Special Note Regarding Forward-Looking Statements

This annual report on Form 10-K contains, and our officers and representatives may from time to time make, “forward-looking statements” within the meaning of the safe harbor provisions of the U.S. Private Securities Litigation Reform Act of 1995. Forward-looking statements can be identified by words such as: “anticipate,” “intend,” “plan,” “goal,” “seek,” “believe,” “project,” “estimate,” “expect,” “strategy,” “future,” “likely,” “may,” “should,” “will,” or the negative of these terms, and similar references to future periods. Examples of forward-looking statements include, among others, statements we make regarding:

our expectations as to our future financial performance, results of operations, or other operational results or metrics;

the benefits that we expect will result from our business activities and certain transactions we have completed, such as product introductions, increased revenue, decreased expenses, and avoided expenses and expenditures;

our expectations of the effect on our financial condition of claims, litigation, contingent liabilities, and governmental investigations, proceedings, and regulations;

our strategies or expectations for product development, market position, financial results, and reserves; and

other expectations, beliefs, plans, strategies, anticipated developments, and other matters that are not historical facts.

Forward-looking statements are neither historical facts nor assurances of future performance. Instead, they are based only on our current beliefs, expectations, and assumptions regarding the future of our business, future plans and strategies, projections, anticipated events and trends, the economy, and other future conditions. Because forward-looking statements relate to the future, they are subject to inherent uncertainties, risks, and changes in circumstances that are difficult to predict and many of which are outside of our control. Our actual results and financial condition may differ materially from those indicated in the forward-looking statements. Therefore, you should not rely on any of these forward-looking statements. Important factors that could cause our actual results and financial condition to differ materially from those indicated in the forward-looking statements include, among others, the following:

our ability to develop and commercialize our instruments and consumables, to deploy new products, services, and applications, and to expand the markets for our technology platforms;

our ability to manufacture robust instrumentation and consumables;

our ability to identify and integrate acquired technologies, products, or businesses successfully;

our expectations and beliefs regarding prospects and growth for the business and its markets;

the assumptions underlying our critical accounting policies and estimates;

our assessments and estimates that determine our effective tax rate;

our assessments and beliefs regarding the outcome of pending legal proceedings and any liability, that we may incur as a result of those proceedings;

uncertainty, or adverse economic and business conditions, including as a result of slowing or uncertain economic growth in the United States or worldwide; and

other factors detailed in our filings with the SEC, including the risks, uncertainties, and assumptions described in Item 1A “Risk Factors” below, or in information disclosed in public conference calls, the date and time of which are released beforehand.

Any forward-looking statement made by us in this annual report on Form 10-K is based only on information currently available to us and speaks only as of the date on which it is made. We undertake no obligation, and do not intend, to publicly update any forward-looking statement, whether written or oral, that may be made from time to time, or to review or confirm analysts’ expectations, or to provide interim reports or updates on the progress of any current financial quarter, in each case whether as a result of new information, future developments, or otherwise.

Available Information

Our annual report on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K, and all amendments to those reports are available free of charge on our website, www.illumina.com. The information on our website is not incorporated by reference into this report. Such reports are made available as soon as reasonably practicable after filing with, or furnishing to, the SEC. The SEC also maintains an Internet site at www.sec.gov that contains reports, proxy and information statements, and other information regarding issuers that electronically file with the SEC. Copies of our annual report on Form 10-K will be made available, free of charge, upon written request.

Illumina®, 24sure®, BaseSpace®, BeadArray, BlueFish®, BlueFuse®, BlueGnome®, cBot, CSPro®, DASL®, DesignStudio, Epicentre®, ForenSeq, Genetic Energy®, GenomeStudio®, GoldenGate®, HiScan®, HiSeq®, HiSeq X®, Infinium®, iScan®, iSelect®, MiniSeq, MiSeq®, MiSeqDx®, MiSeq FGx, NeoPrep, NextBio®, Nextera®, NextSeq®, NovaSeq, SeqMonitor, TruGenome®, TruSeq®, TruSight®, Understand Your Genome®, UYG®, VeraCode®, verifi®, VeriSeq, the pumpkin orange color, and the Genetic Energy streaming bases design are certain of our trademarks. This report also contains brand names, trademarks, or service marks of companies other than Illumina, and these brand names, trademarks, and service marks are the property of their respective holders.

Unless the context requires otherwise, references in this annual report on Form 10-K to “Illumina,” the “Company,” “we,” “us,” and “our” refer to Illumina, Inc. and its subsidiaries.

PART I

ITEM 1. Business.

Overview

We are the global leader in sequencing- and array-based solutions for genetic analysis. Our products and services serve customers in a wide range of markets, enabling the adoption of genomic solutions in research and clinical settings. We were incorporated in California in April 1998 and reincorporated in Delaware in July 2000. Our principal executive offices are located at 5200 Illumina Way, San Diego, California 92122. Our telephone number is (858) 202-4500.

Our customers include leading genomic research centers, academic institutions, government laboratories, and hospitals, as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostic laboratories, and consumer genomics companies.

Our portfolio of integrated systems, consumables, and analysis tools is designed to accelerate and simplify genetic analysis. This portfolio addresses the range of genomic complexity, price points, and throughput, enabling customers to select the best solution for their research or clinical challenge.

Over the past five years, we have made key acquisitions to provide our customers with more comprehensive sample-to-answer solutions and to enable our goal of becoming a leader in the clinical market. These include:

GenoLogics Life Sciences Software Inc., a developer of industry-leading laboratory information management systems, in August 2015;

Myraqa, Inc., a regulatory and quality consulting firm specializing in IVDs and companion diagnostics, in July 2014;

NextBio, a provider of clinical and genomic informatics, in November 2013;

Advanced Liquid Logic Inc., a developer of digital microfluidics and liquid handling solutions, in July 2013;

Verinata Health, Inc., a provider of non-invasive tests for the early identification of fetal chromosomal abnormalities, in February 2013; and

BlueGnome Ltd., a provider of cytogenetics and in vitro fertilization screening solutions, in September ~~2012;~~2012.

We also invest in early-stage companies that are pursuing promising genomics-related technologies. For example, GRAIL, Inc. (GRAIL), formed in January 2016, was created to develop a blood test for early-stage cancer detection, and

~~Epicentre Technologies Corporation, a provider of nucleic-acid sample preparation reagents and specialty enzymes for~~ Helix Holdings I, LLC (Helix) was established in 2015 to enable individuals to explore their genetic information by providing sequencing and ~~array applications, in January 2011.~~services for consumers through third-party partners. GRAIL and Helix are consolidated variable interest entities.

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Genetics Primer

The instruction set for all living cells is encoded in deoxyribonucleic acid, or DNA. The complete set of DNA for any organism is referred to as its genome. DNA contains small regions called genes, which comprise a string of nucleotide bases labeled A, C, G, and T, representing adenine, cytosine, guanine, and thymine, respectively. These nucleotide bases occur in a precise order known as the DNA sequence. When a gene is “expressed,” a partial copy of its DNA sequence called messenger RNA (mRNA) is used as a template to direct the synthesis of a particular protein. Proteins, in turn, direct all cellular function. The illustration below is a simplified gene expression schematic.

Variations among organisms are due, in large part, to differences in their DNA sequences. Changes can result from insertions, deletions, inversions, translocations, or duplications of nucleotide bases. These changes may result in certain genes becoming over-expressed (excessive protein production), under-expressed (reduced protein production), or silenced altogether, sometimes triggering changes in cellular function. These changes can be the result of heredity, but most often they occur at random. The most common form of variation in humans is called a single nucleotide polymorphism (SNP), which is a base change in a single position in a DNA sequence. Another type of variation, copy number variations (CNVs), occur when there are fewer or more copies of certain genes, segments of a gene, or stretches of DNA.

In humans, genetic variation accounts for many of the physical differences we see (e.g., height, hair, eye color, etc.). Genetic variations also can have medical consequences affecting disease susceptibility, including predisposition to complex genetic diseases such as cancer, diabetes, cardiovascular disease, and Alzheimer’s disease. They can affect individual response to certain drug treatments, causing patients to experience adverse side effects, or to respond well or not at all.

Scientists are studying these variations and their consequences in humans, as well as in a broad range of animals, plants, and microorganisms. Such research takes place in government, university, pharmaceutical, biotechnology, and agrigenomics laboratories around the world, where scientists expand our knowledge of the biological functions essential for life. Beginning at the genetic level, Illumina tools are used to elucidate the correlation between gene sequence and biological processes. Life-science research includes the study of the cells, tissues, organs, systems, and other components of living organisms. This research supports the development of new treatments to improve human health. Examples include more tailored clinical treatments, often referred to as precision medicine, as well as advances in agriculture and animal husbandry to meet growing needs for food and energy. Researchers who investigate human, viral, and bacterial genetic variation to understand the mechanisms of disease are enabling the development of more effective diagnostics and therapeutics. They also provide greater insight into genetic variation in plants (e.g., food and biofuel crops) and animals (e.g., livestock and domestic), enabling improvements in crop yields and animal breeding programs.

By empowering genetic analysis and facilitating a deeper understanding of genetic variation and function, our tools advance disease research, drug development, and the creation of molecular diagnostic tests. We believe that this will trigger a fundamental shift in the practice of medicine and health care and that the increased emphasis on preventive and predictive molecular medicine will usher in the era of precision health care.

Our Principal Markets

Our organization is structured to target the markets and customers outlined below.

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Life Sciences

Historically, our core business has been in the life sciences research market. This includes laboratories associated with universities, research centers, and government institutions, along with biotechnology and pharmaceutical companies. Researchers at these institutions use our products and services for basic and translational research across a spectrum of scientific applications, including targeted, exome, and whole-genome sequencing; genetic variation; gene expression; epigenetics; and metagenomics. ~~Increasingly, these techniques are migrating to next-generation~~Next-generation sequencing (NGS) technologies are being adopted due to ~~the~~their declining costs ~~of NGS technologies~~per sample as well as their ability to sequence large sample sizes and ~~the ability of NGS to provide~~generate vast amounts of ~~data, resulting in improved discovery performance as compared to arrays.~~data. Both private and public funding drive this research, along with global initiatives to characterize genetic variation.

We also serve applied markets ~~in life sciences, such as~~including consumer genomics, agrigenomics, forensic genomics, and transplant biology. In consumer genomics, our customers use our technologies to provide personalized genetic data and analysis to individual consumers. In agrigenomics, government and corporate researchers use our ~~sequencing-~~products and ~~array-based tools~~services to explore the genetic and biological basis for productivity and nutritional constitution in crops and livestock. Researchers can identify natural and novel genomic variation and deploy genome-wide marker-based applications to accelerate breeding and production of healthier and higher-yielding crops and livestock. In forensic genomics, major law enforcement agencies use ~~sequencing~~genomic information to investigate criminal cases, as do military and security intelligence agencies. In transplant diagnostics, we offer a sample-to-answer solution to perform high resolution HLA typing in a single assay, which enables users to determine how closely the tissues of one person match the tissues of another person.

Clinical Genomics

We provide sample-to-answer solutions to our customers in two key areas of translational and clinical genomics: reproductive and genetic health, and oncology.

Illumina provides reproductive-health solutions, including noninvasive prenatal testing (NIPT), preimplantation genetic screening and diagnosis (PGS and PGD), ~~noninvasive prenatal testing (NIPT),~~ and neonatal and genetic health testing. Our technology enables NIPT for early identification of fetal chromosomal abnormalities by analyzing cell-free DNA in maternal blood. Our PGS solution is used with in vitro fertilization (IVF) to determine, before implantation, whether an embryo has an abnormal number of chromosomes, which is a major cause of IVF failure and miscarriages. In the case of PGD, the technology determines which embryos are free from gene variants associated with genetic diseases. ~~Our technology enables NIPT for early identification of fetal chromosomal abnormalities by analyzing cell-free DNA in maternal blood.~~

Cancer is a disease of the genome, and the goal of cancer genomics is to identify genomic changes that transform a normal cell into a cancerous one. Understanding these genomic changes improves diagnostic accuracy, increases understanding of the prognosis, and enables oncologists to target therapies to individuals. Customers in the translational and clinical oncology markets use ~~Illumina sequencing- and array-based solutions~~our products to perform research that may help identify individuals who are genetically predisposed to cancer. Customers also utilize our technology to identify the molecular changes in a tumor so that physicians can tailor treatment based on the genetic variation. We believe that circulating tumor DNA (ctDNA) will become an important clinical tool for managing oncology patients during all stages of tumor progression. Our technology is being used to research the implications of ctDNA in treatment determination, treatment monitoring, minimal residual disease, and asymptomatic screening. ~~In early 2016,~~For example, we ~~formed a new company,~~have invested in GRAIL, ~~Inc.,~~ which ~~is majority owned by Illumina and funded by Illumina and outside investors,~~was formed to develop a ~~pan-cancer screening~~blood-based test for early-stage cancer detection, and has been enabled by our sequencing technology.

To advance genomic-based precision oncology care, we are working with key opinion leaders to set standards for NGS-based assays in routine clinical oncology practice and to define regulatory frameworks for this new testing paradigm.

~~Enterprise Informatics~~

Enterprise informatics solutions increase the utility of genomic data by allowing customers to aggregate, analyze, archive, and share genomic data. Integrating our instruments with data-analysis software allows customers to go from their biological sample, through the raw genomic data, to meaningful results. Our BaseSpace platform, which can be hosted onsite or in the cloud, integrates directly with our sequencing instruments. It facilitates data sharing, provides data-storage solutions, and streamlines analysis through a growing number of applications from Illumina and the bioinformatics community.

In 2013, we acquired NextBio, a platform for aggregating and analyzing large quantities of genomic and phenotypic data. Translational researchers use this tool to understand the efficacy of drug therapies and identify trends in patient outcomes. We believe that large-scale genomic databases containing genomic and phenotypic information will enhance the value of human genome sequencing and accelerate the pace of discovery.

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Our Principal Products and Technologies

Our unique technology platforms support the scale of experimentation necessary for population-scale studies, genome-wide discovery, target selection, and validation studies (see Figure 1 below). Customers use our products to analyze the genome at all levels of complexity, from whole-genome sequencing to targeted panels. A large and dynamic Illumina user community has published ~~approximately 32,000~~tens of thousands of customer-authored scientific papers using our technologies. Through rapid innovation, we are changing the economics of genetic research, enabling projects that were previously considered impossible, and supporting clinical advances towards precision medicine.

Most of our product sales consist of instruments and consumables (which include reagents, flow cells, and microarrays) based on our proprietary technologies. For the fiscal years ended January 1, 2017, January 3, 2016, and December 28, 2014, ~~and~~ ~~December 29, 2013~~, instrument sales comprised ~~27%~~20%, ~~30%~~27%, and ~~26%~~30%, respectively, of total revenues, and consumable sales represented ~~58%~~64%, ~~56%~~58%, and ~~62%~~56%, respectively, of total revenues.

Figure 1: Illumina Platform Overview:

Sequencing

DNA sequencing is the process of determining the order of nucleotide bases (A, C, G, or T) in a DNA sample. Our portfolio of sequencing platforms represents a family of systems that we believe set the standard for productivity, cost-effectiveness, and accuracy among NGS technologies. Customers use our platforms to perform whole-genome, de novo, exome and ~~exome~~RNA sequencing, and targeted resequencing of specific gene regions and genes.

Whole-genome sequencing determines the complete DNA sequence of an organism. In de novo sequencing, the goal is to sequence and analyze a sample without using information from prior sequencing of that species. In targeted resequencing, a portion of the sequence of an organism is compared to a standard or reference sequence from previously sequenced samples to identify genetic variation. Understanding the similarities and differences in DNA sequence between and within species helps us understand the function of the structures encoded in the DNA.

Our DNA sequencing technology is based on our proprietary reversible terminator-based sequencing chemistry, referred to as sequencing by synthesis (SBS) biochemistry. SBS tracks the addition of labeled nucleotides as the DNA chain is copied in a massively parallel fashion. Our SBS sequencing technology provides researchers with a broad range of applications and the ability to sequence even large mammalian genomes in a ~~day~~few days rather than weeks or years.

Our sequencing platforms can generate between 500 megabases (Mb) and ~~1.8~~2.0 terabases (Tb) (equivalent to 16 human genomes) of genomic data in a single run, depending on the instrument and application. There are different price points per gigabase (Gb) for each instrument, and for different applications, which range from small-genome, amplicon, and targeted gene-panel sequencing to population-scale whole human genome sequencing. Since we launched our first sequencing system

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in 2007, our systems have reduced the cost of sequencing by more than a factor of 10,000. In addition, the sequencing time per Gb has dropped by a factor of ~~nearly 2,000.~~approximately 3,500.

Our BaseSpace Informatics Suite cloud platform plays a critical role in supporting our sequencing applications. BaseSpace Suite integrates directly with our sequencing instruments, allowing customers to manage their biological sample and sequencing runs, process and analyze the raw genomic data, and derive meaningful results. It facilitates data sharing, provides data-storage solutions and streamlines analysis through a growing number of applications from us and the bioinformatics community. Some components of the BaseSpace Informatics Suite can also be installed for customers on-site.

For the fiscal years ended January 1, 2017, January 3, 2016, and December 28, 2014, ~~and December 29, 2013,~~ sequencing revenue comprised ~~86%~~84%, ~~81%~~86%, and ~~73%~~81%, respectively, of total revenues.

Arrays

Arrays are used for a broad range of DNA and RNA analysis applications, including SNP genotyping, CNV analysis, gene expression analysis, and methylation analysis, and allow for the detection of millions of known genetic markers on a single array.

Our BeadArray technology combines microscopic beads and a substrate in a proprietary manufacturing process to produce arrays that can perform many assays simultaneously. This facilitates large-scale analysis of genetic variation and biological function in a uniquely high-throughput, cost-effective, and flexible manner. Using our BeadArray technology, we achieve high-throughput analysis via a high density of test sites per array and the ability to format arrays in various configurations. Varying the size, shape, and format of the substrate into which the beads self-assemble and creating specific bead types for different applications lets us address multiple markets and market segments. Both our iScan array scanner system and our NextSeq 550 system can be used to image the arrays.

For the fiscal years ended January 1, 2017, January 3, 2016, and December 28, 2014, ~~and December 29, 2013,~~ array revenue comprised ~~14%~~16%, ~~19%~~14%, and ~~27%~~19%, respectively, of total revenues.

Consumables

We have developed various library preparation and sequencing kits to simplify workflows and accelerate analysis. Our sequencing applications include whole-genome sequencing kits, which sequence entire genomes of any size and complexity, and targeted resequencing kits, which can sequence exomes, specific genes, RNA or other genomic regions of interest. Our sequencing kits maximize the ability of our customers to characterize the target genome ~~accurately.~~accurately and are sold in various configurations, which address a wide range of applications.

Customers use Illumina array-based genotyping consumables for a wide range of analyses, including diverse species, disease-related mutations, and genetic characteristics associated with cancer. Customers can select from a range of human, animal, and agriculturally relevant genome panels or create their own custom arrays to investigate millions of genetic markers targeting any species.

Our Services

~~In addition to selling products, we~~We provide whole-genome sequencing, genotyping, NIPT, and ~~NIPT~~support services. Human whole-genome sequencing services are provided through our CLIA-certified, CAP-accredited laboratory. Using our services, customers can perform whole-genome sequencing projects ~~(including phasing and long-read sequencing services)~~ and microarray projects (including large-scale genotyping studies and whole-genome association studies). We also provide NIPT services through our partner laboratories that direct samples to us on a test send-out basis in our CLIA-certified, CAP-accredited laboratory. In addition, we also offer support services to customers who have purchased our products.

Intellectual Property

We have an extensive intellectual property portfolio. As of February 1, ~~2016,~~2017, we own or have exclusive licenses to ~~577~~671 issued U.S. patents and ~~406~~572 pending U.S. patent applications, including 3431 allowed applications that have not yet issued as patents. Our issued and pending patents cover various aspects of our arrays, assays, oligo synthesis, sequencing technology, instruments, digital microfluidics, software, bioinformatics, and chemical-detection technologies, and have terms that expire between ~~2016~~2017 and ~~2036.~~2038. We continue to file new patent applications to protect the full range of our technologies. We have filed or have been granted counterparts for many of these patents and applications in foreign countries.

We protect trade secrets, know-how, copyrights, and trademarks, as well as continuing technological innovation and licensing opportunities to develop and maintain our competitive position. Our success depends in part on obtaining patent protection for our products and processes, preserving trade secrets, patents, copyrights and trademarks, operating without infringing the proprietary rights of third parties, and acquiring licenses for technology or products.

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We are party to various exclusive and nonexclusive license agreements and other arrangements with third parties that grant us rights to use key aspects of our sequencing and array technologies, assay methods, chemical detection methods, reagent kits, and scanning equipment. Our exclusive licenses expire with the termination of the underlying patents, which will occur between ~~2016~~2017 and 2032. We have additional nonexclusive license agreements with various third parties for other components of our products. In most cases, the agreements remain in effect over the term of the underlying patents, may be terminated at our request without further obligation, and require that we pay customary royalties.

Research and Development

Illumina has historically made substantial investments in research and development. Our research and development efforts prioritize continuous innovation coupled with product evolution.

Research and development expenses for fiscal ~~2015~~2016, ~~2014~~2015, and ~~2013~~2014 were $~~401.5~~504.4 million, ~~$388.1~~$401.5 million, and ~~$276.7~~$388.1 million, respectively. We expect research and development expense to increase during fiscal ~~2016~~2017 to support business growth and continuing expansion in research and product-development efforts.

Marketing and Distribution

We market and distribute our products directly to customers in North America, Europe, Latin America, and the Asia-Pacific region. In each of these areas, dedicated sales, service, and application-support personnel are expanding and supporting their respective customer bases. In addition, we sell through life-science distributors in certain markets within Europe, the Asia-Pacific region, Latin America, the Middle East, and South Africa. We expect to continue increasing our sales and distribution resources during ~~2016~~2017 and beyond as we launch new products and expand our potential customer base.

Manufacturing

We manufacture sequencing and array platforms and reagent ~~kits, and scanning equipment.~~kits. In ~~2015,~~2016, we continued to increase our manufacturing capacity to meet customer demand. To address increasing product complexity and volume, we continue to automate manufacturing processes to accelerate throughput and improve quality and yield. We are committed to providing medical devices and related services that consistently meet customer and applicable regulatory requirements. We adhere to access and safety standards required by federal, state, and local health ordinances, such as standards for the use, handling, and disposal of hazardous substances. Our key manufacturing and distribution facilities operate under a quality management system certified to ISO 13485.

Raw Materials

Our manufacturing operations require a wide variety of raw materials, electronic and mechanical components, chemical and biochemical materials, and other supplies. Multiple commercial sources provide many of our components and supplies, but there are some raw materials and components that we obtain from single-source suppliers. To manage potential risks arising from single source suppliers, we believe that we could redesign our products using alternative components or for use with alternative reagents, if necessary. In addition, while we attempt to keep our inventory at minimal levels, we purchase incremental inventory as circumstances warrant to protect our supply chain. If the capabilities of our suppliers and component manufacturers are limited or stopped, due to disasters, quality, regulatory, or other reasons, it could negatively impact our ability to manufacture our products.

Competition

Although we believe that our products and services provide significant advantages over products and services currently available from other sources, we expect continued intense competition. Our competitors offer products and services for sequencing, SNP genotyping, gene expression, and molecular diagnostics markets. They include companies such as ~~Affymetrix, Inc.,~~ Agilent Technologies, Inc., BGI, Oxford Nanopore Technologies Limited, Pacific Biosciences of California, Inc., QIAGEN N.V., Roche Holding AG., and Thermo Fisher Scientific, Inc., among others. Some of these companies have or will have substantially greater financial, technical, research, and other resources than we do, along with larger, more established marketing, sales, distribution, and service organizations. In addition, they may have greater name recognition than we do in the markets we address, and in some cases a larger installed base of systems. We expect new competitors to emerge and the intensity of competition to increase. To compete effectively, we must scale our organization and infrastructure appropriately and demonstrate that our products have superior throughput, cost, and accuracy.

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Segment and Geographic Information

~~In accordance with the authoritative accounting guidance for segment reporting, we have determined that we have one reportable segment~~We are organized into three operating segments for purposes of ~~recording~~evaluating our business operations and ~~reporting~~reviewing our financial results. One segment consists of Illumina’s core operations (Core Illumina). The other two segments relate to the activities of our consolidated variable interest entities (VIEs), GRAIL and Helix. The combined results of operations of our consolidated VIEs became material during the year ended January 1, 2017. As such, we commenced reporting two segments, Core Illumina and Consolidated VIEs, during 2016.

We currently sell our products to a number of customers outside the United States, including customers in other areas of North America, Latin America, Europe, and the Asia-Pacific region. Shipments to customers outside the United States totaled ~~$1,012.4~~$1,104.2 million, or 46% of ~~our~~ total ~~revenue,~~revenues, during fiscal ~~2015~~2016, compared to$1,012.4 million, or 46%, and $910.7 million, or 49%, ~~and~~ ~~$706.5 million, or~~ ~~50%~~, in fiscal ~~2014~~2015 and ~~2013~~2014, respectively. The U.S. dollar has been determined to be the functional currency of the Company’s international operations due to the primary activities of our foreign subsidiaries. We expect that sales to international customers will continue to be an important and growing source of revenue. See note “12. Segment Information, Geographic Data, and Significant Customers” in Part II, Item 8 of this Form 10-K for further information concerning our foreign and domestic operations.

Backlog

Our backlog was approximately $650 million and $560 million as of January 1, 2017 and January 3, ~~2016.~~2016, respectively. Generally, our backlog consists of orders believed to be firm as of the balance-sheet date. However, we may allow customers to make product substitutions as we launch new products. The timing of shipments depends on several factors, including agreed upon shipping schedules, which may span multiple quarters, and whether the product is catalog or custom. We expect ~~most~~approximately two-thirds of ~~the~~our backlog as of January ~~3, 2016,~~1, 2017, to be shipped within the fiscal year ending ~~January 1,~~December 31, 2017~~, with the most notable exception being $130 million in backlog related to the Genomics England sequencing services project.~~. Although we generally recognize revenue upon the transfer of title to a customer, some customer agreements or applicable accounting treatments might require us to defer the recognition of revenue beyond title transfer.

Environmental Matters

We are committed to the protection of our employees and the environment. Our operations require the use of hazardous materials that subject us to various federal, state, and local environmental and safety laws and regulations. We believe that we are in material compliance with current applicable laws and regulations. However, we could be held liable for damages and fines should contamination of the environment or individual exposures to hazardous substances occur. In addition, we cannot predict how changes in these laws and regulations, or the development of new laws and regulations, will affect our business operations or the cost of compliance.

Government Regulation

As we expand product lines to address the diagnosis of disease, regulation by governmental authorities in the United States and other countries will become an increasingly significant factor in development, testing, production, and marketing. Products that we develop in the molecular diagnostic markets, depending on their intended use, may be regulated as medical devices by the FDA and comparable agencies in other countries. In the United States, certain of our products may require FDA clearance following a pre-market notification process, also known as a 510(k) clearance, or premarket approval (PMA) from the FDA before marketing. The usually shorter 510(k) clearance process, which we used for the FDA-cleared assays that are run on our FDA-regulated MiSeqDx instrument, generally takes from three to six months after submission, but it can take significantly longer. The longer PMA process is much more costly and uncertain. It generally takes from 9 to 18 months after a complete filing, but it can take significantly longer and typically requires conducting clinical studies, which are not always needed for a 510(k) clearance. All of the products that are currently regulated by the FDA as medical devices are also subject to the FDA Quality System Regulation (QSR). Obtaining the requisite regulatory approvals, including the FDA quality system inspections that are required for PMA approval, can be expensive and may involve considerable delay.

We cannot be certain which of our planned molecular diagnostic products will be subject to the shorter 510(k) clearance process and, in fact, some of our products may need to go through the PMA process. The regulatory approval process for such products may be significantly delayed, may be significantly more expensive than anticipated, and may conclude without such products being approved by the FDA. Without timely regulatory approval, we may not be able to launch or successfully commercialize such products.

Changes to the current regulatory framework, including the imposition of additional or new regulations, could arise at any time during the development or marketing of our products. This may negatively affect our ability to obtain or maintain FDA or

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comparable regulatory clearance or approval of our products. In addition, the FDA may introduce new requirements that may change the regulatory requirements for either or both Illumina or ~~Illumina~~our customers.

If our products labeled as ~~“Research~~“For Research Use ~~Only,~~Only. Not for use in diagnostic procedures,” or RUO, are used, or could be used, for the diagnosis of disease, the regulatory requirements related to marketing, selling, and supporting such products could

be uncertain. This is true even if such use by our customers occurs without our consent. If the FDA or other regulatory authorities assert that any of our RUO products are subject to regulatory clearance or approval, our business, financial condition, or results of operations could be adversely affected.

Illumina products sold as medical devices in Europe will be regulated under the In Vitro Diagnostics Directive (98/79/EC). This regulation includes requirements for both presentation and review of performance data and quality-system requirements.

Certain of our diagnostic products are currently available through laboratories that are certified under the Clinical Laboratory Improvements Amendments (CLIA) of 1988. These products are commonly called “laboratory developed tests,” or LDTs. For a number of years, the FDA has exercised its regulatory enforcement discretion to not regulate LDTs as medical devices if created and used within a single laboratory. However, ~~as discussed in more detail under “Risk Factors,”~~ the FDA is reexamining this regulatory approach and changes to the agency’s handling of LDTs could impact our business in ways that cannot be predicted at this time. In October 2014, the FDA published two draft guidance documents suggesting an approach for registration and listing of laboratories and assays along with a framework for regulation of LDTs by the FDA based on risk to patients rather than whether the LDTs were made by a conventional manufacturer or a single laboratory. The draft framework guidance includes pre-market review for higher-risk LDTs, including many used to guide treatment decisions, as well as companion diagnostics that have entered the market as LDTs. We cannot predict the nature or extent of the FDA's final guidance or regulation of LDTs, in general, or with respect to our or our customers’ LDTs, in particular.

Certification of CLIA laboratories includes standards in the areas of personnel qualifications, administration, and participation in proficiency testing, patient test management, and quality control procedures. CLIA also mandates that, for high complexity labs such as ours, to operate as a lab, we must have an accreditation by an organization recognized by CLIA such as the College of Pathologists (CAP), which we have obtained and must maintain. If we were to lose our CLIA certification or CAP accreditation, our business, financial condition, or results of operations could be adversely affected. In addition, state laboratory licensing and inspection requirements may also apply to our products, which, in some cases, are more stringent than CLIA requirements.

Employees

As of January ~~3, 2016,~~1, 2017, we had more than ~~4,600~~5,500 employees. We consider our employee relations to be positive. Our success will depend in large part upon our ability to attract and retain employees. In addition, we employ a number of temporary and contract employees. We face competition in this regard from other companies, research and academic institutions, government entities, and other organizations.


ITEM 1A.	Risk Factors.

Our business is subject to various risks, including those described below. In addition to the other information included in this Form 10-K, the following issues could adversely affect our operating results or our stock price.

If we do not successfully manage the development, manufacturing, and launch of new products or services, including product transitions, our financial results could be adversely affected.

We face risks associated with launching new products and pre-announcing products and services when the products or services have not been fully developed or tested. In addition, we may experience difficulty in managing or forecasting customer reactions, purchasing decisions, or transition requirements or programs with respect to newly launched products (or products in development), which could adversely affect sales of our existing products. For instance, in January ~~2016~~2017 we announced ~~an expansion to~~ our ~~sequencing~~NovaSeq 5000 and 6000 instrument ~~platforms, the MiniSeq system, and we previewed a~~systems, which were developed using our new sequencing ~~system currently under development that will deploy SBS chemistry on a semiconductor chip.~~architecture. If our products and services are not able to deliver the performance or results expected by our target markets or are not delivered on a timely basis, our reputation and credibility may suffer. If we encounter development challenges or discover errors in our products late in our development cycle, we may delay the product launch date. The expenses or losses associated with unsuccessful product development or launch activities or lack of market acceptance of our new products could adversely affect our business, financial condition, or results of operations.

When we introduce or announce new or enhanced products, we face numerous risks relating to product transitions, including the inability to accurately forecast demand (including with respect to our existing products), manage excess and obsolete inventories, address new or higher product cost structures, and manage different sales and support requirements due to the type or complexity of the new or enhanced products. Announcements of currently planned or other new products may cause customers to defer or stop purchasing our products until new products become available. Our failure to effectively manage product transitions or introductions could adversely affect our business, financial condition, or results of operations.

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Our success depends upon the continued emergence and growth of markets for analysis of genetic variation and biological function.

We design our products primarily for applications in the life sciences, diagnostic, agricultural, and pharmaceutical industries. The usefulness of our technologies depends in part upon the availability of genetic data and its usefulness in identifying or treating disease. We are focusing on markets for analysis of genetic variation ~~and~~or biological function, namely sequencing, genotyping, and gene expression profiling. These markets are relatively new and emerging, and they may not develop as quickly as we anticipate, or reach their full potential. Other methods of analysis of genetic variation and biological function may emerge and displace the methods we are developing. Also, researchers may not be able to successfully analyze raw genetic data or be able to convert raw genetic data into medically valuable information. In addition, factors affecting research and development spending generally, such as changes in the regulatory environment affecting life sciences and pharmaceutical companies, and changes in government programs that provide funding to companies and research institutions, could harm our business. If useful genetic data is not available or if our target markets do not develop in a timely manner, demand for our products may grow at a slower rate than we expect.

~~We face intense competition, which could render our products obsolete, result in significant price reductions, or substantially limit the volume of products that we sell.~~

We compete with life sciences companies that design, manufacture, and market products for analysis of genetic variation and biological function and other applications using a wide range of competing technologies. We anticipate that we will continue to face increased competition as existing companies develop new or improved products and as new companies enter the market with new technologies. One or more of our competitors may render one or more of our technologies obsolete or uneconomical. Some of our competitors have greater financial and personnel resources, broader product lines, a more established customer base, and more experience in research and development than we do. Furthermore, life sciences, clinical genomics, and pharmaceutical companies, which are our potential customers and strategic partners, could also develop competing products. We believe that customers in our markets display a significant amount of loyalty to their initial supplier of a particular product; therefore, it may be difficult to generate sales to potential customers who have purchased products from competitors. To the extent we are unable to be the first to develop or supply new products, our competitive position may suffer.

The market for molecular diagnostics products is currently limited and highly competitive, with several large companies already having significant market share, intellectual property portfolios, and regulatory expertise. Established diagnostic companies also have an installed base of instruments in several markets, including clinical and reference laboratories, which could deter acceptance of our products. In addition, some of these companies have formed alliances with genomics companies that provide them access to genetic information that may be incorporated into their diagnostic tests.

Our continued growth is dependent on continuously developing and commercializing new products.

Our target markets are characterized by rapid technological change, evolving industry standards, changes in customer needs, existing and emerging competition, strong price competition, and frequent new product introductions. Accordingly, our continued growth depends on developing and commercializing new products and services, including improving our existing products and services, in order to address evolving market requirements on a timely basis. If we fail to innovate or adequately invest in new technologies, our products and services will become dated, and we could lose our competitive position in the markets that we serve as customers purchase new products offered by our competitors. We believe that successfully introducing new products and technologies in our target markets on a timely basis provides a significant competitive advantage because customers make an investment of time in selecting and learning to use a new product and may be reluctant to switch once that selection is made.

To the extent that we fail to introduce new and innovative products, or such products are not accepted in the market or suffer significant delays in development, we may lose market share to our competitors, which will be difficult or impossible to regain. An inability, for technological or other reasons, to successfully develop and introduce new products on a timely basis could reduce our growth rate or otherwise have an adverse effect on our business. In the past, we have experienced, and are likely to experience in the future, delays in the development and introduction of new products. There can be no assurance that we will keep pace with the rapid rate of change in our markets or that our new products will adequately meet the requirements of the marketplace, achieve market acceptance, or compete successfully with competing technologies. Some of the factors affecting market acceptance of new products and services include:

availability, quality, and price relative to competing products and services;

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the functionality and performance of new and existing products and services;

the timing of introduction of new products or services relative to competing products and services;

scientists’ and customers’ opinions of the utility of new products or services;

citation of new products or services in published research;

regulatory trends and approvals; and

general trends in life sciences research and applied markets.

We may also have to write off excess or obsolete inventory if sales of our products are not consistent with our expectations or the market requirements for our products change due to technical innovations in the marketplace.

If defects are discovered in our products, we may incur additional unforeseen costs, our products may be subject to recalls, customers may not purchase our products, our reputation may suffer, and ultimately our~~sales and operating earnings could be negativelyimpacted.~~

Our products incorporate complex, precision-manufactured mechanical parts, electrical components, optical components, and fluidics, as well as computer software, any of which may contain errors or failures, especially when first introduced. In the course of conducting our business, we must adequately address quality issues associated with our products and services, including defects in our engineering, design, and manufacturing processes, as well as defects in third-party components included in our products. In addition, new products or enhancements may contain undetected errors or performance problems that, despite testing, are discovered only after commercial shipment. Defects or errors in our products may discourage customers from purchasing our products. The costs incurred in correcting any defects or errors may be substantial and could adversely affect our operating margins. Identifying the root cause of quality issues, particularly those affecting reagents and third-party components, may be difficult, which increases the time needed to address quality issues as they arise and increases the risk that similar problems could recur. Because our products are designed to be used to perform complex genomic analysis, we expect that our customers will have an increased sensitivity to such defects. If we do not meet applicable regulatory or quality standards, our products may be subject to recall, and, under certain circumstances, we may be required to notify applicable regulatory authorities about a recall. If our products are subject to recall or shipment holds, our reputation, business, financial condition, or results of operations could be adversely affected.

As we develop, market, or sell diagnostic tests, we may encounter delays in receipt, or limits in the amount, of reimbursement approvals and public health funding, which will impact our ability to grow revenues in the healthcare market.

Physicians and patients may not order diagnostic tests that we develop, market, or sell, such as our verifi prenatal test, unless third-party payors, such as managed care organizations as well as government payors such as Medicare and Medicaid and governmental payors outside of the United States, pay a substantial portion of the test price. Third-party payors are often reluctant to reimburse healthcare providers for the use of medical tests that involve new technologies or provide novel diagnostic information. In addition, third-party payors are increasingly limiting reimbursement coverage for medical diagnostic products and, in many instances, are exerting pressure on diagnostic product suppliers to reduce their prices. Reimbursement by a payor may depend on a number of factors, including a payor's determination that tests using our technologies are:

~~not experimental or investigational;~~

~~medically necessary;~~

~~appropriate for the specific patient;~~

~~cost-effective;~~

~~supported by peer-reviewed publications; and~~

~~included in clinical practice guidelines.~~

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process can delay the broad market introduction of new products, and could have a negative effect on our results of operations. As a result, third-party reimbursement may not be consistent or financially adequate to cover the cost of diagnostic products that we develop, market, or sell. This could limit our ability to sell our products or cause us to reduce prices, which would adversely affect our results of operations.

Even if our tests are being reimbursed, third party payors may withdraw their coverage policies, cancel their contracts with our customers at any time, review and adjust the rate of reimbursement, require co-payments from patients, or stop paying for our tests, which would reduce our revenues. In addition, insurers, including managed care organizations as well as government payors such as Medicare and Medicaid, have increased their efforts to control the cost, utilization, and delivery of healthcare services. These measures have resulted in reduced payment rates and decreased utilization for the clinical laboratory industry. Reductions in the reimbursement rate of payors may occur in the future. Reductions in the prices at which our tests are reimbursed could have a negative impact on our results of operations.

We depend on third-party manufacturers and suppliers for some of our products, or sub-assemblies, components, and materials used in our products, and if shipments from these manufacturers or suppliers are delayed or interrupted, or if the quality of the products, components, or materials supplied do not meet our requirements, we may not be able to launch, manufacture, or ship our products in a timely manner, or at all.

The complex nature of our products requires customized, precision-manufactured sub-assemblies, components, and materials that currently are available from a limited number of sources, and, in the case of some sub-assemblies, components, and materials, from only a single source. If deliveries from these vendors are delayed or interrupted for any reason, or if we are otherwise unable to secure a sufficient supply, we may not be able to obtain these sub-assemblies, components, or materials on a timely basis or in sufficient quantities or qualities, or at all, in order to meet demand for our products. We may need to enter into contractual relationships with manufacturers for commercial-scale production of some of our products, in whole or in part, or develop these capabilities internally, and there can be no assurance that we will be able to do this on a timely basis, in sufficient quantities, or on commercially reasonable terms. In addition, the lead time needed to establish a relationship with a new supplier can be lengthy, and we may experience delays in meeting demand in the event we must switch to a new supplier. The time and effort required to qualify a new supplier could result in additional costs, diversion of resources, or reduced manufacturing yields, any of which would negatively impact our operating results. Accordingly, we may not be able to establish or maintain reliable, high-volume manufacturing at commercially reasonable costs or at all. In addition, the manufacture or shipment of our products may be delayed or interrupted if the quality of the products, sub-assemblies, components, or materials supplied by our vendors does not meet our requirements. Current or future social and environmental regulations or critical issues, such as those relating to the sourcing of conflict minerals from the Democratic Republic of the Congo or the need to eliminate environmentally sensitive materials from our products, could restrict the supply of components and materials used in production or increase our costs. Any delay or interruption to our manufacturing process or in shipping our products could result in lost revenue, which would adversely affect our business, financial condition, or results of operations.

If defects are discovered in our products, we may incur additional unforeseen costs, our products may be subject to recalls, customers may not purchase our products, our reputation may suffer, and ultimately oursales and operating earnings could be negativelyimpacted.

We face intense competition, which could render our products obsolete, result in significant price reductions, or substantially limit the volume of products that we sell.

not experimental or investigational;

medically necessary;

appropriate for the specific patient;

cost-effective;

supported by peer-reviewed publications; and

included in clinical practice guidelines.

Since each third-party payor often makes reimbursement decisions on an individual patient basis, obtaining such approvals is a time-consuming and costly process that requires us to provide scientific and clinical data supporting the clinical benefits of each of our products. As a result, there can be no assurance that reimbursement approvals will be obtained. This process can delay the broad market introduction of new products, and could have a negative effect on our results of operations. As a result, third-party reimbursement may not be consistent or financially adequate to cover the cost of diagnostic products that we develop, market, or sell. This could limit our ability to sell our products or cause us to reduce prices, which would adversely affect our results of operations.

Litigation, other proceedings, or third party claims of intellectual property infringement could require us to spend significant time and money and could prevent us from selling our products or services.

Our success depends in part on our non-infringement of the patents or proprietary rights of third parties. Third parties have asserted and may in the future assert that we are employing their proprietary technology without authorization. As we enter new markets or introduce new products, we expect that competitors will likely claim that our products infringe their intellectual property rights as part of a business strategy to impede our successful competition. In addition, third parties may have obtained and may in the future obtain patents allowing them to claim that the use of our technologies infringes these patents. We could incur substantial costs and divert the attention of our management and technical personnel in defending ourselves against any of these claims. Any adverse ruling or perception of an adverse ruling in defending ourselves against these claims could have an adverse impact on our stock price, which may be disproportionate to the actual impact of the ruling itself. Furthermore, parties making claims against us may be able to obtain injunctive or other relief, which effectively could block our ability to develop further, commercialize, or sell products or services, and could result in the award of substantial damages against us. In the event of a successful infringement claim against us, we may be required to pay damages and obtain

one or more licenses from third parties, or be prohibited from selling certain products or services. In addition, we may be unable to obtain these licenses at a reasonable cost, if at all. We could therefore incur substantial costs related to royalty payments for licenses obtained from third parties, which could negatively affect our gross margins and earnings per share. In addition, we could encounter delays in product introductions while we attempt to develop alternative methods or products. Defense of any lawsuit or failure to obtain any of these licenses on favorable terms could prevent us from commercializing

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products, and the prohibition of sale of any of our products or services could adversely affect our ability to grow or maintain profitability.

Reduction or delay in research and development budgets and government funding may adversely affect our revenue.

The timing and amount of revenues from customers that rely on government and academic research funding may vary significantly due to factors that can be difficult to forecast, and there remains significant uncertainty concerning government and academic research funding worldwide as governments in the United States and Europe, in particular, focus on reducing fiscal deficits while at the same time confronting uncertain economic growth. Funding for life science research has increased more slowly during the past several years compared to previous years and has declined in some countries. Government funding of research and development is subject to the political process, which is inherently fluid and unpredictable. Other programs, such as defense, entitlement programs, or general efforts to reduce budget deficits could be viewed by governments as a higher priority. These budgetary pressures may result in reduced allocations to government agencies that fund research and development activities, such as the U.S. National Institute of Health, or NIH. Past proposals to reduce budget deficits have included reduced NIH and other research and development allocations. Any shift away from the funding of life sciences research and development or delays surrounding the approval of government budget proposals may cause our customers to delay or forego purchases of our products, which could adversely affect our business, financial condition, or results of operations.

Our acquisitions expose us to risks that could adversely affect our business, and we may not achieve the anticipated benefits of acquisitions of businesses or technologies.

As part of our strategy to develop and identify new products, services, and technologies, we have made, and may continue to make, acquisitions of technologies, products, or businesses. Acquisitions involve numerous risks and operational, financial, and managerial challenges, including the following, any of which could adversely affect our business, financial condition, or results of operations:

difficulties in integrating new operations, technologies, products, and personnel;

lack of synergies or the inability to realize expected synergies and cost-savings;

difficulties in managing geographically dispersed operations;

underperformance of any acquired technology, product, or business relative to our expectations and the price we paid;

negative near-term impacts on financial results after an acquisition, including acquisition-related earnings charges;

the potential loss of key employees, customers, and strategic partners of acquired companies;

claims by terminated employees and shareholders of acquired companies or other third parties related to the transaction;

the issuance of dilutive securities, assumption or incurrence of additional debt obligations or expenses, or use of substantial portions of our cash;

diversion of management’s attention and company resources from existing operations of the business;

inconsistencies in standards, controls, procedures, and policies;

the impairment of intangible assets as a result of technological advancements, or worse-than-expected performance of acquired companies; and

assumption of, or exposure to, known or unknown contingent liabilities or liabilities that are difficult to identify or accurately quantify.

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In addition, the successful integration of acquired businesses requires significant efforts and expense across all operational areas, including sales and marketing, research and development, manufacturing, finance, legal, and information technologies. There can be no assurance that any of the acquisitions we make will be successful or will be, or will remain, profitable. Our failure to successfully address the above risks may prevent us from achieving the anticipated benefits from any acquisition in a reasonable time frame, or at all.

If we are unable to increase our manufacturing or service capacity and develop and maintain operation of our manufacturing or service capability, we may not be able to launch or support our products or services in a timely manner, or at all.

We continue to rapidly increase our manufacturing and service capacity to meet the anticipated demand for our products. Although we have significantly increased our manufacturing and service capacity and we believe we have plans in place sufficient to ensure we have adequate capacity to meet our current business plans, there are uncertainties inherent in expanding our manufacturing and service capabilities, and we may not be able to sufficiently increase our capacity in a timely manner. For example, manufacturing and product quality issues may arise as we increase production rates at our manufacturing facilities and launch new products. Also, we may not manufacture the right product mix to meet customer demand, especially as we introduce new products. As a result, we may experience difficulties in meeting customer, collaborator, and internal demand, in which case we could lose customers or be required to delay new product introductions, and demand for our products could decline. Additionally, in the past, we have experienced variations in manufacturing conditions and quality control issues that have temporarily reduced or suspended production of certain products. Due to the intricate nature of manufacturing complex instruments, consumables, and products that contain DNA and enzymes, we may encounter similar or previously unknown manufacturing difficulties in the future that could significantly reduce production yields, impact our ability to launch or sell these products (or to produce them economically), prevent us from achieving expected performance levels, any of which could adversely affect our business, financial condition, or results of operations.

An interruption in our ability to manufacture our products or an inability to obtain key components or raw materials due to a catastrophic disaster or infrastructure could adversely affect our business.

We currently manufacture in a limited number of locations. Our manufacturing facilities are located in San Diego and the San Francisco Bay Area in California; Madison, Wisconsin; and Singapore. These areas are subject to natural disasters such as earthquakes, wildfires, or floods. If a natural disaster were to damage one of our facilities significantly or if other events were to cause our operations to fail, we may be unable to manufacture our products, provide our services, or develop new products. In addition, if the capabilities of our suppliers and component manufacturers are limited or stopped, due to disasters, quality, regulatory, or other reasons, it could negatively impact our ability to manufacture our products.

Many of our manufacturing processes are automated and are controlled by our custom-designed laboratory information management system (LIMS). Additionally, the decoding process in our array manufacturing requires significant network and storage infrastructure. If either our LIMS system or our networks or storage infrastructure were to fail for an extended period of time, it may adversely impact our ability to manufacture our products on a timely basis and could prevent us from achieving our expected shipments in any given period.

We also rely on our technology infrastructure, among other functions, to interact with suppliers; sell our products and services; fulfill orders; bill, collect, and make payments; ship products; provide services and support to customers; fulfill contractual obligations; and otherwise conduct business. Our systems may be vulnerable to damage or interruption from natural disasters, power loss, telecommunication failures, terrorist attacks, computer viruses, computer denial-of-service attacks, unauthorized access to customer or employee data or company trade secrets, and other attempts to harm our systems. Certain of our systems are not redundant, and our disaster recovery planning is not sufficient for every eventuality. Despite any precautions we may take, such problems could result in, among other consequences, interruptions in our services, which could harm our reputation and financial results.

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If we lose our key personnel or are unable to attract and retain additional personnel, we may be unable to achieve our goals.

Our future success depends upon the continuing services of members of our senior management team and scientific and engineering personnel. The loss of their services could adversely impact our ability to achieve our business objectives. In addition, the continued growth of our business depends on our ability to hire additional qualified personnel with expertise in molecular biology, chemistry, biological information processing, software, engineering, sales, marketing, and technical support. We compete for qualified management and scientific personnel with other life science and technology companies, universities, and research institutions. Competition for these individuals, particularly in the San Diego and San Francisco areas, is intense,

and the turnover rate can be high. Moreover, changes in immigration policies, laws and regulations in the United States or other jurisdictions may make it more difficult for us to hire and retain members of management and scientific and engineering personnel. Failure to attract and retain management and scientific and engineering personnel could prevent us from pursuing collaborations or developing our products or technologies. Additionally, integration of acquired companies and businesses can be disruptive, causing key employees of the acquired business to leave. Further, we use share-based compensation, including restricted stock units and performance stock units to attract key personnel, incentivize them to remain with us, and align their interests with those of the Company by building long-term stockholder value. If our stock price decreases, the value of these equity awards decreases and therefore reduces a key employee’s incentive to stay.

Any inability to effectively protect our proprietary technologies could harm our competitive position.

The proprietary positions of companies developing tools for the life sciences, genomics, forensics, agricultural, and pharmaceutical industries, including our proprietary position, generally are uncertain and involve complex legal and factual questions. Our success depends to a large extent on our ability to develop proprietary products and technologies and to obtain patents and maintain adequate protection of our intellectual property in the United States and other countries. The laws of some foreign countries do not protect proprietary rights to the same extent as the laws of the United States, and many companies have encountered significant challenges in establishing and enforcing their proprietary rights outside of the United States. These challenges can be caused by the absence of rules and methods for the establishment and enforcement of intellectual property rights outside of the United States.

We will be able to protect our proprietary rights from unauthorized use by third parties only to the extent that our proprietary technologies are covered by valid and enforceable patents or are effectively maintained as trade secrets. Any finding that our patents or applications are unenforceable could harm our ability to prevent others from practicing the related technology, and a finding that others have inventorship or ownership rights to our patents and applications could require us to obtain certain rights to practice related technologies, which may not be available on favorable terms, if at all. Furthermore, as issued patents expire, we may lose some competitive advantage as others develop competing products, and, as a result, we may lose revenue.

In addition, our existing patents and any future patents we obtain may not be sufficiently broad to prevent others from practicing our technologies or from developing competing products and may therefore fail to provide us with any competitive advantage. We may need to initiate lawsuits to protect or enforce our patents, or litigate against third party claims, which would be expensive, and, if we lose, may cause us to lose some of our intellectual property rights and reduce our ability to compete in the marketplace. Furthermore, these lawsuits may divert the attention of our management and technical personnel. There is also the risk that others may independently develop similar or alternative technologies or design around our patented technologies. In that regard, certain patent applications in the United States may be maintained in secrecy until the patents issue, and publication of discoveries in the scientific or patent literature tend to lag behind actual discoveries by several months.

We also rely upon trade secrets and proprietary know-how protection for our confidential and proprietary information, and we have taken security measures to protect this information. These measures, however, may not provide adequate protection for our trade secrets, know-how, or other confidential information.

Our strategic investments and joint ventures may result in losses.

We periodically make strategic investments in various public and private companies with businesses or technologies that may complement our business. In addition, we periodically form companies, such as GRAIL and Helix, that remain consolidated ~~with~~within our financial statements but receive substantial funding from third-party investors who are granted certain control and governance rights. The market values of these strategic investments may fluctuate due to market conditions and other conditions over which we have no control. Other-than-temporary declines in the market price and valuations of the securities that we hold in other companies would require us to record losses related to our investment. This could result in future charges to our earnings. It is uncertain whether or not we will realize any long-term benefits associated with these strategic investments.

~~Table~~In January 2017, we announced that GRAIL has received indications of ~~Contents~~interest to invest approximately $1 billion for GRAIL’s Series B financing, primarily from undisclosed private and strategic investors. GRAIL intends to raise additional capital in the Series B financing from other investors and has engaged a placement agent in connection with the contemplated additional financing. GRAIL intends to close the Series B prior to the end of March 2017. As of the closing of this transaction, we expect our voting interest to become less than 20 percent and that our remaining interest in GRAIL will be treated as a cost-method investment. In addition, we will no longer have representation on GRAIL’s board of directors. Any failure by GRAIL to close the contemplated financing transactions would have a significant, negative impact on its ability to grow. Such a failure

could also result in the continued consolidation of GRAIL within our financial statements, which would result in incremental dilution compared to fiscal year 2016.

Security breaches, including with respect to cyber-security, and other disruptions could compromise our information, products, and services and expose us to liability, which could cause our business and reputation to suffer.

In the ordinary course of our business, we collect and store sensitive data, including intellectual property, our proprietary business information (and that of our customers), and personally identifiable information of our customers and employees, in our data centers and on our networks. The secure maintenance of this information is important to our operations and business strategy. Despite our security measures, our information technology and infrastructure may be vulnerable to cyber-attacks by hackers or breached due to employee error, malfeasance, or other disruptions. As a leader in the field of genetic analysis, we may face cyber-attacks that attempt to penetrate our network security, including our data centers; sabotage or otherwise disable our research, products, and services, including instruments at our customers’ sites; misappropriate our or our customers' and partners' proprietary information, which may include personally identifiable information; or cause interruptions of our internal systems and services. Any such breach could compromise our networks and the information stored there could be accessed, publicly disclosed, lost, or stolen. Any such access, disclosure, or other loss of information could result in legal claims or proceedings, liability under laws that protect the privacy of personal information, and damage to our reputation.

Our products, if used for the diagnosis of disease, could be subject to government regulation, and the regulatory approval and maintenance process for such products may be expensive, time-consuming, and uncertain both in timing and in outcome.

Our products are not subject to FDA clearance or approval if they are not intended to be used for the diagnosis, treatment or prevention of disease. However, as we expand our product line to encompass products that are intended to be used for the diagnosis of disease, such as our FDA-regulated MiSeqDx, certain of our products will become subject to regulation by the FDA, or comparable international agencies, including requirements for regulatory clearance or approval of such products before they can be marketed. Such regulatory approval processes or clearances may be expensive, time-consuming, and uncertain, and our failure to obtain or comply with such approvals and clearances could have an adverse effect on our business, financial condition, or operating results. In addition, changes to the current regulatory framework, including the imposition of additional or new regulations, could arise at any time during the development or marketing of our products, which may negatively affect our ability to obtain or maintain FDA or comparable regulatory approval of our products, if required.

Molecular diagnostic products ~~in particular, depending on their intended use, may be~~are regulated as medical devices by the FDA and comparable international agencies and may require either clearance from the FDA following the 510(k) pre-market notification process or premarket approval from the FDA, in each case prior to marketing. Obtaining the requisite regulatory approvals can be expensive and may involve considerable delay. If we fail to obtain, or experience significant delays in obtaining, regulatory approvals for molecular diagnostic products that we develop, we may not be able to launch or successfully commercialize such products in a timely manner, or at all.

In addition, if our products labeled as ~~“Research~~“For Research Use ~~Only,~~Only. Not for use in diagnostic procedures,” or RUO, are used, or could be used, for the diagnosis of disease, the regulatory requirements related to marketing, selling, and supporting such products could change or be uncertain, even if such use by our customers is without our consent. If the FDA or other regulatory authorities assert that any of our RUO products are subject to regulatory clearance or approval, our business, financial condition, or results of operations could be adversely affected.

If the FDA requires in the future that any of our LDT products be subject to regulatory clearance or approval, our business, financial condition, or results of operations could be adversely affected.

Certain of our diagnostic products are currently available through laboratories that are certified under the Clinical Laboratory Improvements Amendments (CLIA) of 1988. These products are commonly called “laboratory developed tests,” or LDTs. For a number of years, the FDA has exercised its regulatory enforcement discretion to not regulate LDTs as medical devices if created and used within a single laboratory. However, the FDA has been reconsidering its enforcement discretion policy and has commented that regulation of LDTs may be warranted because of the growth in the volume and complexity of testing services utilizing LDTs. In October 2014, the FDA published two draft guidance documents suggesting an approach for registration and listing of laboratories and assays along with a framework for regulation of LDTs by the FDA based on risk to patients rather than whether the LDTs were made by a conventional manufacturer or a single laboratory. The draft framework guidance includes pre-market review for higher-risk LDTs, including many used to guide treatment decisions, as well as companion diagnostics that have entered the market as LDTs. We cannot predict the nature or extent of the FDA's final guidance or regulation of LDTs, in general, or with respect to our LDTs, in particular. If the FDA requires in the future that

LDT products are subject to regulatory clearance or approval, our business, financial condition, or results of operations could be adversely affected.

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If product or service liability lawsuits are successfully brought against us, we may face reduced demand for our products and incur significant liabilities.

Our products and services are used for sensitive applications, and we face an inherent risk of exposure to product or service liability claims if our products or services are alleged to have caused harm, resulted in false negatives or false positives, or do not perform in accordance with specifications. Product liability claims filed against us or against third parties ~~who~~to whom we may have an obligation could be costly and time-consuming to defend and result in substantial damages or reputational risk. We cannot be certain that we would be able to successfully defend any product or service liability lawsuit brought against us. Regardless of merit or eventual outcome, product or service liability claims may result in:

decreased demand for our products;

injury to our reputation;

increased product liability insurance costs;

costs of related litigation; and

substantial monetary awards to plaintiffs.

Although we carry product and service liability insurance, if we become the subject of a successful product or service liability lawsuit, our insurance may not cover all substantial liabilities, which could have an adverse effect on our business, financial condition, or results of operations.

Doing business internationally creates operational and financial risks for our business.

Conducting and launching operations on an international scale requires close coordination of activities across multiple jurisdictions and time zones and consumes significant management resources. If we fail to coordinate and manage these activities effectively, including the risks noted below, our business, financial condition, or results of operations could be adversely affected. We have sales offices located internationally throughout Europe, the Asia-Pacific region, and Brazil, as well as manufacturing facilities in Singapore. Shipments to customers outside the United States comprised 46%, ~~49%~~46%, and ~~50%~~49% of our total revenue for fiscal years ~~2015~~2016, ~~2014~~2015, and ~~2013~~2014, respectively.

During ~~2015~~2016, a significant portion of our sales were denominated in foreign currencies while the majority of our purchases of raw materials were denominated in U.S. dollars. Changes in the value of the relevant currencies may affect the cost of certain items required in our operations. Changes in currency exchange rates may also affect the relative prices at which we are able sell products in the same market. Our revenues from international customers may be negatively impacted as increases in the U.S. dollar relative to our international customers local currency could make our products more expensive, impacting our ability to compete. Our costs of materials from international suppliers may increase if, in order to continue doing business with us, they raise their prices as the value of the U.S. dollar decreases relative to their local currency. Foreign policies and actions regarding currency valuation could result in actions by the United States and other countries to offset the effects of such fluctuations. Recent global financial conditions have led to a high level of volatility in foreign currency exchange rates and that level of volatility may continue, which could adversely affect our business, financial condition, or results of operations.

In addition to the foregoing risks, international operations entail the following risks:

longer payment cycles and difficulties in collecting accounts receivable outside of the United States;

longer sales cycles due to the volume of transactions taking place through public tenders;

challenges in staffing and managing foreign operations;

tariffs and other trade barriers;

unexpected changes in legislative or regulatory requirements of foreign countries into which we sell our products;

difficulties in obtaining export licenses or in overcoming other trade barriers and restrictions resulting in delivery delays; and

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significant taxes or other burdens of complying with a variety of foreign laws.

Additionally, we must comply with complex foreign and U.S. laws and regulations, such as the U.S. Foreign Corrupt Practices Act, the U.K. Bribery Act, and other local laws prohibiting corrupt payments to governmental officials, anti-competition regulations and sanctions imposed by the U.S. Office of Foreign Assets Control and other similar laws and regulations. Violations of these laws and regulations could result in fines and penalties, criminal sanctions, restrictions on our business conduct and on our ability to offer our products in one or more countries, and could also materially affect our brand, our ability to attract and retain employees, our international operations, our business and our operating results. Although we have implemented policies and procedures designed to ensure compliance with these laws and regulations, there can be no assurance that our employees, contractors, or agents will not violate our policies.

We are subject to risks related to taxation in multiple jurisdictions.

We are subject to income taxes in both the United States and numerous foreign jurisdictions. Significant judgments based on interpretations of existing tax laws or regulations are required in determining the provision for income taxes. Our effective income tax rate could be adversely affected by various factors, including, but not limited to, changes in the mix of earnings in tax jurisdictions with different statutory tax rates, changes in the valuation of deferred tax assets and liabilities, changes in existing tax policies, laws, regulations, or ~~tax~~ rates, changes in the level of non-deductible expenses (including share-based compensation), location of operations, changes in our future levels of research and development spending, mergers and acquisitions, or the result of examinations by various tax authorities. Although we believe our tax estimates are reasonable, if the U.S. Internal Revenue Service or other taxing authority disagrees with the positions taken by the Company on its tax returns, we could have additional tax liability, including interest and penalties. If material, payment of such additional amounts upon final adjudication of any disputes could have a material impact on our results of operations and financial position.

Our operating results may vary significantly from period to period, and we may not be able to sustain operating profitability.

Our revenue is subject to fluctuations due to the timing of sales of high-value products and services, the effects of new product launches and related promotions, the timing and availability of our customers’ funding, the impact of seasonal spending patterns, the timing and size of research projects our customers perform, changes in overall spending levels in the life sciences industry, and other unpredictable factors that may affect customer ordering patterns. Given the difficulty in predicting the timing and magnitude of sales for our products and services, we may experience quarter-to-quarter fluctuations in revenue resulting in the potential for a sequential decline in quarterly revenue. While we anticipate future growth, there is some uncertainty as to the timing of revenue recognition on a quarterly basis. This is because a substantial portion of our quarterly revenue is typically recognized in the last month of a quarter and because the pattern for revenue generation during that month is normally not linear, with a concentration of orders in the final weeks of the quarter. In light of that, our revenue cut-off and recognition procedures, together with our manufacturing and shipping operations, may experience increased pressure and demand during the time period shortly before the end of a fiscal quarter.

A large portion of our expenses are relatively fixed, including expenses for facilities, equipment, and personnel. To meet the anticipated growth in our business, we may incur fixed expenses, such as costs related to facility expansions, before we generate revenue sufficient to fully support such expenses. In addition, we expect operating expenses to continue to increase significantly in absolute dollars, and we expect that our research and development and selling and marketing expenses will increase at a higher rate in the future as a result of the development and launch of new products. Accordingly, our ability to sustain profitability will depend in part on the rate of growth, if any, of our revenue and on the level of our expenses, and if revenue does not grow as anticipated, we may not be able to maintain annual or quarterly profitability. Any significant delays in the commercial launch of our products, unfavorable sales trends in our existing product lines, or impacts from the other factors mentioned above, could adversely affect our future revenue growth or cause a sequential decline in quarterly revenue. In addition, non-cash share-based compensation expense and expenses related to prior and future acquisitions are also likely to continue to adversely affect our future profitability. Due to the possibility of significant fluctuations in our revenue and expenses, particularly from quarter to quarter, we believe that quarterly comparisons of our operating results are not a good indication of our future performance. If our operating results fluctuate or do not meet the expectations of stock market analysts and investors, our stock price could decline.

From time to time, we receive large orders that have a significant effect on our operating results in the period in which the order is recognized as revenue. The timing of such orders is difficult to predict, and the timing of revenue recognition from

such orders may affect period to period changes in net sales. As a result, our operating results could vary materially from quarter to quarter based on the receipt of such orders and their ultimate recognition as revenue.

We may not be able to convert our order backlog into revenue.

Our backlog consists of orders believed to be firm as of the balance-sheet date. However, we may allow customers to make product substitutions as we launch new products. We may not receive revenue from some of these orders, and the order backlog we report may not be indicative of our future revenue. Many events can cause an order to be delayed or not completed at all, some of which may be out of our control. If we delay fulfilling customer orders, or if customers reconsider their orders, those customers may seek to cancel or modify their orders with us. Customers may otherwise seek to cancel or delay their orders even if we are prepared to fulfill them. If our orders in backlog do not result in sales, our operating results may suffer.

Disruption of critical information technology systems or material breaches in the security of our systems could have an adverse effect on our operations, business, customer relations, and financial condition.

Information technology systems (IT) help us operate efficiently, interface with customers, maintain financial accuracy and efficiency, and accurately produce our financial statements. IT systems are used extensively in virtually all aspects of our business, including product manufacturing and supply chain, sales forecast, order fulfillment and billing, customer service, logistics, and management of financial reports and data. Our success depends, in part, on the continued and uninterrupted performance of our IT systems. IT systems may be vulnerable to damage from a variety of sources, including telecommunications or network failures, power loss, natural disasters, human acts, computer viruses, computer ~~denial-of-~~

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~~service~~denial-of-service attacks, unauthorized access to customer or employee data or company trade secrets, and other attempts to harm our systems. Certain of our systems are not redundant, and our disaster recovery planning is not sufficient for every eventuality. Despite any precautions we may take, such problems could result in, among other consequences, disruption of our operations, which could harm our reputation and financial results.

If we do not allocate and effectively manage the resources necessary to build and sustain the proper IT infrastructure, we could be subject to transaction errors, processing inefficiencies, the loss of customers, business disruptions, or the loss of or damage to intellectual property through security breach. If our data management systems do not effectively collect, store, process, and report relevant data for the operation of our business, whether due to equipment malfunction or constraints, software deficiencies, or human error, our ability to effectively plan, forecast, and execute our business plan and comply with applicable laws and regulations will be impaired. Any such impairment could adversely affect our reputation, financial condition, results of operations, cash flows, and the timeliness with which we report our internal and external operating results.

As ~~a part of our ongoing effort to upgrade our IT systems, in 2015~~ we ~~implemented new enterprise resource planning software and other software applications to manage certain of our business operations. As we continue to~~continuously adjust our work-flow and business practices and add additional functionality to our enterprise resource planning software and other software applications, problems could arise that we have not foreseen, including interruptions in service, loss of data, or reduced functionality. Such problems could adversely impact our ability to provide quotes, take customer orders, and otherwise run our business in a timely manner. In addition, if our new systems fail to provide accurate and increased visibility into pricing and cost structures, it may be difficult to improve or maximize our profit margins. As a result, our results of operations and cash flows could be adversely affected.

Changes in accounting standards and subjective assumptions, estimates, and judgments by management related to complex accounting matters could significantly affect our financial results or financial condition.

Generally accepted accounting principles and related accounting pronouncements, implementation guidelines, and interpretations with regard to a wide range of matters that are relevant to our business, such as revenue recognition, asset impairment and fair value determinations, inventories, business combinations and intangible asset valuations, and litigation, are highly complex and involve many subjective assumptions, estimates, and judgments. In particular, accounting rules related to companies that we form together with, or that receive substantial funding from, third-party investors such as GRAIL and Helix are highly complex and involve many subjective assumptions, estimates, and judgments. Changes in these rules or their interpretation or changes in underlying assumptions, estimates, or judgments could significantly change our reported or expected financial performance or financial condition.

Ethical, legal, and social concerns related to the use of genetic information could reduce demand for our products or services.

Our products may be used to provide genetic information about humans, agricultural crops, other food sources, and other living organisms. The information obtained from our products could be used in a variety of applications, which may have underlying ethical, legal, and social concerns regarding privacy and the appropriate uses of the resulting information, including preimplantation genetic screening of embryos, prenatal genetic testing, genetic engineering or modification of agricultural products, or testing genetic predisposition for certain medical conditions, particularly for those that have no known cure. Governmental authorities could, for social or other purposes, call for limits on or regulation of the use of genetic testing or prohibit testing for genetic predisposition to certain conditions, particularly for those that have no known cure. Similarly, such concerns may lead individuals to refuse to use genetics tests even if permissible. These and other ethical, legal, and social concerns about genetic testing may limit market acceptance of our technology for certain applications or reduce the potential markets for our technology, either of which could have an adverse effect on our business, financial condition, or results of operations.

Conversion of our outstanding convertible notes may result in losses.

As of January ~~3, 2016,~~1, 2017, we had ~~$75.5 million aggregate principal amount of convertible notes due 2016,~~ $632.5 million aggregate principal amount of convertible notes due 2019, and $517.5 million aggregate principal amount of convertible notes due 2021 outstanding. The notes are convertible into cash, and if applicable, shares of our common stock under certain circumstances, including trading price conditions related to our common stock. ~~If the trading price of our common stock remains significantly above the conversion price of~~ ~~$83.55~~ ~~with respect to convertible notes due 2016, we believe that some noteholders will elect to convert the applicable notes.~~ Upon conversion, we are required to record a gain or loss for the difference between the fair value of the notes to be extinguished and their corresponding net carrying value. The fair value of the notes to be extinguished depends on our current incremental borrowing rate. The net carrying value of our notes has an implicit interest rate of ~~4.5% with respect to convertible notes due 2016,~~ 2.9% with respect to convertible notes due 2019, and

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3.5% with respect to convertible notes due 2021. If our incremental borrowing rate at the time of conversion is lower than the implied interest rate of the notes, we will record a loss in our consolidated statement of income during the period in which the notes are converted.

Our Certificate of Incorporation and Bylaws include anti-takeover provisions that may make it difficult for another company to acquire control of us or limit the price investors might be willing to pay for our stock.

Certain provisions of our Certificate of Incorporation and Bylaws could delay the removal of incumbent directors and could make it more difficult to successfully complete a merger, tender offer, or proxy contest involving us. Our Certificate of Incorporation has provisions that give our Board the ability to issue preferred stock and determine the rights and designations of the preferred stock at any time without stockholder approval. The rights of the holders of our common stock will be subject to, and may be adversely affected by, the rights of the holders of any preferred stock that may be issued in the future. The issuance of preferred stock, while providing flexibility in connection with possible acquisitions and other corporate purposes, could have the effect of making it more difficult for a third party to acquire, or of discouraging a third party from acquiring, a majority of our outstanding voting stock. In addition, the staggered terms of our board of directors could have the effect of delaying or deferring a change in control.

In addition, certain provisions of the Delaware General Corporation Law (DGCL), including Section 203 of the DGCL, may have the effect of delaying or preventing changes in the control or management of Illumina. Section 203 of the DGCL provides, with certain exceptions, for waiting periods applicable to business combinations with stockholders owning at least 15% and less than 85% of the voting stock (exclusive of stock held by directors, officers, and employee plans) of a company.

The above factors may have the effect of deterring hostile takeovers or otherwise delaying or preventing changes in the control or management of Illumina, including transactions in which our stockholders might otherwise receive a premium over the fair market value of our common stock.


ITEM 1B.	Unresolved Staff Comments.

None.


ITEM 2.	Properties.

The following table summarizes the facilities we lease as of January ~~3, 2016,~~1, 2017, including the location and size of each principal facility, and their designated use. We believe our facilities are adequate for our current and near-term needs, and will be able to locate additional facilities as needed.

Location

Approximate Square Feet

Operation

Lease

Expiration Dates

Approximate Square Feet

Operation

Lease

Expiration Dates

San Diego, CA

876,000

R&D, Manufacturing, Warehouse, Distribution, and Administrative

2017 – 2031

San Diego, CA*

902,000

R&D, Manufacturing, Warehouse, Distribution, and Administrative

2018 – 2031

San Francisco Bay Area, CA*

268,000

R&D, Manufacturing, Warehouse, and Administrative

2016 – 2024

274,000

R&D, Manufacturing, Warehouse, and Administrative

2018 – 2026

Singapore

167,000

R&D, Manufacturing, Warehouse, Distribution, and Administrative

2016 – 2021

211,000

R&D, Manufacturing, Warehouse, Distribution, and Administrative

2018 – 2021

Cambridge, United Kingdom*

94,000

R&D, Manufacturing, and Administrative

2017 – 2024

105,000

R&D, Manufacturing, and Administrative

2017 – 2024

Eindhoven, the Netherlands

42,000

Distribution and Administrative

2020

42,000

Distribution and Administrative

2020

Madison, WI

38,000

R&D, Manufacturing, Distribution, and Administrative

2019

73,000

R&D, Manufacturing, Warehouse, Distribution, and Administrative

2018 – 2019

Other

39,000

Administrative

2016 - 2019

47,000

Administrative

2017 – 2019

________________

*Excludes approximately ~~360,000 and 155,000~~885,000 square feet ~~in Foster City, California, and Cambridge, United Kingdom, respectively, as~~for which the leases do not commence until ~~2017.~~2017 and beyond.

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ITEM 3.	Legal Proceedings.

We are involved in various lawsuits and claims arising in the ordinary course of business, including actions with respect to intellectual property, employment, and contractual matters. In connection with these matters, we assesses, on a regular basis, the probability and range of possible loss based on the developments in these matters. A liability is recorded in the financial statements if it is believed to be probable that a loss has been incurred and the amount of the loss can be reasonably estimated. Because litigation is inherently unpredictable and unfavorable results could occur, assessing contingencies is highly subjective and requires judgments about future events. We regularly review outstanding legal matters to determine the adequacy of the liabilities accrued and related disclosures. The amount of ultimate loss may differ from these estimates. Each matter presents its own unique circumstances, and prior litigation does not necessarily provide a reliable basis on which to predict the outcome, or range of outcomes, in any individual proceeding. Because of the uncertainties related to the occurrence, amount, and range of loss on any pending litigation or claim, we are currently unable to predict their ultimate outcome, and, with respect to any pending litigation or claim where no liability has been accrued, to make a meaningful estimate of the reasonably possible loss or range of loss that could result from an unfavorable outcome. In the event that opposing litigants in outstanding litigations or claims ultimately succeed at trial and any subsequent appeals on their claims, any potential loss or charges in excess of any established accruals, individually or in the aggregate, could have a material adverse effect on our business, financial condition, results of operations, and/or cash flows in the period in which the unfavorable outcome occurs or becomes probable, and potentially in future periods.


ITEM 4.	Mine Safety Disclosures.

Not applicable.

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PART II


ITEM 5.	Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities.

Market Information

Our common stock has been quoted on The NASDAQ Global Select Market under the symbol “ILMN” since July 28, 2000. Prior to that time, there was no public market for our common stock. The following table sets forth, for the fiscal periods indicated, the quarterly high and low sales prices per share of our common stock as reported on The NASDAQ Global Select Market.


	2015				2014				2016				2015
	High		Low		High		Low		High		Low		High		Low
First Quarter	$	213.33	$	178.52	$	183.30	$	106.79	$	188.25	$	130.37	$	213.33	$	178.52
Second Quarter	$	223.08	$	178.68	$	178.19	$	127.69	$	178.77	$	127.10	$	223.08	$	178.68
Third Quarter	$	242.37	$	170.29	$	185.00	$	156.85	$	182.67	$	132.65	$	242.37	$	170.29
Fourth Quarter	$	196.47	$	130.00	$	197.37	$	145.12	$	186.88	$	119.37	$	196.47	$	130.00

Stock Performance Graph

The graph below compares the cumulative total stockholder returns on our common stock for the last five fiscal years with the cumulative total stockholder returns on the NASDAQ Composite Index, the NASDAQ Biotechnology Index, and the S&P 500 Index for the same period. The graph assumes that $100 was invested on January ~~2, 2011~~1, 2012 in our common stock and in each index and that all dividends were reinvested. No cash dividends have been declared on our common stock. Stockholder returns over the indicated period should not be considered indicative of future stockholder returns.

Compare 5-Year Cumulative Total Return among Illumina, NASDAQ Composite Index,

NASDAQ Biotechnology Index, and S&P 500 Index

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Holders

As of February ~~19, 2016,~~3, 2017, we had ~~195~~184 record holders of our common stock.

Dividends

We have never paid cash dividends and have no present intention to pay cash dividends in the foreseeable future. The indentures for our ~~0.25% convertible senior notes due 2016,~~ 0% convertible senior notes due 2019 and 0.5% convertible senior notes due in 2021, which notes are convertible into cash and, in certain circumstances, shares of our common stock, require us to increase the conversion rate applicable to the notes if we pay any cash dividends.

Purchases of Equity Securities by the Issuer

On ~~May 1, 2015, the Company’s Board of Directors authorized share repurchases for up to $150.0 million of repurchases under a Rule 10b5-1 plan. In addition, on October 29, 2015,~~July 28, 2016, the Company’s Board of Directors authorized a new ~~discretionary~~ share repurchase program, which supersedes all prior and available repurchase authorizations, to repurchase $250.0 million of ~~$250.0 million.~~outstanding common stock. The following table summarizes shares repurchased pursuant to ~~these programs~~this program during the three months ended January ~~3, 2016.~~1, 2017.

Period

Total Number
of Shares
Purchased (1)

Average Price
Paid per Share Total Number of
Shares Purchased as
Part of Publicly
Announced Programs Approximate Dollar
Value of Shares
that May Yet Be
Purchased Under
the Programs
September 28, 2015 - October 25, 2015 56,772
$ 153.59
56,772
$ 199,402,046
October 26, 2015 - November 22, 2015 1,210,271
$ 149.79
1,210,271
$ 268,110,431
November 23, 2015 - January 3, 2016 66,930
$ 179.29
66,930
$ 256,110,853
Total 1,333,973
$ 151.44
1,333,973
$ 256,110,853



Period	Total Number of Shares Purchased (1)	Average Price Paid per Share		Total Number of Shares Purchased as Part of Publicly Announced Programs	Approximate Dollar Value of Shares that May Yet Be Purchased Under the Programs
October 3, 2016 - October 30, 2016	—	—		—	$	236,926,941
October 31, 2016 - November 27, 2016	—	—		—	$	236,926,941
November 28, 2016 - January 1, 2017	1,056,021	$	129.02	1,056,021	$	100,680,660
Total	1,056,021	$	129.02	1,056,021	$	100,680,660

___________

(1) All shares purchased during the three months ended January ~~3, 2016,~~1, 2017, were made in open-market transactions.

Sales of Unregistered Securities

None during the fiscal quarter ended January ~~3, 2016.~~1, 2017.

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ITEM 6.	Selected Financial Data.

The following table sets forth selected historical consolidated financial data for each of our last five fiscal years during the period ended January ~~3, 2016.~~1, 2017. This information should be read in conjunction with the consolidated financial statements of the Company and notes thereto included in in Part II, Item 8 of this Form 10-K.

Statement of Income Data


	Years Ended										Years Ended
	January 3, 2016 (53 weeks)		December 28, 2014 (52 weeks)		December 29, 2013 (52 weeks)		December 30, 2012 (52 weeks)		January 1, 2012 (52 weeks)		January 1, 2017 (52 weeks)		January 3, 2016 (53 weeks)		December 28, 2014 (52 weeks)		December 29, 2013 (52 weeks)		December 30, 2012 (52 weeks)
	(In thousands, except per share data)										(In thousands, except per share data)
Total revenue	$	2,219,762	$	1,861,358	$	1,421,178	$	1,148,516	$	1,055,535	$	2,398,373	$	2,219,762	$	1,861,358	$	1,421,178	$	1,148,516
Income from operations	$	612,841	$	514,711	$	134,107	$	200,752	$	199,461	$	587,032	$	612,841	$	514,711	$	134,107	$	200,752
Consolidated net income	$	457,390	$	353,351	$	125,308	$	151,254	$	86,628	$	428,090	$	457,390	$	353,351	$	125,308	$	151,254
Net loss attributable to noncontrolling interests	$	4,169	—		—		—		—
Net income attributable to Illumina stockholders	$	461,559	$	353,351	$	125,308	$	151,254	$	86,628	$	462,649	$	461,559	$	353,351	$	125,308	$	151,254
Net income attributable to Illumina stockholders for earnings per share											$	454,106	$	461,526	$	353,351	$	125,308	$	151,254
Earnings per share attributable to Illumina stockholders:
Basic	$	3.19	$	2.61	$	1.00	$	1.23	$	0.70	$	3.09	$	3.19	$	2.61	$	1.00	$	1.23
Diluted	$	3.10	$	2.37	$	0.90	$	1.13	$	0.62	$	3.07	$	3.10	$	2.37	$	0.90	$	1.13
Shares used in calculating earnings per share:	Shares used in calculating earnings per share:										Shares used in calculating earnings per share:
Basic	144,826		135,553		125,076		122,999		123,399		146,788		144,826		135,553		125,076		122,999
Diluted	149,069		148,977		139,936		133,693		138,937		148,040		149,069		148,977		139,936		133,693

Balance Sheet Data


	January 3, 2016		December 28, 2014		December 29, 2013		December 30, 2012		January 1, 2012		January 1, 2017		January 3, 2016		December 28, 2014		December 29, 2013		December 30, 2012
	(In thousands)										(In thousands)
Cash, cash equivalents and short-term investments	$	1,386,220	$	1,338,371	$	1,165,603	$	1,350,204	$	1,189,568	$	1,558,724	$	1,386,220	$	1,338,371	$	1,165,603	$	1,350,204
Total assets	$	3,687,747	$	3,339,640	$	3,019,006	$	2,566,085	$	2,195,840	$	4,280,600	$	3,687,747	$	3,339,640	$	3,019,006	$	2,566,085
Long-term debt, less current portion	$	1,015,649	$	986,780	$	839,305	$	805,406	$	807,369	$	1,047,805	$	1,015,649	$	986,780	$	839,305	$	805,406
Redeemable noncontrolling interest	$	32,546	—		—		—		—		$	43,940	$	32,546	—		—		—
Total stockholders’ equity	$	1,848,553	$	1,462,798	$	1,533,202	$	1,318,581	$	1,075,215	$	2,197,229	$	1,848,553	$	1,462,798	$	1,533,202	$	1,318,581


ITEM 7.	Management’s Discussion and Analysis of Financial Condition and Results of Operations.

Our Management’s Discussion and Analysis of Financial Condition and Results of Operations (MD&A) will help readers understand our results of operations, financial condition, and cash flow. It is provided in addition to the accompanying consolidated financial statements and notes. This MD&A is organized as follows:

Business Overview and Outlook. High level discussion of our operating results and significant known trends that affect our business.

Results of Operations. Detailed discussion of our revenues and expenses.

Liquidity and Capital Resources. Discussion of key aspects of our statements of cash flows, changes in our financial position, and our financial commitments.

Off-Balance Sheet Arrangements. We have no ~~significant~~ off-balance sheet arrangements.

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Contractual Obligations. Tabular disclosure of known contractual obligations as of January ~~3, 2016.~~1, 2017.

Critical Accounting Policies and Estimates. Discussion of significant changes we believe are important to understanding the assumptions and judgments underlying our financial statements.

Recent Accounting Pronouncements.

This MD&A discussion contains forward-looking statements that involve risks and uncertainties. See “Special Note Regarding Forward-Looking Statements” for additional factors relating to such statements. See “Risk Factors” in Item 1A of this report for a discussion of certain risk factors applicable to our business, financial condition, and results of operations. Operating results are not necessarily indicative of results that may occur in future periods.

Business Overview and Outlook

Our Company is organized into three operating segments for purposes of evaluating our business operations and reviewing our financial results. One segment consists of Illumina’s core operations (Core Illumina). The other two segments relate to the activities of our consolidated variable interest entities (VIEs), GRAIL and Helix. The combined results of operations of our consolidated VIEs became material during the year ended January 1, 2017. As such, we commenced reporting two segments, Core Illumina and Consolidated VIEs, during 2016. For information on GRAIL and Helix, refer to note “12. Segment Information, Geographic Data, and Significant Customers” in Part II, Item 8 of this Form 10-K.

Our focus on innovation has established us as the global leader in ~~sequencing~~sequencing- and array-based technologies, serving customers in a wide range of markets, enabling the adoption of genomic solutions in research and clinical settings.

Our customers include leading genomic research centers, academic institutions, government laboratories, and ~~applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture,~~hospitals, as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostic laboratories, and ~~other emerging market segments.~~consumer genomics companies.

Our portfolio of integrated systems, consumables, and analysis tools is designed to accelerate and simplify genetic analysis. This portfolio addresses athe range of genomic complexity, price points, and throughput, enabling customers to select the best solution for their research or clinical challenge.

~~Financial~~Consolidated financial highlights ~~for~~ ~~2015~~ include the following:

Net revenue increased ~~19.3%~~8.0% in ~~2015~~2016 over ~~2014~~2015~~. Our~~ due to the growth in sales ~~increased across~~of our ~~portfolio~~sequencing consumables and services, partially offset by lower shipments of ~~sequencing products, including consumables, instruments, and services.~~our high-throughput platforms. We expect our revenue to continue to increase in ~~2016.~~2017.

Gross profit as a percentage of revenue (gross margin) ~~increased~~decreased to69.5% in 2016 from 69.8% in 2015 ~~from~~ ~~69.7%~~ in ~~2014~~. Gross margins in ~~2015~~2016 ~~increased~~decreased primarily due to our increased manufacturing capacity, which was partially offset by a ~~positive shift in product~~greater mix toof sequencing consumables. Gross margin in 2014 was favorably impacted by the litigation settlement with Syntrix, which resulted in reversal of cost of sales of $10.4 million. See detailed discussions on this matter in note “9. Legal Proceedings” in Part II, Item 8 of this Form 10-K. We believe ourOur gross margin in future periods will depend on several factors, including: market conditions that may impact our pricing power; sales mix changes among consumables, instruments, and services; product mix changes between established products and new products in new markets; excess and obsolete inventories; royalties; our cost structure for manufacturing operations; and product support obligations.

Income from operations as a percentage of revenue ~~increased$98.1 million~~decreased to 24.5% in 2016 compared to 27.6% in 2015 ~~compared~~primarily due to~~2014~~ ~~as a result of higher revenue, despite~~ the increase in research and development and selling, general, and administrative expenses ~~which we~~as a percentage of revenue. We expect ~~will~~research and development and selling, general and administrative expenses to continue to grow.

Our effective tax rate was 23.7% and 21.6% in 2016 and ~~21.3% in~~ 2015, ~~and 2014,~~ respectively. The variance from the U.S. federal statutory tax rate of 35% was primarily attributable to a discrete tax benefit of $24.8 million, related to the exclusion of stock compensation from prior period cost-sharing charges as a result of a recent tax court opinion in which an unrelated third party was successful in challenging such charges. If this tax court opinion is overturned, our tax rate will be adversely impacted by the reversal of the discrete tax benefit recorded this year and any stock compensation that should have been included in the cost-sharing charges from this year going forward. The decrease from the U.S. federal statutory tax rate also resulted from the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore and the United ~~Kingdom.~~Kingdom, partially offset by the tax impact associated with the investments in our consolidated variable interest entities.

Our future effective tax rate may vary from the U.S. federal statutory tax rate due to the mix of earnings in tax jurisdictions with different statutory tax rates and the other factors discussed in the risk factor “We are subject to risks related to taxation in multiple jurisdictions” in Part I Item 1A “Risk Factors” of this Form 10-K. We may

also be adversely impacted in the future if the tax court opinion regarding the exclusion of stock compensation from cost-sharing charges is overturned. We anticipate that our effective tax rate will trend lower than the U.S. federal statutory tax rate in the future due to the portion of our earnings that will be subject to lower statutory tax rates.

We ended ~~2015~~2016 with cash, cash equivalents, and short-term investments totaling $~~1.4~~1.6 billion., of which approximately $749.7 million was held by our foreign subsidiaries. Cash and cash equivalents held by our consolidated VIEs as of January 1, 2017 were $75.9 million.

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This overview and outlook provides a high-level discussion of our operating results and significant known trends that affect our business. We believe that an understanding of these trends is important to understanding our financial results for the periods reported herein as well as our future financial performance. This summary is not intended to be exhaustive, nor is it intended to be a substitute for the detailed discussion and analysis provided elsewhere in this Annual Report on Form 10-K.

Results of Operations

To enhance comparability, the following table sets forth audited consolidated statement of operations data for the years ended January 1, 2017, January 3, 2016~~December 28, 2014~~, and December ~~29, 2013~~28, 2014, stated as a percentage of total revenue.


	2015		2014		2013		2016		2015		2014
Revenue:
Product revenue	85.2	%	87.0	%	89.0	%	84.7	%	85.2	%	87.0	%
Service and other revenue	14.8		13.0		11.0		15.3		14.8		13.0
Total revenue	100.0		100.0		100.0		100.0		100.0		100.0
Cost of revenue:
Cost of product revenue	22.1		23.2		28.7		22.3		22.1		23.2
Cost of service and other revenue	6.0		5.0		4.8		6.4		6.0		5.0
Amortization of acquired intangible assets	2.1		2.1		2.3		1.8		2.1		2.1
Total cost of revenue	30.2		30.3		35.8		30.5		30.2		30.3
Gross profit	69.8		69.7		64.2		69.5		69.8		69.7
Operating expense:
Research and development	18.1		20.8		19.5		21.0		18.1		20.8
Selling, general and administrative	23.6		25.1		26.8		24.3		23.6		25.1
Legal contingencies	0.9		(4.0	)	8.1		(0.4	)	0.9		(4.0	)
Acquisition related gain, net	(0.3	)	(0.1	)	(0.8	)	—		(0.3	)	(0.1	)
Headquarter relocation	(0.1	)	0.3		0.2		0.1		(0.1	)	0.3
Unsolicited tender offer related expense	—		—		1.0
Total operating expense	42.2		42.1		54.8		45.0		42.2		42.1
Income from operations	27.6		27.6		9.4		24.5		27.6		27.6
Other income (expense):
Interest income	0.2		0.3		0.3		0.4		0.2		0.3
Interest expense	(1.9	)	(2.2	)	(2.7	)	(1.4	)	(1.9	)	(2.2	)
Cost-method investment gain, net	0.7		0.2		4.3		—		0.7		0.2
Other expense, net	(0.3	)	(1.8	)	(0.1	)	(0.1	)	(0.3	)	(1.8	)
Total other (expense) income, net	(1.3	)	(3.5	)	1.8
Total other expense, net							(1.1	)	(1.3	)	(3.5	)
Income before income taxes	26.3		24.1		11.2		23.4		26.3		24.1
Provision for income taxes	5.7		5.1		2.4		5.6		5.7		5.1
Consolidated net income	20.6		19.0		8.8		17.8		20.6		19.0
Add: Net loss attributable to noncontrolling interests	0.2		—		—		1.5		0.2		—
Net income attributable to Illumina stockholders	20.8	%	19.0	%	8.8	%	19.3	%	20.8	%	19.0	%

Our fiscal year is the 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. Fiscal year 2016 was 52 weeks, fiscal year 2015 was 53 weeks, and ~~each of~~ fiscal ~~years~~year 2014 ~~and 2013 were~~was 52 weeks.

~~Table of Contents~~

Revenue


	2015 - 2014								2014 - 2013						2016 - 2015								2015 - 2014
(Dollars in thousands)	2015		2014		Change		% Change		2013		Change		% Change		2016		2015		Change		% Change		2014		Change		% Change
Product revenue	$	1,890,633	$	1,619,511	$	271,122	17	%	$	1,264,656	$	354,855	28	%	$	2,031,997	$	1,890,633	$	141,364	7	%	$	1,619,511	$	271,122	17	%
Service and other revenue	329,129		241,847		87,282		36		156,522		85,325		55		366,376		329,129		37,247		11		241,847		87,282		36
Total revenue	$	2,219,762	$	1,861,358	$	358,404	19	%	$	1,421,178	$	440,180	31	%	$	2,398,373	$	2,219,762	$	178,611	8	%	$	1,861,358	$	358,404	19	%

Product revenue consists primarily of revenue from sales of consumables and instruments. Service and other revenue consists primarily of sequencing and genotyping service revenue as well as instrument service contract revenue. Our consolidated VIEs are in the development stage and have no revenues to date.

2016 Compared to 2015

Revenue increased$178.6 million, or 8%, to $2,398.4 million in 2016 compared to $2,219.8 million in 2015.

Consumables revenue increased$263.6 million, or 21%, to $1,543.5 million in 2016 compared to $1,279.9 million in 2015, driven by growth in the sequencing instrument installed base.

Instrument revenue decreased$125.2 million, or 21%, to $469.5 million in 2016 compared to $594.7 million in 2015, primarily due to lower shipments of our high-throughput platforms.

Service and other revenue increased $37.2 million, or 11%, to $366.4 million in 2016 compared to $329.1 million in 2015, driven by revenue from genotyping services and instrument service contracts associated with a larger sequencing installed base, partially offset by our NIPT customers shifting to in-house testing on our sequencers.

2015 Compared to 2014

Revenue increased $358.4 million, or 19%, to $2,219.8 million in 2015 compared to $1,861.4 million in 2014.

Consumables revenue increased~~$238.9~~ $238.9 million,, or 23%, to ~~$1,279.9~~$1,279.9 million in 2015 compared to ~~$1,041.0~~$1,041.0 million in ~~2014,~~the prior year, driven by growth in the sequencing instrument installed base.

Instrument revenue increased~~$32.5~~ $32.5 million,, or 6%, to ~~$594.7~~$594.7 million in 2015 compared to ~~$562.2~~$562.2 million in ~~2014,~~the prior year, driven by shipments of HiSeq X and NextSeq systems.

Service and other revenue increased $87.3 million, or 36%, to $329.1 million in 2015 compared to $241.8 million in ~~2014,~~the prior year, driven by the growth in NIPT service test volumes. Revenue from ~~extended~~ instrument service contracts also contributed to the increase as our sequencing instrument installed base continues to grow.

Overall, these increases were negatively impacted by the foreign exchange fluctuations in the comparative periods. Absent these fluctuations, revenues would have grown 23% on a constant currency basis from 2014 to 2015.

~~2014~~ ~~Compared to~~ ~~2013~~

~~Revenue~~ ~~increased$440.2 million, or~~ ~~31%, to~~ ~~$1,861.4 million~~ ~~in 2014 compared to $1,421.2 million in 2013.~~

Consumables revenue increased $160.7 million, or 18%, to $1,041.0 million in 2014 compared to $880.3 million in the prior year. The increase was primarily attributable to sales of sequencing consumables, driven by the growth in the installed base, including HiSeq X and NextSeq systems introduced in January 2014. Such increase was partially offset by a decrease in array consumables.

Instrument revenue increased $190.7 million, or 51%, to $562.2 million in 2014 compared to $371.5 million in the prior year, driven primarily by shipments of sequencing instruments, in particular HiSeq X and NextSeq systems introduced in January 2014.

Service and other revenue increased $85.3 million, or 55%, to $241.8 million in 2014 compared to $156.5 million in the prior year, driven primarily by sequencing services and extended service contracts for our instruments as our installed base continues to grow.

Gross Margin


	2015 - 2014										2014 - 2013							2016 - 2015										2015 - 2014
(Dollars in thousands)	2015			2014			Change		% Change		2013			Change		% Change		2016			2015			Change		% Change		2014			Change		% Change
Total gross profit	$	1,549,290		$	1,297,710		$	251,580	19	%	$	911,887		$	385,823	42	%	$	1,666,448		$	1,549,290		$	117,158	8	%	$	1,297,710		$	251,580	19	%
Total gross margin	69.8		%	69.7		%					64.2		%					69.5		%	69.8		%					69.7		%

2016 Compared to 2015

Gross margin decreased to 69.5% in 2016 compared to 69.8% in 2015. Gross margin decreased primarily due to our increased manufacturing capacity, which was partially offset by a greater mix of sequencing consumables.

2015 Compared to 2014

Gross margin increased to 69.8% ~~in 2015~~ compared to 69.7% in ~~2014.~~the prior year. Gross margin increased primarily due to a positive shift in product mix to sequencing consumables. Gross margin in 2014 was favorably impacted by the litigation settlement

~~Table of Contents~~

with Syntrix, which included a reversal of cost of sales of $10.4 million. See detailed discussions on this matter in note “9. Legal Proceedings” in Part II, Item 8 of this Form 10-K.

Operating Expense



	2016 - 2015											2015 - 2014
(Dollars in thousands)	2016			2015			Change			% Change		2014			Change			% Change
Research and development	$	504,415		$	401,527		$	102,888		26	%	$	388,055		$	13,472		3	%
Selling, general and administrative	583,005			524,657			58,348			11		466,283			58,374			13
Legal contingencies	(9,490		)	19,000			(28,490		)	(150	)	(74,338		)	93,338			(126	)
Acquisition related gain, net	—			(6,124		)	6,124			(100	)	(2,639		)	(3,485		)	132
Headquarter relocation	1,486			(2,611		)	4,097			(157	)	5,638			(8,249		)	(146	)
Total operating expense	$	1,079,416		$	936,449		$	142,967		15	%	$	782,999		$	153,450		20	%

2016 Compared to 2015

Research and development (R&D) expense increased by $102.9 million, or 26%, in 2016 from 2015. Core Illumina R&D expense increased by $59.9 million, or 15%, primarily due to increased headcount and outside services as we continue to invest in the development of new products as well as enhancements to existing products. Our consolidated VIEs contributed $43.0 million to the increase, primarily due to $33.7 million incurred by GRAIL.

~~2014~~Selling, general and administrative (SG&A) expense increased by $58.3 million, or 11% in 2016 from 2015. Core Illumina SG&A expense increased $35.5 million, or 7%, primarily due to headcount and facilities investment to support the continued growth and scale of our operations, as well as outside services. GRAIL and Helix contributed $13.7 million and $9.1 million to the increase, respectively.

Legal contingencies in 2016 represent a reversal of prior year expense related to the settlement of patent litigation.

2015 Compared to ~~2013~~2014

Gross margin increased to 69.7% compared to 64.2% in the prior year, primarily due to the increase in revenue. Also contributing to the increase in gross margin was our litigation settlement with Syntrix in 2014, which resulted in reversal of cost of sales of $10.4 million. See detailed discussions on this matter in note “9. Legal Proceedings” in Part II, Item 8 of this Form 10-K. In addition, higher margins on sequencing instrument sales and efficiencies in manufacturing contributed to the increase in gross margin. In 2013, gross margin was negatively affected by a $25.2 million impairment charge associated with the discontinuation of the Eco and NuPCR product lines.

~~Operating Expense~~

2015 - 2014 2014 - 2013
(Dollars in thousands) 2015 2014 Change % Change 2013 Change % Change
Research and development $ 401,527
$ 388,055
$ 13,472
3 % $ 276,743
$ 111,312
40 %
Selling, general and administrative 524,657
466,283
58,374
13
381,040
85,243
22
Legal contingencies 19,000
(74,338 ) 93,338
(126 ) 115,369
(189,707 ) (164 )
Acquisition related gain, net (6,124 ) (2,639 ) (3,485 ) 132
(11,617 ) 8,978
(77 )
Headquarter relocation (2,611 ) 5,638
(8,249 ) (146 ) 2,624
3,014
115
Unsolicited tender offer related expense —
—
—
—
13,621
(13,621 ) (100 )
Total operating expense $ 936,449
$ 782,999
$ 153,450
20 % $ 777,780
$ 5,219
1 %

~~2015 Compared to 2014~~

Research and development expense increased by $13.5 million, or 3%, in 2015 from 2014, primarily due to increased headcount and related expenses as we continue to invest in the development of our products as well as enhancements to existing products. Research and development expense in 2014 included our litigation settlement and patent pooling agreement with Sequenom, as $48.8 million was recorded to research and development expense for an upfront payment. See detailed discussion on this matter in note “9. Legal Proceedings” to our financial statements in Part II, Item 8 of this Form 10-K.

Selling, general and administrative expense increased by ~~$58.4~~$58.4 million,, or 13%, in 2015 from 2014, primarily driven by increased headcount and consulting services to support our continued growth, investments in scaling our operations, and start-up costs related to ~~our Helix joint venture.~~Helix.

Legal contingencies in 2015 represent charges related to patent litigation. Legal contingencies in 2014 reflected predominantly the $82.1 million gain from our litigation settlement with Syntrix, offset by other legal contingency charges.

Acquisition related gain, net, in 2015 and 2014 consisted of changes in fair value of contingent consideration. The changes in the fair value of the contingent consideration during the periods were primarily due to changes in the estimated payments and a shorter discounting period.

Headquarter relocation costs for 2015 include a net gain related to a change in a lease exit liability, partially offset by accretion of interest on such liability.

~~2014~~ ~~Compared to~~ ~~2013~~

Research and development expense increased by $111.3 million, or 40%, in 2014 from 2013. The increase is partially attributable to our litigation settlement and patent pooling agreement with Sequenom in 2014, as $48.8 million was recorded to research and development expense for the upfront payment. See detailed discussion on this matter in note “9. Legal Proceedings” to our financial statements in Part II, Item 8 of this Form 10-K. In addition, headcount increases and other expenses related to our new product launches contributed to the increase in research and development expenses, reflecting our continued investment in the development of new products as well as enhancements to existing products.

~~Table of Contents~~

Selling, general and administrative expense increased by $85.2 million, or 22%, in 2014 from 2013. The increase is primarily driven by increases in headcount, consulting services, and infrastructure investment to support the growth of our Company.

~~Acquisition related gain, net, in 2014 and 2013 consisted of changes in fair value of contingent consideration and transaction related costs.~~

We completed the relocation of our headquarters in 2012. During 2014 and 2013, we incurred $5.6 million and $2.6 million, respectively, in additional headquarter relocation expense, consisting primarily of changes in estimated lease exit liability recorded upon vacating our former headquarters, and accretion expense related to such facility exit obligation.

Legal contingencies in 2014 reflected predominantly the $82.1 million gain from our litigation settlement with Syntrix, offset by other legal contingency charges. The $115.4 million in legal contingencies in 2013 were primarily charges recorded for the Syntrix litigation matter. See detailed discussion on this matter in note “9. Legal Proceedings” in Part II, Item 8 of this Form 10-K.

In 2013, we recorded $13.6 million of expenses incurred in relation to an unsolicited tender offer in Q1 2012. The expenses consisted primarily of advisory and legal fees. The advisory service arrangement was completed in 2013.

Other (Expense) Income, Net


	2015 - 2014											2014 - 2013								2016 - 2015											2015 - 2014
(Dollars in thousands)	2015			2014			Change			% Change		2013			Change			% Change		2016			2015			Change			% Change		2014			Change			% Change
Interest income	$	5,024		$	3,901		$	1,123		29	%	$	4,887		$	(986	)	(20	)%	$	9,799		$	5,024		$	4,775		95	%	$	3,901		$	1,123		29	%
Interest expense	(42,121		)	(41,728		)	(393		)	1		(39,690		)	(2,038		)	5		(33,181		)	(42,121		)	8,940			(21	)	(41,728		)	(393		)	1
Cost-method investment gain, net	15,601			4,427			11,174			252		61,357			(56,930		)	(93	)	—			15,601			(15,601		)	(100	)	4,427			11,174			252
Other expense, net	(8,203		)	(32,553		)	24,350			(75	)	(1,347		)	(31,206		)	2,317		(2,472		)	(8,203		)	5,731			(70	)	(32,553		)	24,350			(75	)
Total other (expense) income, net	$	(29,699	)	$	(65,953	)	$	36,254		(55	)%	$	25,207		$	(91,160	)	(362	)%
Total other expense, net																				$	(25,854	)	$	(29,699	)	$	3,845		(13	)%	$	(65,953	)	$	36,254		(55	)%

2016 Compared to 2015

Interest income increased in 2016 compared to 2015 as a result of higher yields on our investments and higher savings and money market balances. Interest expense consisted primarily of accretion of discount on our convertible senior notes. The decrease in interest expense in 2016 compared to 2015 was due to a lower outstanding principal balance on the 2016 Notes, which matured in March 2016.

Other expense, net, in 2016 is primarily attributable to $1.0 million related to equity method investment losses and $0.9 million in net foreign exchange loss. Other expense, net, in 2015 consisted primarily of $4.3 million in net foreign exchange loss and a $4.1 million loss on extinguishment of debt.

2015 Compared to 2014

Interest income primarily consisted of returns from our investment portfolio. Interest income increased slightly in 2015 compared to 2014 as a result of higher yields and higher investment balances throughout the period. Interest expense consisted primarily of accretion of discount on our convertible senior notes. The increase in interest expense in 2015 compared to 2014 was due to the issuance of our 2019 and 2021 Notes in June 2014, partially offset by the impact from the concurrent repurchase of $600.0 million in principal amount of our 2016 Notes.

Cost-method investment gain, net in 2015 consisted primarily of gains on dispositions of cost-method investments, partially offset by impairment charges on other investments.

Other expense, net,, in 2015 consisted primarily of $4.3 million in foreign exchange loss and $4.1 million in loss on extinguishment of our 2016 notes. Other expense, net, in 2014, was negatively impacted by $31.4 million loss on extinguishment of debt recorded as a result of the repurchase of $600.0 million in principal amount of our 2016 Notes.

~~2014~~ ~~Compared to~~ ~~2013~~

Interest income primarily consisted of returns from our investment portfolio. Interest income decreased slightly in 2014 compared to 2013 as a result of lower yields, partially offset by the impact from a larger investment portfolio. Interest expense in 2014 remained relatively consistent to 2013 and consisted primarily of accretion on our convertible senior notes.

Cost-method investment gain, net in 2014 consisted of a gain associated with additional proceeds received for a cost-method investment sold in a prior year. In 2013, we recognized $61.4 million in gains from sales of cost-method investments, of which $55.2 million related to the sale of our minority ownership interest in Oxford Nanopore Technologies Ltd.

Other expense, net, in 2014 and 2013 primarily consisted of loss on extinguishment of debt and net foreign exchange gains and losses. In conjunction with the issuance of the 2019 and 2021 Notes, we used $1,244.7 million in cash to repurchase

~~Table of Contents~~

$600.0 million in principal amount of the outstanding 2016 Notes in privately negotiated transactions. As a result, we recorded $31.4 million in loss on extinguishment of debt calculated as the difference between the fair value and carrying value of the liability component of the debt.

Provision for Income Taxes


	2015 - 2014										2014 - 2013							2016 - 2015											2015 - 2014
(Dollars in thousands)	2015			2014			Change		% Change		2013			Change		% Change		2016			2015			Change			% Change		2014			Change		% Change
Income before income taxes	$	583,142		$	448,758		$	134,384	30	%	$	159,314		$	289,444	182	%	$	561,178		$	583,142		$	(21,964	)	(4	)%	$	448,758		$	134,384	30	%
Provision for income taxes	125,752			95,407			30,345		32		34,006			61,401		181		133,088			125,752			7,336			6		95,407			30,345		32
Consolidated net income	$	457,390		$	353,351		$	104,039	29	%	$	125,308		$	228,043	182	%	$	428,090		$	457,390		$	(29,300	)	(6	)%	$	353,351		$	104,039	29	%
Effective tax rate	21.6		%	21.3		%					21.3		%					23.7		%	21.6		%						21.3		%

~~2015~~2016 Compared to 2015

Our effective tax rate was 23.7% and 21.6% in 2016 and 2015, respectively. In 2016, the variance from the U.S. federal statutory tax rate of 35% was primarily attributable to the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore and the United Kingdom, partially offset by the tax impact associated with the investments in our consolidated variable interest entities. In 2015, the variance from the U.S. federal statutory tax rate of 35% was primarily attributable to a discrete tax benefit of $24.8 million, related to the exclusion of stock compensation from

prior period cost-sharing charges as a result of a tax court opinion in which an unrelated third party was successful in challenging such charges. The decrease from the U.S. federal statutory tax rate also resulted from the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as in Singapore and the United Kingdom.

2015 Compared to 2014

Our effective tax rate was 21.6% and 21.3% in 2015 and 2014, respectively. In 2015, the variance from the U.S. federal statutory tax rate of 35% was attributable to a discrete tax benefit of $24.8 million, related to the exclusion of stock compensation from prior period cost-sharing charges as a result of a ~~recent~~ tax court opinion in which an unrelated third party was successful in challenging such charges. In 2015 and 2014, the variance from the U.S. federal statutory tax rate of 35% was also attributable to the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as Singapore and the United Kingdom.

~~2014~~ ~~Compared to~~ ~~2013~~

Our effective tax rate was 21.3% in 2014 and 2013. The variance from the U.S. federal statutory tax rate of 35% was primarily attributable to the mix of earnings in jurisdictions with lower statutory tax rates than the U.S. federal statutory tax rate, such as Singapore and the United Kingdom. In addition, the variance in 2014 was also attributable to the benefit from research and development credits and foreign tax credits, and the variance in 2013 was also attributable to the retroactive reinstatement of the federal research and development credit for 2012 which was enacted in January 2013. These items offset the impact of recording a valuation allowance which was primarily related to the estimated limitation on utilizing foreign tax credits in the U.S.

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Recent Accounting Pronouncements

For summary of recent accounting pronouncements applicable to our consolidated financial statement see note “1“1. Organization and Summary of Significant Accounting Policies” in Part II, Item 8, Notes to Consolidated Financial Statements, which is incorporated herein by reference.


ITEM 7A.	Quantitative and Qualitative Disclosures About Market Risk.

Interest Rate Sensitivity

Our investment portfolio is exposed to market risk from changes in interest rates. The fair market value of fixed rate securities may be adversely impacted by fluctuations in interest rates while income earned on floating rate securities may decline as a result of decreases in interest rates. Under our current policies, we do not use interest rate derivative instruments to manage exposure to interest rate changes. We attempt to ensure the safety and preservation of our invested principal funds by limiting default risk, market risk, and reinvestment risk. We mitigate default risk by investing in investment grade securities. We have historically maintained a relatively short average maturity for our investment portfolio, and we believe a hypothetical 100 basis point adverse move in interest rates along the entire interest rate yield curve would not materially affect the fair value of our interest sensitive financial instruments.

Changes in interest rates may impact gains or losses from the conversion of our outstanding convertible senior notes. In June 2014, we issued $632.5 million aggregate principal amount of 0% convertible senior notes due 2019 (2019 Notes) and $517.5 million aggregate principal amount of 0.5% convertible senior notes due 2021 (2021 Notes). ~~Similar to our 0.25% convertible senior notes due 2016, at~~At our election, the notes are convertible into cash, shares of our common stock, or a combination of cash and shares of our common stock under certain circumstances, including trading price conditions related to our common stock. If the trading price of our common stock reaches a price at 130% above the conversion price, the notes will become convertible. Upon conversion, we are required to record a gain or loss for the difference between the fair value of the debt to be extinguished and its corresponding net carrying value. The fair value of the debt to be extinguished depends on our then-current incremental borrowing rate. If our incremental borrowing rate at the time of conversion is higher or lower than the implied interest rate of the notes, we will record a gain or loss in our consolidated statement of income during the period in which the notes are converted. The implicit interest rates for the 2019 and 2021 Notes were 2.9% and 3.5%, respectively. An incremental borrowing rate that is a hypothetical 100 basis points lower than the implicit interest rate upon conversion of $100.0 million aggregate principal amount of each of the 2019 and 2021 Notes would result in losses of approximately ~~$3.3~~$2.5 million and ~~$4.8~~$4.1 million, respectively.

Foreign Currency Exchange Risk

We conduct a portion of our business in currencies other than the company’s U.S. dollar functional currency. These transactions give rise to monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. The value of these monetary assets and liabilities are subject to changes in currency exchange rates from the time the transactions are originated until settlement in cash. Our foreign currency exposures are primarily concentrated in the Euro, Yen, and Australian dollar. Both realized and unrealized gains or losses on the value of these monetary assets and liabilities are included in the determination of net income.

We use forward exchange contracts to manage foreign currency risks related to monetary assets and liabilities denominated in currencies other than the U.S. dollar. We only use derivative financial instruments to reduce foreign currency exchange rate risks; we do not hold any derivative financial instruments for trading or speculative purposes. We primarily use forward exchange contracts to hedge foreign currency exposures, and they generally have terms of one month or less. Realized and unrealized gains or losses on the value of financial contracts entered into to hedge the exchange rate exposure of these monetary assets and liabilities are also included in the determination of net income, as they have not been designated for hedge accounting. These contracts, which settle monthly, effectively fix the exchange rate at which these specific monetary assets and liabilities will be settled, so that gains or losses on the forward contracts offset the gains or losses from changes in the value of the underlying monetary assets and liabilities. As of January ~~3, 2016,~~1, 2017, the total notional amount of outstanding forward contracts in place for foreign currency purchases was $~~61.3~~68.8 million.

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ITEM 8.	Financial Statements and Supplementary Data.

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS



	Page
Report of Independent Registered Public Accounting Firm	42
Consolidated Balance Sheets	43
Consolidated Statements of Income	44
Consolidated Statements of Comprehensive Income	45
Consolidated Statements of Stockholders’ Equity	46
Consolidated Statements of Cash Flows	47
Notes to Consolidated Financial Statements	48

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REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Board of Directors and Stockholders of

Illumina, Inc.

We have audited the accompanying consolidated balance sheets of Illumina, Inc. as of January 1, 2017 and January 3, 2016, ~~and December 28, 2014,~~ and the related consolidated statements of income, comprehensive income, stockholders’ equity, and cash flows for each of the three fiscal years in the period ended January ~~3, 2016.~~1, 2017. Our audits also included the financial statement schedule listed in the Index at Item 15. These financial statements and schedule are the responsibility of the Company’s management. Our responsibility is to express an opinion on these financial statements and schedule based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements. An audit also includes assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the financial statements referred to above present fairly, in all material respects, the consolidated financial position of Illumina, Inc. at January 1, 2017 and January 3, 2016, ~~and December 28, 2014,~~ and the consolidated results of its operations and its cash flows for each of the three fiscal years in the period ended January ~~3, 2016,~~1, 2017, in conformity with U.S. generally accepted accounting principles. Also, in our opinion, the related financial statement schedule, when considered in relation to the basic financial statements taken as a whole, presents fairly in all material respects the information set forth therein.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), Illumina, Inc.’s internal control over financial reporting as of January ~~3, 2016,~~1, 2017, based on criteria established in Internal Control-Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) and our report dated ~~March 2, 2016~~February 13, 2017 expressed an unqualified opinion thereon.

/s/ ERNST & YOUNG LLP

San Diego, California

~~March 2, 2016~~February 13, 2017

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ILLUMINA, INC.

CONSOLIDATED BALANCE SHEETS

(in thousands, except par value)


	January 3, 2016			December 28, 2014			January 1, 2017			January 3, 2016
ASSETS
Current assets:
Cash and cash equivalents	$	768,770		$	636,154		$	734,516		$	768,770
Short-term investments	617,450			702,217			824,208			617,450
Accounts receivable, net	385,529			289,458			381,316			385,529
Inventory	270,777			191,144			300,170			270,777
Deferred tax assets, current portion	—			40,786
Prepaid expenses and other current assets	54,297			29,844			77,881			54,297
Total current assets	2,096,823			1,889,603			2,318,091			2,096,823
Property and equipment, net	342,694			265,264			713,334			342,694
Goodwill	752,629			724,904			775,995			752,629
Intangible assets, net	273,621			314,500			242,652			273,621
Deferred tax assets, long-term portion	134,515			49,848
Deferred tax assets							123,317			134,515
Other assets	87,465			95,521			107,211			87,465
Total assets	$	3,687,747		$	3,339,640		$	4,280,600		$	3,687,747
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	139,226		$	82,626		$	137,930		$	139,226
Accrued liabilities	396,339			335,276			342,751			386,844
Build-to-suit lease liability							222,734			9,495
Long-term debt, current portion	74,929			304,256			1,250			74,929
Total current liabilities	610,494			722,158			704,665			610,494
Long-term debt	1,015,649			986,780			1,047,805			1,015,649
Other long-term liabilities	180,505			167,904			213,955			180,505
Commitments and contingencies
Redeemable noncontrolling interests	32,546			—			43,940			32,546
Stockholders’ equity:
Preferred stock, $0.01 par value, 10,000 shares authorized; no shares issued and outstanding at January 3, 2016 and December 28, 2014	—			—
Common stock, $0.01 par value, 320,000 shares authorized; 186,663 shares issued and 146,584 outstanding at January 3, 2016; 181,332 shares issued and 143,629 outstanding at December 28, 2014	1,859			1,805
Preferred stock, $0.01 par value, 10,000 shares authorized; no shares issued and outstanding at January 1, 2017 and January 3, 2016							—			—
Common stock, $0.01 par value, 320,000 shares authorized; 188,759 shares issued and 146,196 outstanding at January 1, 2017; 186,663 shares issued and 146,584 outstanding at January 3, 2016							1,887			1,859
Additional paid-in capital	2,497,501			2,172,940			2,733,394			2,497,501
Accumulated other comprehensive income (loss)	36			(1,080		)
Accumulated other comprehensive (loss) income							(1,037		)	36
Retained earnings	1,022,765			561,206			1,485,414			1,022,765
Treasury stock, 40,079 shares and 37,703 shares at cost at January 3, 2016 and December 28, 2014, respectively	(1,673,608		)	(1,272,073		)
Treasury stock, 42,563 shares and 40,079 shares at cost at January 1, 2017 and January 3, 2016, respectively							(2,022,429		)	(1,673,608		)
Total Illumina stockholders’ equity							2,197,229			1,848,553
Noncontrolling interests							73,006			—
Total stockholders’ equity	1,848,553			1,462,798			2,270,235			1,848,553
Total liabilities and stockholders’ equity	$	3,687,747		$	3,339,640		$	4,280,600		$	3,687,747

See accompanying notes to consolidated financial statements.

~~Table of Contents~~

ILLUMINA, INC.

CONSOLIDATED STATEMENTS OF INCOME

(In thousands, except per share amounts)


	Years Ended									Years Ended
	January 3, 2016			December 28, 2014			December 29, 2013			January 1, 2017			January 3, 2016			December 28, 2014
Revenue:
Product revenue	$	1,890,633		$	1,619,511		$	1,264,656		$	2,031,997		$	1,890,633		$	1,619,511
Service and other revenue	329,129			241,847			156,522			366,376			329,129			241,847
Total revenue	2,219,762			1,861,358			1,421,178			2,398,373			2,219,762			1,861,358
Cost of revenue:
Cost of product revenue	490,812			431,920			407,877			534,199			490,812			431,920
Cost of service and other revenue	133,850			92,355			67,811			154,762			133,850			92,355
Amortization of acquired intangible assets	45,810			39,373			33,603			42,964			45,810			39,373
Total cost of revenue	670,472			563,648			509,291			731,925			670,472			563,648
Gross profit	1,549,290			1,297,710			911,887			1,666,448			1,549,290			1,297,710
Operating expense:
Research and development	401,527			388,055			276,743			504,415			401,527			388,055
Selling, general and administrative	524,657			466,283			381,040			583,005			524,657			466,283
Legal contingencies	19,000			(74,338		)	115,369			(9,490		)	19,000			(74,338		)
Acquisition related gain, net	(6,124		)	(2,639		)	(11,617		)	—			(6,124		)	(2,639		)
Headquarter relocation	(2,611		)	5,638			2,624			1,486			(2,611		)	5,638
Unsolicited tender offer related expense	—			—			13,621
Total operating expense	936,449			782,999			777,780			1,079,416			936,449			782,999
Income from operations	612,841			514,711			134,107			587,032			612,841			514,711
Other income (expense):
Interest income	5,024			3,901			4,887			9,799			5,024			3,901
Interest expense	(42,121		)	(41,728		)	(39,690		)	(33,181		)	(42,121		)	(41,728		)
Cost-method investment gain, net	15,601			4,427			61,357			—			15,601			4,427
Other expense, net	(8,203		)	(32,553		)	(1,347		)	(2,472		)	(8,203		)	(32,553		)
Total other (expense) income, net	(29,699		)	(65,953		)	25,207
Total other expense, net										(25,854		)	(29,699		)	(65,953		)
Income before income taxes	583,142			448,758			159,314			561,178			583,142			448,758
Provision for income taxes	125,752			95,407			34,006			133,088			125,752			95,407
Consolidated net income	457,390			353,351			125,308			428,090			457,390			353,351
Add: Net loss attributable to noncontrolling interests	4,169			—			—			34,559			4,169			—
Net income attributable to Illumina stockholders	$	461,559		$	353,351		$	125,308		$	462,649		$	461,559		$	353,351
Net income attributable to Illumina stockholders for earnings per share										$	454,106		$	461,526		$	353,351
Earnings per share attributable to Illumina stockholders:
Basic	$	3.19		$	2.61		$	1.00		$	3.09		$	3.19		$	2.61
Diluted	$	3.10		$	2.37		$	0.90		$	3.07		$	3.10		$	2.37
Shares used in computing earnings per common share:
Basic	144,826			135,553			125,076			146,788			144,826			135,553
Diluted	149,069			148,977			139,936			148,040			149,069			148,977

See accompanying notes to consolidated financial statements.

~~Table of Contents~~

ILLUMINA, INC.

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME

(In thousands)


	Years Ended								Years Ended
	January 3, 2016		December 28, 2014			December 29, 2013			January 1, 2017			January 3, 2016		December 28, 2014
Consolidated net income	$	457,390	$	353,351		$	125,308		$	428,090		$	457,390	$	353,351
Unrealized gain (loss) on available-for-sale securities, net of deferred tax	1,116		(2,314		)	(889		)
Unrealized (loss) gain on available-for-sale securities, net of deferred tax									(1,073		)	1,116		(2,314		)
Total consolidated comprehensive income	458,506		351,037			124,419			427,017			458,506		351,037
Add: Comprehensive loss attributable to noncontrolling interests	4,169		—			—			34,559			4,169		—
Comprehensive income attributable to Illumina stockholders	$	462,675	$	351,037		$	124,419		$	461,576		$	462,675	$	351,037

See accompanying notes to consolidated financial statements.

~~Table of Contents~~

ILLUMINA, INC.

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY


				Additional			Accumulated Other										Total			Illumina Stockholders
	Common Stock			Paid-In			Comprehensive			Retained		Treasury Stock					Stockholders’						Additional			Accumulated Other													Total
	Shares	Amount		Capital			Income (Loss)			Earnings		Shares		Amount			Equity			Common Stock			Paid-In			Comprehensive			Retained		Treasury Stock					Noncontrolling			Stockholders’
	(in thousands)																			Shares	Amount		Capital			Income (Loss)			Earnings		Shares		Amount			Interests			Equity
Balance as of December 30, 2012	170,171	$	1,703	$	2,419,831		$	2,123		$	82,547	(46,228	)	$	(1,187,623	)	$	1,318,581
Net income	—	—		—			—			125,308		—		—			125,308
Unrealized loss on available-for-sale securities, net of deferred tax	—	—		—			(889		)	—		—		—			(889		)
Issuance of common stock, net of repurchases	5,034	50		98,215			—			—		(1,254	)	(52,722		)	45,543
Reclassification of conversion option subject to cash settlement	—	—		2,338			—			—		—		—			2,338
Share-based compensation	—	—		105,771			—			—		—		—			105,771
Net incremental tax benefit related to share-based compensation	—	—		53,032			—			—		—		—			53,032
Equity based contingent compensation	—	—		8,278			—			—		—		—			8,278
Fair value of options assumed in acquisition	—	—		240			—			—		—		—			240
Warrant retirement	—	—		(125,000		)	—			—		—		—			(125,000		)
																				(in thousands)
Balance as of December 29, 2013	175,205	1,753		2,562,705			1,234			207,855		(47,482	)	(1,240,345		)	1,533,202			175,205	$	1,753	$	2,562,705		$	1,234		$	207,855	(47,482	)	$	(1,240,345	)	$	—		$	1,533,202
Net income	—	—		—			—			353,351		—		—			353,351			—	—		—			—			353,351		—		—			—			353,351
Unrealized loss on available-for-sale securities, net of deferred tax	—	—		—			(2,314		)	—		—		—			(2,314		)	—	—		—			(2,314		)	—		—		—			—			(2,314		)
Issuance of common stock, net of repurchases	6,127	52		96,204			—			—		(2,696	)	(247,221		)	(150,965		)	6,127	52		96,204			—			—		(2,696	)	(247,221		)	—			(150,965		)
Tax impact from the issuance, repurchase and conversion of convertible notes	—	—		(58,354		)	—			—		—		—			(58,354		)	—	—		(58,354		)	—			—		—		—			—			(58,354		)
Reclassification of conversion option subject to cash settlement	—	—		282			—			—		—		—			282			—	—		282			—			—		—		—			—			282
Share-based compensation	—	—		153,189			—			—		—		—			153,189			—	—		153,189			—			—		—		—			—			153,189
Net incremental tax benefit related to share-based compensation	—	—		126,477			—			—		—		—			126,477			—	—		126,477			—			—		—		—			—			126,477
Equity based contingent compensation	—	—		2,621			—			—		—		—			2,621			—	—		2,621			—			—		—		—			—			2,621
Warrant exercises	—	—		(215,493		)	—			—		12,475		215,493			—			—	—		(215,493		)	—			—		12,475		215,493			—			—
Repurchase of convertible notes, net of issuances	—	—		(494,691		)	—			—		—		—			(494,691		)	—	—		(494,691		)	—			—		—		—			—			(494,691		)
Balance as of December 28, 2014	181,332	1,805		2,172,940			(1,080		)	561,206		(37,703	)	(1,272,073		)	1,462,798			181,332	1,805		2,172,940			(1,080		)	561,206		(37,703	)	(1,272,073		)	—			1,462,798
Net income attributable to Illumina stockholders	—	—		—			—			461,559		—		—			461,559
Net income																				—	—		—			—			461,559		—		—			—			461,559
Unrealized gain on available-for-sale securities, net of deferred tax	—	—		—			1,116			—		—		—			1,116			—	—		—			1,116			—		—		—			—			1,116
Issuance of common stock, net of repurchases	5,331	54		69,870			—			—		(2,376	)	(401,535		)	(331,611		)	5,331	54		69,870			—			—		(2,376	)	(401,535		)	—			(331,611		)
Tax impact from the conversion of convertible notes	—	—		373			—			—		—		—			373			—	—		373			—			—		—		—			—			373
Share-based compensation	—	—		133,454			—			—		—		—			133,454			—	—		133,454			—			—		—		—			—			133,454
Net incremental tax benefit related to share-based compensation	—	—		125,451			—			—		—		—			125,451			—	—		125,451			—			—		—		—			—			125,451
Reclassification of vested Helix stock units	—	—		(418		)	—			—		—		—			(418		)
Vesting of redeemable equity awards																				—	—		(418		)	—			—		—		—			—			(418		)
Adjustment to the carrying value of redeemable noncontrolling interests	—	—		(4,169		)	—			—		—		—			(4,169		)	—	—		(4,169		)	—			—		—		—			—			(4,169		)
Balance as of January 3, 2016	186,663	$	1,859	$	2,497,501		$	36		$	1,022,765	(40,079	)	$	(1,673,608	)	$	1,848,553		186,663	1,859		2,497,501			36			1,022,765		(40,079	)	(1,673,608		)	—			1,848,553
Net income (loss)																				—	—		—			—			462,649		—		—			(13,817		)	448,832
Unrealized loss on available-for-sale securities, net of deferred tax																				—	—		—			(1,073		)	—		—		—			—			(1,073		)
Issuance of common stock, net of repurchases																				2,096	28		47,599			—			—		(2,506	)	(349,167		)	—			(301,540		)
Tax impact from the conversion of convertible notes																				—	—		(8		)	—			—		—		—			—			(8		)
Share-based compensation																				—	—		128,538			—			—		—		—			—			128,538
Net incremental tax benefit related to share-based compensation																				—	—		86,872			—			—		—		—			—			86,872
Adjustment to the carrying value of redeemable noncontrolling interests																				—	—		(21,194		)	—			—		—		—			—			(21,194		)
Vesting of redeemable equity awards																				—	—		(1,942		)	—			—		—		—			—			(1,942		)
Vesting of non-redeemable equity awards																				—	—		(67		)	—			—		—		—			67			—
Issuance of subsidiary shares in business combination																				—	—		2,102			—			—		—		—			198			2,300
Issuance of treasury stock																				—	—		3,554			—			—		22		346			—			3,900
Contributions from noncontrolling interest owners																				—	—		—			—			—		—		—			80,000			80,000
Proceeds from early exercise of equity awards from a subsidiary																				—	—		—			—			—		—		—			6,558			6,558
Tax impact of deemed dividend from GRAIL, Inc.																				—	—		(9,561		)	—			—		—		—			—			(9,561		)
Balance as of January 1, 2017																				188,759	$	1,887	$	2,733,394		$	(1,037	)	$	1,485,414	(42,563	)	$	(2,022,429	)	$	73,006		$	2,270,235

See accompanying notes to consolidated financial statements.

~~Table of Contents~~

ILLUMINA, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands)	ILLUMINA, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands)									ILLUMINA, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (In thousands)

	Years Ended									Years Ended
	January 3, 2016			December 28, 2014			December 29, 2013			January 1, 2017			January 3, 2016			December 28, 2014
Cash flows from operating activities:
Consolidated net income	$	457,390		$	353,351		$	125,308		$	428,090		$	457,390		$	353,351
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation expense	72,687			61,905			50,810			89,955			72,687			61,905
Amortization of intangible assets	53,732			50,669			47,115			50,960			53,732			50,669
Share-based compensation expense	132,593			152,551			105,826			129,065			132,593			152,551
Accretion of debt discount	38,517			38,069			36,237			29,732			38,517			38,069
Loss on extinguishment of debt	4,062			31,360			555			113			4,062			31,360
Incremental tax benefit related to share-based compensation	(126,659		)	(126,479		)	(56,678		)	(91,332		)	(126,659		)	(126,479		)
Deferred income taxes	80,504			99,846			(36,663		)
Deferred income tax expense										93,562			80,504			99,846
Change in fair value of contingent consideration	(6,124		)	(5,356		)	(18,784		)	(1,161		)	(6,124		)	(5,356		)
(Gain) impairment related to discontinued product line	—			(2,000		)	25,214
Change in estimated cease-use loss	(2,611		)	5,651			2,624
Cost-method investment gain, net	(15,601		)	(4,427		)	(61,357		)	—			(15,601		)	(4,427		)
Gain on litigation settlement	—			(109,363		)	—			(11,490		)	—			(109,363		)
Other	9,548			11,967			12,811			14,759			6,937			15,618
Changes in operating assets and liabilities:
Accounts receivable	(95,913		)	(50,381		)	(15,928		)	3,239			(95,913		)	(50,381		)
Inventory	(80,545		)	(36,542		)	6,217			(29,686		)	(80,545		)	(36,542		)
Prepaid expenses and other current assets	(10,876		)	6,619			1,783			(1,204		)	(10,876		)	6,619
Other assets	(1,418		)	(36,256		)	(16,357		)	(6,882		)	(1,418		)	(36,256		)
Accounts payable	46,296			(2,106		)	2,389			(1,969		)	46,296			(2,106		)
Accrued liabilities	79,791			83,902			38,550			(24,250		)	98,791			60,332
Accrued legal contingencies	19,000			(23,570		)	132,933
Other long-term liabilities	5,223			1,861			3,816			15,737			5,223			1,861
Net cash provided by operating activities	659,596			501,271			386,421			687,238			659,596			501,271
Cash flows from investing activities:
Purchases of available-for-sale securities	(797,022		)	(791,252		)	(364,001		)	(894,369		)	(797,022		)	(791,252		)
Sales of available-for-sale securities	582,528			391,655			523,635			543,252			582,528			391,655
Maturities of available-for-sale securities	294,224			150,229			289,197			139,642			294,224			150,229
Net cash paid for acquisitions	(36,581		)	(3,285		)	(523,501		)	(17,841		)	(36,581		)	(3,285		)
Net (purchases of) sales proceeds from strategic investments	(6,048		)	(11,755		)	95,580
Net purchases of strategic investments										(13,842		)	(6,048		)	(11,755		)
Purchases of property and equipment	(142,847		)	(105,996		)	(79,215		)	(259,891		)	(142,847		)	(105,996		)
Cash paid for intangible assets	(400		)	(36,220		)	(11,344		)	(11,490		)	(400		)	(36,220		)
Net cash used in investing activities	(106,146		)	(406,624		)	(69,649		)	(514,539		)	(106,146		)	(406,624		)
Cash flows from financing activities:
Payments on financing obligations	(244,952		)	(29,991		)	(10,852		)	(65,897		)	(244,952		)	(29,991		)
Payments on acquisition related contingent consideration liability	(2,900		)	—			(3,985		)	(29,200		)	(2,900		)	—
Proceeds from issuance of convertible notes	—			1,132,378			—
Proceeds from issuance of debt										5,000			—			1,132,378
Repurchase of convertible notes	—			(1,244,721		)	—			—			—			(1,244,721		)
Incremental tax benefit related to share-based compensation	126,659			126,479			56,678			91,332			126,659			126,479
Common stock repurchases	(274,324		)	(237,183		)	(50,020		)	(249,342		)	(274,324		)	(237,183		)
Taxes paid related to net share settlement of equity awards	(127,212		)	(10,038		)	—			(99,825		)	(127,212		)	(10,038		)
Payments on retirement of warrants	—			—			(125,000		)
Proceeds from issuance of common stock	71,839			96,328			94,460			47,661			71,839			96,328
Proceeds from early exercise of equity awards from a subsidiary										6,558			—			—
Contributions from noncontrolling interest owners	32,128			—			—			89,000			32,128			—
Net cash used in financing activities	(418,762		)	(166,748		)	(38,719		)	(204,713		)	(418,762		)	(166,748		)
Effect of exchange rate changes on cash and cash equivalents	(2,072		)	(3,382		)	(397		)	(2,240		)	(2,072		)	(3,382		)
Net increase (decrease) in cash and cash equivalents	132,616			(75,483		)	277,656
Net (decrease) increase in cash and cash equivalents										(34,254		)	132,616			(75,483		)
Cash and cash equivalents at beginning of year	636,154			711,637			433,981			768,770			636,154			711,637
Cash and cash equivalents at end of year	$	768,770		$	636,154		$	711,637		$	734,516		$	768,770		$	636,154

Supplemental cash flow information:
Cash paid for income taxes	$	16,913		$	17,886		$	50,086		$	59,749		$	16,913		$	17,886

See accompanying notes to consolidated financial statements.

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NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

Unless the context requires otherwise, references in this report to “Illumina,” “we,” “us,” the “Company,” and “our” refer to Illumina, Inc. and its consolidated subsidiaries.


1.	Organization and Summary of Significant Accounting Policies

Organization and Business

Illumina, Inc. is a provider of sequencing- and array-based solutions, which serves customers in a board range of markets, enabling the adoption of genomic solutions in research and clinical settings. The Company’s customers include leading genomic research centers, academic institutions, government laboratories, and hospitals, as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostic laboratories, and consumer genomics companies.

Basis of Presentation

The consolidated financial statements of the Company have been prepared in conformity with U.S. generally accepted accounting principles and include the accounts of the Company and its wholly-owned subsidiaries, majority-owned or controlled companies, and variable interest entities (VIEs) for which the Company is the primary beneficiary. All intercompany transactions and balances have been eliminated in consolidation.

The Company evaluates its ownership, contractual and other interests in entities that are not wholly-owned by the Company to determine if these entities are VIEs, and, if so, whether the Company is the primary beneficiary of the VIE. In determining whether the Company is the primary beneficiary of a VIE and is therefore required to consolidate the VIE, the Company applies a qualitative approach that determines whether it has both (1) the power to direct the activities of the VIE that most significantly impact the VIE’s economic performance and (2) the obligation to absorb losses of, or the rights to receive benefits from, the VIE that could potentially be significant to that VIE. The Company continuously assesses whether it is the primary beneficiary of a VIE as changes to existing relationships or future transactions may result in the consolidation or deconsolidation, as the case may be. The Company has not provided financial or other support during the periods presented to its VIEs that it was not previously contractually required to provide.

The equity method is used to account for investments in which the Company has the ability to exercise significant influence, but not control, over the investee. Such investments are recorded within other assets, and the share of net income or losses of equity investments is recognized on a one quarter lag in other expense, net.

Redeemable Noncontrolling Interests

Noncontrolling interests represent the portion of equity (net assets) in ana consolidated entity that is not wholly-owned by the Company that is not attributable, directly or indirectly, to the Company. Noncontrolling interests with embedded contingent redemption features, such as put rights, that are not solely within the Company’s control are considered redeemable noncontrolling interests. Redeemable noncontrolling interests are presented outside of stockholders’ equity on the ~~condensed~~ consolidated balance sheets.

Segment Information

The Company is organized into three operating segments for purposes of evaluating its business operations and reviewing its financial results. One segment consists of Illumina’s core operations (Core Illumina). The other two segments relate to the activities of the Company’s consolidated VIEs, GRAIL and Helix. The combined results of operations of the Company’s consolidated VIEs became material during the year ended January 1, 2017. As such, the Company commenced reporting two segments, Core Illumina and Consolidated VIEs, during 2016. Financial information for all periods presented has been classified to reflect these changes to our reportable segments. For further information on the Company’s segments, refer to note “12. Segment Information, Geographic Data, and Significant Customers”.

Fiscal Year

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The Company’s fiscal year is 52 or 53 weeks ending the Sunday closest to December 31, with quarters of 13 or 14 weeks ending the Sunday closest to March 31, June 30, September 30, and December 31. The year ended January 1, 2017 was 52 weeks; the year ended January 3, 2016 was 53 weeks; and the ~~years~~year ended December 28, 2014 ~~and~~ ~~December 29, 2013~~ ~~were~~ was 52 weeks.

Reclassifications

Certain prior period amounts have been reclassified to conform to the current period presentation.

Use of Estimates

The preparation of financial statements requires that management make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, expenses, and related disclosures of contingent assets and liabilities. Actual results could differ from those estimates.

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board issued ASU 2014-09, Revenue from Contracts with Customers (Topic 606). The new standard is based on the principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. Since its initial release, the FASB has issued several amendments to the standard, which include clarification of accounting guidance related to identification of performance obligations, intellectual property licenses, and principal vs. agent considerations.

ASU 2014-09 and all subsequent amendments (collectively, the “new standards”) will be effective for the Company beginning in the first quarter of 2018 and may be applied using either the full retrospective method, in which case the standard would be applied to each prior reporting period presented, or the modified retrospective method, in which case the cumulative effect of applying the standard would be recognized at the date of initial application.

The Company formed an implementation team in 2016 to oversee adoption of the new standards. The implementation team has completed its initial assessment of the new standards, including a detailed review of the Company’s contract portfolio and revenue streams, particularly around product revenues, to identify potential differences in accounting as a result of the new standards. It performed an analysis of those differences and formed preliminary conclusions on the expected changes. While the team’s analysis to date suggests the impact of adoption will not have a material impact on the Company’s existing revenue accounting policies or financial statements, there are a number of steps in the team’s project plan that remain to be completed including: finalizing contract reviews, evaluating the impact on the company’s services and other revenue streams, and working through anticipated changes to systems, business processes and controls to support the adoption of the new standards. Assuming the impact is not material, the Company expects to adopt the new standards using the modified retrospective method with an adjustment to beginning retained earnings for the cumulative effect of the change.

In February 2016, the Financial Accounting Standards Board issued Accounting Standard Update (ASU) 2016-02, Leases (Topic 842). The new standard requires lessees to recognize most leases on their balance sheets as lease liabilities with corresponding right-of-use assets and eliminates certain real estate-specific provisions. ASU 2016-02 will be effective for the Company beginning in the first quarter of 2019. ASU 2016-02 will be adopted on a modified retrospective transition basis for

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leases existing at, or entered into after, the beginning of the earliest comparative period presented in the financial statements. The Company is currently evaluating the impact of ASU 2016-02 on its consolidated financial statements.

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In ~~February 2015,~~March 2016, the Financial Accounting Standards Board issued Accounting Standard Update (ASU) ~~2015-02,~~2016-09, ~~Consolidation~~Compensation - Stock Compensation (Topic ~~810): Amendments~~718), which aims to simplify the ~~Consolidation Analysis. The new standard modifies current guidance~~accounting for share-based payment transactions, including accounting for income taxes, classification on ~~consolidation under~~ the ~~variable interest model~~statement of cash flows, accounting for forfeitures, and ~~the voting model.~~classification of awards as either liabilities or equity. This ASU ~~2015-02 will be~~is effective for the Company beginning in the first quarter of ~~2016.~~2017 and the Company will classify excess tax benefits from share-based payment arrangements as a discrete item within the provision for income taxes on the consolidated statement of income, rather than recognizing excess tax benefits on the consolidated statement of stockholders’ equity.

In addition, under the ASU, excess income tax benefits from share-based compensation arrangements are classified as cash flow from operations, rather than cash flow from financing activities. The Company has elected to apply the cash flow classification guidance retrospectively.

If this standard had been adopted in fiscal year 2016, the provision for income taxes would have been reduced by $86.9 million and cash flows from operating activities would have been increased by $91.3 million. Further, the Company had $46.4 million of unrealized excess tax benefits associated with share-based compensation as of January 1, 2017. These tax benefits will be accounted for as a credit to retained earnings when this ASU becomes effective in the first quarter of 2017.

The actual benefit realized in the future periods is inherently uncertain and will vary based on the timing and value realized for future share-based payment arrangements. Other than these reclassifications, the effect of excess tax benefits on the provision for income taxes, and the adjustment to retained earnings, the Company does not ~~anticipate a material~~believe the adoption of this ASU will materially impact on its consolidated financial ~~statements at the time of adoption of this standard.~~statements.

In ~~May 2014,~~June 2016, the ~~Financial~~FASB issued Accounting Standards ~~Board issued ASU 2014-09,~~Update (ASU) 2016-13, ~~Revenue from Contracts with Customers (Topic 606)~~Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments~~. The new standard is~~, which amends the impairment model by requiring entities to use a forward-looking approach based on ~~the principle that revenue should be recognized~~expected losses to ~~depict the transfer~~estimate credit losses on certain types of ~~promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange~~financial instruments, including trade receivables and available for ~~those goods or services.~~sale debt securities. The ASU ~~2014-09 will be~~is effective for the Company beginning in the first quarter of ~~2018 and allows for a full retrospective or a modified retrospective~~2020, with early adoption ~~approach.~~permitted. The Company is currently evaluating the impact of ASU ~~2014-09~~2016-13 on its consolidated financial statements.

Concentrations of Risk

The Company operates in markets that are highly competitive and rapidly changing. Significant technological changes, shifting customer needs, the emergence of competitive products or services with new capabilities, and other factors could negatively impact the Company’s operating results. A portion of the Company’s customers consist of university and research institutions that management believes are, to some degree, directly or indirectly supported by the United States Government. A significant change in current research funding, particularly with respect to the U.S. National Institutes of Health, could have an adverse impact on the Company’s future revenues and results of operations.

The Company is also subject to risks related to its financial instruments including its cash and cash equivalents, investments, and accounts receivable. Most of the Company’s cash and cash equivalents as of January ~~3, 2016~~1, 2017 were deposited with U.S. financial institutions, either domestically or with their foreign branches. The Company’s investment policy restricts the amount of credit exposure to any one issuer to 5% of the portfolio or 5% of the total issue size outstanding at the time of purchase and to any one industry sector, as defined by ~~Bloomberg classifications,~~Clearwater Analytics (Industry Sector Report), to 30% of the portfolio at the time of purchase. There is no limit to the percentage of the portfolio that may be maintained in debt securities in U.S. government-sponsored entities, U.S. Treasury securities, and money market funds.

The ~~Company’s products require~~Company requires customized products and components that currently are available from a limited number of sources. The Company sources certain key products and components included in its products from single vendors.

The Company performs a regular review of customer activity and associated credit risks and does not require collateral or enter into netting arrangements. Shipments to customers outside the United States comprised 46%, ~~49%~~46%, and ~~50%~~49% of the Company’s revenue for the years ended January 1, 2017, January 3, 2016~~December 28, 2014~~, and December ~~29, 2013~~28, 2014, respectively. Customers outside the United States represented 48% of the Company’s gross trade accounts receivable balance as of both January ~~3, 2016~~1, 2017 and ~~December 28, 2014~~January 3, 2016.

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International sales entail a variety of risks, including currency exchange fluctuations, longer payment cycles, and greater difficulty in accounts receivable collection. The Company is also subject to general geopolitical risks, such as political, social and economic instability, and changes in diplomatic and trade relations. The risks of international sales are mitigated in part by the extent to which sales are geographically distributed. The Company has historically not experienced significant credit losses from investments and accounts receivable.

Fair Value Measurements

The Company determines the fair value of its assets and liabilities based on the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value maximize the use of observable inputs and minimize the use of unobservable inputs. The Company uses a fair value hierarchy with three levels of inputs, of which the first two are considered observable and the last unobservable, to measure fair value:

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Level 1 — Quoted prices in active markets for identical assets or liabilities.

Level 2 — Inputs, other than Level 1, that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The carrying amounts of financial instruments such as cash and cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable, and accrued liabilities, excluding acquisition related contingent consideration liabilities, approximate the related fair values due to the short-term maturities of these instruments.

Functional Currency

The U.S. dollar is the functional currency of the Company’s international operations. The Company re-measures its foreign subsidiaries’ monetary assets and liabilities to the U.S. dollar and records the net gains or losses resulting from re-measurement in other expense, net in the consolidated statements of income.

Acquisitions

The Company measures all assets acquired and liabilities assumed, including contingent considerations and all contractual contingencies, at fair value as of the acquisition date. Contingent purchase considerations to be settled in cash are re-measured to estimated fair value at each reporting period with the change in fair value recorded in acquisition related gain, net, a component of operating expenses. In addition, the Company capitalizes in-process research and development (IPR&D) and either amortizes it over the life of the product upon commercialization, or impairs it if the project is abandoned. Post-acquisition adjustments in deferred tax asset valuation allowances and liabilities for uncertain tax positions are recorded in current period income tax expense.

In January 2016, the Company closed two acquisitions consisting of $17.8 million in upfront cash payments, equity

instruments, and certain contingent consideration provisions.

Cash Equivalents and Short-Term Investments

Cash equivalents are comprised of short-term, highly liquid investments with maturities of 90 days or less at the date of purchase.

Short-term investments consist predominantly of debt securities in U.S. government-sponsored entities, corporate debt securities, and U.S. Treasury securities. Management classifies short-term investments as available-for-sale at the time of purchase and evaluates such classification as of each balance sheet date. All short-term investments are recorded at estimated fair value. Unrealized gains and losses for available-for-sale securities are included in accumulated other comprehensive income, a component of stockholders’ equity. The Company evaluates its investments to assess whether those with unrealized loss positions are other than temporarily impaired. Impairments are considered to be other than temporary if they are related to deterioration in credit risk or if it is likely that the Company will sell the securities before the recovery of their cost basis.

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Realized gains, losses, and declines in value judged to be other than temporary are determined based on the specific identification method and are reported in interest income in the consolidated statements of income.

Accounts Receivable

Trade accounts receivable are recorded at the net invoice value and are not interest bearing. The Company considers receivables past due based on the contractual payment terms. The Company reserves specific receivables if collectibility is no longer reasonably assured. The Company also reserves a percentage of its trade receivable balance based on collection history and current economic trends that might impact the level of future credit losses. The Company re-evaluates such reserves on a regular basis and adjusts its reserves as needed. Once a receivable is deemed to be uncollectible, such balance is charged against the reserve.

Inventory

Inventory is stated at the lower of cost or market, on a first in, first out basis. Inventory includes raw materials and finished goods that may be used in the research and development process and such items are expensed as consumed or expired. Provisions for slow moving, excess, and obsolete inventories are estimated based on product life cycles, quality issues, historical experience, and usage forecasts.

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Property and Equipment

Property and equipment are stated at cost, subject to review for impairment, and depreciated over the estimated useful lives of the assets, ~~which generally range from~~ ~~three~~ to ~~seven years~~, using the straight-line method. Amortization of leasehold improvements is recorded over the shorter of the lease term or the estimated useful life of the related assets. Amortization of assets that are recorded under capital leases are included in depreciation expense. Maintenance and repairs are charged to operations as incurred. When assets are sold, or otherwise disposed of, the cost and related accumulated depreciation are removed from the accounts and any gain or loss is included in operating expense.

The estimated useful lives of the major classes of property and equipment are generally as follows:



	Estimated Useful Lives
Building and leasehold improvements	4 to 30 years
Machinery and equipment	3 to 5 years
Computer hardware and software	3 to 7 years
Furniture and fixtures	7 years

In 2015, as a part of the Company’s ongoing effort to upgrade its ~~current~~ information systems, the Company ~~finished the implementation of the initial phase of~~implemented a new enterprise resource planning software and applications to manage parts of its business operations. Certain costs incurred in the development of such internal-use software and software applications, including external direct costs of materials and services and applicable compensation costs of employees devoted to specific software development were capitalized as computer software costs. Costs incurred outside of the application development stage were expensed as incurred.

Leases

Leases are reviewed and classified as capital or operating at their inception. Additionally, the Company evaluates whether it is the accounting owner during the construction period when the Company is involved in the construction of leased assets. ~~The~~For operating leases, the Company records rent expense on a straight-line basis over the term of the lease, which includes the construction build-out period and lease extension periods, if appropriate. The difference between rent payments and straight-line rent expense is recorded as deferred rent in accrued liabilities and other long-term liabilities. ~~Landlord allowances~~Lease incentives are amortized on a straight-line basis over the lease term as a reduction to rent expense. The Company capitalizes leasehold improvements and amortizes the value over the shorter of the lease term or expected useful lives.

Headquarter relocation expenses consisted of expenses such as accelerated depreciation expense, impairment of assets, additional rent expense during the transition period in 2012 when both the new and former headquarter facilities were occupied, moving expenses, cease-use losses, and accretion of interest expense on lease exit liability. The Company completed the

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relocation of its headquarters in 2012 to another facility in San Diego, California and recorded cease-use losses and the corresponding facility exit obligation upon vacating its former headquarters in 2011 and 2012, calculated as the present value of the remaining lease obligation offset by estimated sublease rental receipts during the remaining lease period, adjusted for deferred items and estimated lease incentives. The Company reassesses the facility exit obligation on a quarterly basis and the key assumptions used in the calculation include the amount and timing of estimated sublease rental receipts, and the risk-adjusted discount rate.

Goodwill, Intangible Assets and Other Long-Lived Assets

Goodwill, which has an indefinite useful life, represents the excess of cost over fair value of net assets acquired. The change in the carrying value of goodwill during the year ended January ~~3, 2016,~~1, 2017, was due to a current year ~~acquisition.~~acquisitions. Goodwill is reviewed for impairment at least annually during the second quarter, or more frequently if an event occurs indicating the potential for impairment. During its goodwill impairment review, the Company may assess qualitative factors to determine whether it is more likely than not that the fair value of its reporting unit is less than its carrying amount, including goodwill. The qualitative factors include, but are not limited to, macroeconomic conditions, industry and market considerations, and the overall financial performance of the Company. If, after assessing the totality of these qualitative factors, the Company determines that it is not more likely than not that the fair value of its reporting unit is less than its carrying amount, then no additional assessment is deemed necessary. Otherwise, the Company proceeds to perform the two-step test for goodwill impairment. The first step involves comparing the estimated fair value of the reporting unit with its carrying value, including goodwill. If the carrying amount of the reporting unit exceeds its fair value, the Company performs the second step of the goodwill impairment test to determine the amount of loss, which involves comparing the implied fair value of the goodwill to the carrying value of the goodwill. The Company may also elect to bypass the qualitative assessment in a period and elect to proceed to perform the first step of the goodwill impairment test. The Company performed its annual assessment for goodwill impairment in the second quarter of ~~2015,~~2016, noting no impairment.

The Company’s identifiable intangible assets are typically comprised of acquired core technologies, licensed technologies, customer relationships, license agreements, and trade names. The cost of identifiable intangible assets with finite lives is generally amortized on a straight-line basis over the assets’ respective estimated useful lives.

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The Company regularly performs reviews to determine if any event has occurred that may indicate its intangible assets with finite useful lives and other long-lived assets are potentially impaired. If indicators of impairment exist, the Company performs an impairment test to assess the recoverability of the affected assets by determining whether the carrying amount of such assets exceeds the undiscounted expected future cash flows. If the affected assets are not recoverable, the Company estimates the fair value of the assets and records an impairment loss if the carrying value of the assets exceeds the fair value. Factors that may indicate potential impairment include a significant decline in the Company’s stock price and market capitalization compared to its net book value, significant changes in the ability of a particular asset to generate positive cash flows the Company’s strategic business objectives, and the pattern of utilization of a particular asset.

During 2013, the Company decided to discontinue its Eco and NuPCR product lines to better align its product portfolio with its core strategy. As a result, the Company recorded a total impairment charge of $25.2 million in cost of product revenue, $22.9 million of which related to identifiable intangible assets.

Derivatives

The Company is exposed to foreign exchange rate risks in the normal course of business. The Company enters into foreign exchange contracts to manage foreign currency risks related to monetary assets and liabilities that are denominated in currencies other than the U.S. dollar. These foreign exchange contracts are carried at fair value in other assets or other liabilities and are not designated as hedging instruments. Changes in the value of the derivatives are recognized in other expense, net, along with the re-measurement gain or loss on the foreign currency denominated assets or liabilities.

As of January ~~3, 2016,~~1, 2017, the Company had foreign exchange forward contracts in place to hedge exposures in the euro, Japanese yen, and Australian dollar. As of January ~~3, 2016~~1, 2017 and ~~December 28, 2014~~January 3, 2016, the total notional amount of outstanding forward contracts in place for foreign currency purchases was $~~61.3~~68.8 million and $~~61.0~~61.3 million, respectively.

Warranties

The Company generally provides a ~~one-year~~one-year warranty on instruments. Additionally, the Company provides a warranty on consumables through the expiration date, which generally ranges from six to twelve months after the manufacture date. At the time revenue is recognized, the Company establishes an accrual for estimated warranty expenses based on historical experience as well as anticipated product performance. The Company periodically reviews its warranty reserve for adequacy and adjusts

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the warranty accrual, if necessary, based on actual experience and estimated costs to be incurred. Warranty expense is recorded as a component of cost of product revenue.

Revenue Recognition

The Company’s revenue is generated primarily from the sale of products and services. Product revenue primarily consists of sales of instruments and consumables used in genetic analysis. Service and other revenue primarily consists of revenue generated from genotyping and sequencing services and instrument service contracts.

The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the seller’s price to the buyer is fixed or determinable, and collectibility is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all the acceptance criteria have been met. The Company occasionally offers discounts on newly introduced products to recent customers of existing products. These promotions sometimes involve the trade-in of existing products in exchange for a discount on new products. Where applicable, the Company defers a portion of revenue on the sales of existing products in recognition of the promotional discounts until the delivery of new products. All revenue is recorded net of discounts and sales taxes collected on behalf of governmental authorities.

Revenue from product sales is recognized generally upon transfer of title to the customer, provided that no significant obligations remain and collection of the receivable is reasonably assured. Revenue from instrument service contracts is recognized as the services are rendered, typically evenly over the contract term. Revenue from genotyping and sequencing services is recognized when earned, which is generally at the time the genotyping or sequencing analysis data is made available to the customer or agreed upon milestones are reached.

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In order to assess whether the price is fixed or determinable, the Company evaluates whether an arrangement is cancellable or subject to future changes in price, deliverables, or other terms. If it is determined that the price is not fixed or determinable, the Company defers revenue recognition until the price becomes fixed or determinable. The Company assesses collectibility based on a number of factors, including past transaction history with, and the creditworthiness of, the customer. If the Company determines that collection of a payment is not reasonably assured, revenue recognition is deferred until receipt of payment.

The Company regularly enters into contracts where revenue is derived from multiple deliverables including products or services. These products or services are generally delivered within a short time frame, approximately three to six months, after the contract execution date. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when the delivered item has value to the customer on a stand-alone basis. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis.

For transactions with multiple deliverables, consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence (VSOE) of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable.

In order to establish VSOE of selling price, the Company must regularly sell the product or service on a standalone basis with a substantial majority priced within a relatively narrow range. VSOE of selling price is usually the midpoint of that range. If there are not a sufficient number of standalone sales and VSOE of selling price cannot be determined, then the Company considers whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within the industry, the Company has rarely established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, the Company determines its best estimate of selling price using average selling prices over a rolling 12-month period coupled with an assessment of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by the Company’s pricing committee adjusted for applicable discounts. The Company recognizes revenue for delivered elements only when it determines there are no uncertainties regarding customer acceptance.

In certain markets, the Company sells products and provides services to customers through distributors that specialize in life science products. In most sales through distributors, the product is delivered directly to customers. In cases where the product is delivered to a distributor, revenue recognition is deferred until acceptance is received from the distributor, and/or the

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end-user, if required by the applicable sales contract. The terms of sales transactions through distributors are consistent with the terms of direct sales to customers. These transactions are accounted for in accordance with the Company’s revenue recognition policy described herein.

Share-Based Compensation

The Company incurs share-based compensation expense related to restricted stock, its Employee Stock Purchase Plan (ESPP), and stock options.

Restricted stock units (RSU), restricted stock awards (RSA), and performance stock units (PSU) are all considered restricted stock. The fair value of restricted stock is determined by the closing market price of the Company’s common stock on the date of grant. The Company recognizes share-based compensation expense based on the fair value on a straight-line basis over the requisite service periods of the awards, taking into consideration estimated forfeitures. PSU represents a right to receive a certain number of shares of common stock based on the achievement of corporate performance goals and continued employment during the vesting period. At each reporting period, the Company reassesses the probability of the achievement of such corporate performance goals and any additional expenses resulting from an adjustment in the estimated shares to be released are treated as a cumulative catch-up in the period of adjustment.

The Company uses the Black-Scholes-Merton option-pricing model to estimate the fair value of stock purchases under ESPP and stock options granted. The model assumptions include expected volatility, term, dividends, and the risk-free interest rate. The Company determines the expected volatility by equally weighing the historical and implied volatility of the Company’s common stock. The historical volatility is generally commensurate with the estimated expected term of the Company’s stock awards, adjusted for the impact of unusual fluctuations and other relevant factors. The implied volatility is calculated from the implied market volatility of exchange-traded call options on the Company’s common stock. The expected

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~~ILLUMINA, INC.~~

~~NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)~~

term of an award is based on historical forfeiture experience, exercise activity, and on the terms and conditions of the stock awards. The expected dividend yield is determined to be 0% given that the Company has never declared or paid cash dividends on its common stock and does not anticipate paying such cash dividends. The risk-free interest rate is based upon U.S. Treasury securities with remaining terms similar to the expected term of the share-based awards.

Shipping and Handling Expenses

Shipping and handling expenses are included in cost of product revenue.

Research and Development

Research and development expenses include personnel expenses, contractor fees, license fees, facilities costs, and utilities. Expenditures relating to research and development are expensed in the period incurred.

Advertising Costs

The Company expenses advertising costs as incurred. Advertising costs were $~~18.5~~19.5 million, $~~16.4~~18.5 million, and $~~14.5~~16.4 million for the years ended January 1, 2017, January 3, 2016~~December 28, 2014~~, and December ~~29, 2013~~28, 2014, respectively.

Income Taxes

The provision for income taxes is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. The effect of a change in tax rates on deferred tax assets and liabilities is recognized in the provision for income taxes in the period that includes the enactment date.

Deferred tax assets are regularly assessed to determine the likelihood they will be recovered from future taxable income. A valuation allowance is established when the Company believes it is more likely than not the future realization of all or some of a deferred tax asset will not be achieved. In evaluating the ability to recover deferred tax assets within the jurisdiction which they arise the Company considers all available positive and negative evidence. Factors reviewed include the cumulative pre-tax book income for the past three years, scheduled reversals of deferred tax liabilities, history of earnings and reliable forecasting,

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ILLUMINA, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)

projections of pre-tax book income over the foreseeable future, and the impact of any feasible and prudent tax planning strategies.

The Company recognizes excess tax benefits associated with share-based compensation to stockholders’ equity only when realized. When assessing whether excess tax benefits relating to share-based compensation have been realized, the Company follows the with-and-without approach excluding any indirect effects of the excess tax deductions. Under this approach, excess tax benefits related to share-based compensation are not deemed to be realized until after the utilization of all other tax benefits available to the Company.

The Company recognizes the impact of a tax position in the financial statements only if that position is more likely than not of being sustained upon examination by taxing authorities, based on the technical merits of the position. Any interest and penalties related to uncertain tax positions will be reflected in income tax expense.

Earnings per Share

Basic earnings per share attributable to Illumina stockholders is computed based on the weighted average number of common shares outstanding during the period. Diluted earnings per share attributable to Illumina stockholders is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. Per-share earnings of our VIEs are included in the Company’s consolidated basic and diluted earnings per share computations based on the Company’s share of the VIE’s securities.

Potentially dilutive common shares consist of shares issuable under convertible senior notes, equity awards, and warrants. Convertible senior notes have a dilutive impact when the average market price of the Company’s common stock exceeds the applicable conversion price of the respective notes. Potentially dilutive common shares from equity awards and warrants are determined using the average share price for each period under the treasury stock method. In addition, the following amounts

~~Table of Contents~~

~~ILLUMINA, INC.~~

~~NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)~~

are assumed to be used to repurchase shares: proceeds from exercise of equity awards and warrants; the average amount of unrecognized compensation expense for equity awards; and estimated tax benefits that will be recorded in additional paid-in capital when expenses related to equity awards become deductible. In loss periods, basic net loss per share and diluted net loss per share are identical because the otherwise dilutive potential common shares become anti-dilutive and are therefore excluded.

The following table presents the calculation of weighted average shares used to calculate basic and diluted earnings per share (in thousands):


	Years Ended			Years Ended
	January 3, 2016	December 28, 2014	December 29, 2013	January 1, 2017	January 3, 2016	December 28, 2014
Weighted average shares outstanding	144,826	135,553	125,076	146,788	144,826	135,553
Effect of potentially dilutive common shares from:
Convertible senior notes	1,661	3,489	1,340	60	1,661	3,489
Equity awards	2,582	4,340	4,404	1,192	2,582	4,340
Warrants	—	5,595	9,116	—	—	5,595
Weighted average shares used in calculating diluted earnings per share	149,069	148,977	139,936	148,040	149,069	148,977
Potentially dilutive shares excluded from calculation due to anti-dilutive effect	139	124	996	459	139	124

Accumulated Other Comprehensive (Loss) Income ~~(Loss)~~

Comprehensive income is comprised of net income and other comprehensive income. Accumulated other comprehensive (loss) income ~~(loss)~~ on the consolidated balance sheets at January ~~3, 2016~~1, 2017 and ~~December 28, 2014~~January 3, 2016 includes accumulated foreign currency translation adjustments and unrealized gains and losses on the Company’s available-for-sale securities.

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ILLUMINA, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)

The components of accumulated other comprehensive income (loss) are as follows (in thousands):

January 3,
2016 December 28,
2014
Foreign currency translation adjustments $ 1,289
$ 1,289
Unrealized loss on available-for-sale securities, net of deferred tax (1,253 ) (2,369 )
Total accumulated other comprehensive income (loss) $ 36
$ (1,080 )



	January 1, 2017			January 3, 2016
Foreign currency translation adjustments	$	1,289		$	1,289
Unrealized (loss) gain on available-for-sale securities, net of deferred tax	(2,326		)	(1,253		)
Total accumulated other comprehensive (loss) income	$	(1,037	)	$	36


2.	Balance Sheet Account Details

Short-Term Investments

The following is a summary of short-term investments (in thousands):


	January 3, 2016									December 28, 2014									January 1, 2017									January 3, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Available-for-sale securities:
Debt securities in government-sponsored entities	$	14,634	$	—	$	(8	)	$	14,626	$	51,308	$	10	$	(55	)	$	51,263	$	33,862	$	—	$	(162	)	$	33,700	$	14,634	$	—	$	(8	)	$	14,626
Corporate debt securities	422,177		44		(1,127		)	421,094		502,924		46		(2,882		)	500,088		478,159		42		(1,959		)	476,242		422,177		44		(1,127		)	421,094
U.S. Treasury securities	182,144		3		(417		)	181,730		151,255		5		(394		)	150,866		315,502		31		(1,267		)	314,266		182,144		3		(417		)	181,730
Total available-for-sale securities	$	618,955	$	47	$	(1,552	)	$	617,450	$	705,487	$	61	$	(3,331	)	$	702,217	$	827,523	$	73	$	(3,388	)	$	824,208	$	618,955	$	47	$	(1,552	)	$	617,450

~~Table of Contents~~

~~ILLUMINA, INC.~~

~~NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)~~

Contractual maturities of available-for-sale debt securities as of January ~~3, 2016~~1, 2017 are as follows (in thousands):


	Estimated Fair Value		Estimated Fair Value
Due within one year	$	276,219	$	362,143
After one but within five years	341,231		462,065
Total	$	617,450	$	824,208

The Company has the ability, if necessary, to liquidate any of its cash equivalents and short-term investments in order to meet its liquidity needs in the next 12 months. Accordingly, those investments with contractual maturities greater than one year from the date of purchase nonetheless are classified as short-term on the accompanying Consolidated Balance Sheets.

~~Cost-Method~~Strategic Investments

As of January ~~3, 2016~~1, 2017 and ~~December 28, 2014~~January 3, 2016, the aggregate carrying amounts of the Company’s cost-method investments in non-publicly traded companies were $~~56.6~~57.4 million and $~~37.2~~56.6 million, respectively, included in other assets. Revenue recognized from transactions with such companies were $55.7 million, $61.0 million, ~~$39.8 million,~~ and ~~$31.7~~$39.8 million for the years ended January 1, 2017, January 3, 2016, and December 28, 2014, ~~and December 29, 2013,~~ respectively.

The Company’s cost-method investments are assessed for impairment quarterly. The Company determines that it is not practicable to estimate the fair value of its cost-method investments on a regular basis and does not reassess the fair value of cost-method investments if there are no identified events or changes in circumstances that may have a significant adverse effect on the fair value of the investments. No material impairment losses were recorded during the years ended January 1, 2017, January 3, 2016, and December 28, ~~2014, and December 29, 2013.~~2014.

During the year ended January 3, 2016, the Company recognized gains on dispositions of cost-method investments of $18.1 million. During the year ended December 28, 2014, the Company recorded a gain of $4.4 million associated with additional proceeds received for a cost-method investment sold in a prior period.

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ILLUMINA, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS — (Continued)

On April 14, 2016, the Company announced that it has committed to invest $100.0 million in the Fund. The capital commitment is callable over ten years, and up to $40.0 million can be drawn down during the first year. The Company’s investment in the Fund is accounted for as an equity method investment, and had a balance of $9.7 million as of January 1, 2017. During the year ended ~~December 29, 2013,~~January 1, 2017, the Company ~~recorded cost-method investment related gains of $61.4~~transferred $3.2 million of ~~which $55.2 million related~~its cost-method investments to the ~~sale of the Company’s minority interest~~Fund and contributed $7.4 million in ~~Oxford Nanopore Technologies Ltd.~~cash.

Accounts Receivable

Accounts receivable, net consist of the following (in thousands):


	January 3, 2016			December 28, 2014			January 1, 2017			January 3, 2016
Accounts receivable from product and service sales	$	393,106		$	292,847		$	385,164		$	393,106
Other receivables	636			2,070			386			636
Total accounts receivable, gross	393,742			294,917			385,550			393,742
Allowance for doubtful accounts	(8,213		)	(5,459		)	(4,234		)	(8,213		)
Total accounts receivable, net	$	385,529		$	289,458		$	381,316		$	385,529

~~Table of Contents~~

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

The Board of Directors and Stockholders of Illumina, Inc.

We have audited Illumina, Inc.’s internal control over financial reporting as of January ~~3, 2016,~~1, 2017, based on criteria established in Internal Control — Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). Illumina, Inc.’s management is responsible for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Report on Internal Control over Financial Reporting. Our responsibility is to express an opinion on the company’s internal control over financial reporting based on our audit.

We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion.

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

In our opinion, Illumina, Inc. maintained, in all material respects, effective internal control over financial reporting as of January ~~3, 2016,~~1, 2017, based on the COSO criteria.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the accompanying consolidated balance sheets of Illumina, Inc. as of January 1, 2017 and January 3, 2016, ~~and December 28, 2014,~~ and the related consolidated statements of income, comprehensive income, stockholders’ equity, and cash flows for each of the three fiscal years in the period ended January ~~3, 2016~~1, 2017 of Illumina, Inc. and our report dated ~~March 2, 2016~~February 13, 2017 expressed an unqualified opinion thereon.

/s/ ERNST & YOUNG LLP

San Diego, California

~~March 2, 2016~~February 13, 2017

~~Table of Contents~~


ITEM 9B.	Other Information.

None.

PART III


ITEM 10.	Directors, Executive Officers, and Corporate Governance.

(a) Identification of Directors. Information concerning our directors is incorporated by reference from the section entitled “Proposal One: Election of Directors,” “Information About Directors,” “Director Compensation,” and “Board of Directors and Corporate Governance” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

(b) Identification of Executive Officers. Information concerning our executive officers is incorporated by reference from the section entitled “Executive Officers” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

(c) Compliance with Section 16(a) of the Exchange Act. Information concerning compliance with Section 16(a) of the Securities Exchange Act of 1934 is incorporated by reference from the section entitled “Section 16(a) Beneficial Ownership Reporting Compliance” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

(d) Information concerning the audit committee financial expert as defined by the SEC rules adopted pursuant to the Sarbanes-Oxley Act of 2002 is incorporated by reference from the section entitled “Board of Directors and Corporate Governance” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

Code of Ethics

We have adopted a code of ethics for our directors, officers, and employees, which is available on our website at www.illumina.com in the Corporate Governance portal of the Investor Relations section under “Company.” A copy of the Code of Ethics is available in print free of charge to any stockholder who requests a copy. Interested parties may address a written request for a printed copy of the Code of Ethics to: Corporate Secretary, Illumina, Inc., 5200 Illumina Way, San Diego, California 92122. We intend to satisfy the disclosure requirement regarding any amendment to, or a waiver from, a provision of the Code of Ethics for our principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions, by posting such information on our website. The information on, or that can be accessed from, our website is not incorporated by reference into this report.


ITEM 11.	Executive Compensation.

Information concerning executive compensation is incorporated by reference from the sections entitled “Compensation Discussion and Analysis,” “Director Compensation,” and “Executive Compensation” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.


ITEM 12.	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters.

Information concerning the security ownership of certain beneficial owners and management and information covering securities authorized for issuance under equity compensation plans is incorporated by reference from the sections entitled “Stock Ownership of Principal Stockholders and Management,” “Executive Compensation,” and “Equity Compensation Plan Information” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.


ITEM 13.	Certain Relationships and Related Transactions, and Director Independence.

Information concerning certain relationships and related transactions, and director independence is incorporated by reference from the sections entitled “Proposal One: Election of Directors,” “Information About Directors,” “Director Compensation,” “Executive Compensation,” and “Certain Relationships and Related Party Transactions” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

~~Table of Contents~~


ITEM 14.	Principal Accountant Fees and Services.

Information concerning principal accountant fees and services is incorporated by reference from the sections entitled “Proposal Two: Ratification of Appointment of Independent Registered Public Accounting Firm” and “Independent Registered Public Accountants” to be contained in our definitive Proxy Statement with respect to our ~~2016~~2017 Annual Meeting of Stockholders to be filed with the SEC no later than May ~~2, 2016~~1, 2017.

PART IV


ITEM 15.	Exhibits, Financial Statement Schedules.

1. Financial Statements: See “Index to Consolidated Financial Statements” in Part II, Item 8 of this Form 10-K.

2. Financial Statement Schedule: See “Schedule II — Valuation and Qualifying Accounts and Reserves” in this section of this Form 10-K.

3. Exhibits: The exhibits listed in the accompanying index to exhibits are filed or incorporated by reference as part of this Form 10-K.

~~Table of Contents~~

SCHEDULE II — VALUATION AND QUALIFYING ACCOUNTS AND RESERVES


	Balance at Beginning of Period		Additions Charged to Expenses/(Reductions from Revenue)(1)		Deductions(2)		Balance at End of Period		Balance at Beginning of Period		Additions Charged to Expenses/(Reductions from Revenue)(1)	Deductions(2)		Balance at End of Period
	(In thousands)								(In thousands)
Year ended January 1, 2017
Allowance for doubtful accounts									$	8,213	2,953	(6,932	)	$	4,234
Year ended January 3, 2016
Allowance for doubtful accounts	$	5,459	3,213		(459	)	$	8,213	$	5,459	3,213	(459	)	$	8,213
Year ended December 28, 2014
Allowance for doubtful accounts	$	3,680	1,870		(91	)	$	5,459	$	3,680	1,870	(91	)	$	5,459
Year ended December 29, 2013
Allowance for doubtful accounts	$	4,280	(422	)	(178	)	$	3,680


(1)	Additions to and reductions from allowance for doubtful accounts are recorded to selling, general and administrative expense.


(2)	Deductions for allowance for doubtful accounts are for accounts receivable written off.

~~Table of Contents~~

INDEX TO EXHIBITS
Incorporated by Reference
Exhibit Filing Filed
Number Exhibit Description Form File Number Exhibit Date Herewith
2.1 Agreement and Plan of Merger by and among Illumina, Inc., TP Corporation, Verinata Health, Inc. and Shareholder Representative Services LLC (as the Stockholder Representative), dated as of January 6, 2013 10-K 001-35406 2.1
2/15/2013
3.1 Amended and Restated Certificate of Incorporation 8-K 000-30361 3.1
9/23/2008
3.2 Amended and Restated Bylaws 8-K 000-30361 3.1
11/5/2014
4.1 Specimen Common Stock Certificate S-1/A 333-33922 4.1
7/3/2000
4.2 Indenture related to the 0.25% Convertible Senior Notes due 2016, dated as of March 18, 2011, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee 10-Q 000-30361 4.1
5/4/2011
4.3 Indenture related to the 0% Convertible Senior Notes due 2019, dated as of June 11, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee 8-K 001-35406 4.1
6/11/2014
4.4 Indenture related to the 0.5% Convertible Senior Notes due 2021, dated as of June 11, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee 8-K 001-35406 4.2
6/11/2014
4.5 First Supplemental Indenture related to the 0.5% Convertible Senior Notes due 2021, dated as of August 27, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee 10-Q 001-35406 4.1
10/29/2014
+10.1 Form of Indemnification Agreement between Illumina and each of its directors and executive officers 10-Q 000-30361 10.55
7/25/2008
+10.2 Amended and Restated Change in Control Severance Agreement between Illumina and Jay T Flatley, dated October 22, 2008 10-K 000-30361 10.33
2/26/2009
+10.3 Form of Change in Control Severance Agreement between Illumina and each of its executive officers 10-K 000-30361 10.34
2/26/2009
+10.4 2000 Employee Stock Purchase Plan, as amended and restated through February 2, 2012 10-K 001-35406 10.4
2/24/2012
+10.5 2005 Stock and Incentive Plan, as amended and restated through May 29, 2013 S-8 333-190322 4.5
8/2/2013
+10.6 Form of Restricted Stock Unit Agreement for Non-Employee Directors under 2005 Stock and Incentive Plan 10-K 001-35406 10.6
2/24/2012
+10.7 Form of Stock Option Agreement for Non-Employee Directors under 2005 Stock and Incentive Plan 10-K 001-35406 10.7
2/24/2012
+10.8 Form of Restricted Stock Unit Agreement for Employees under 2005 Stock and Incentive Plan 10-K 001-35406 10.8
2/24/2012

INDEX TO EXHIBITS

Incorporated by Reference

Exhibit

Filing

Filed

Number

Exhibit Description

Form

File Number

Exhibit

Date

Herewith

3.1

Amended and Restated Certificate of Incorporation

8-K

000-30361

3.1

9/23/2008

3.2

Amended and Restated Bylaws

8-K

001-35406

3.2

1/11/2017

4.1

Specimen Common Stock Certificate

S-1/A

333-33922

4.1

7/3/2000

4.2

Indenture related to the 0% Convertible Senior Notes due 2019, dated as of June 11, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee

8-K

001-35406

4.1

6/11/2014

4.3

Indenture related to the 0.5% Convertible Senior Notes due 2021, dated as of June 11, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee

8-K

001-35406

4.2

6/11/2014

4.4

First Supplemental Indenture related to the 0.5% Convertible Senior Notes due 2021, dated as of August 27, 2014, between Illumina and The Bank of New York Mellon Trust Company, N.A., as trustee

10-Q

001-35406

4.1

10/29/2014

+10.1

Form of Indemnification Agreement between Illumina and each of its directors and executive officers

10-Q

000-30361

10.55

7/25/2008

+10.2

Amended and Restated Change in Control Severance Agreement between Illumina and Jay T Flatley, dated October 22, 2008

10-K

000-30361

10.33

2/26/2009

+10.3

Form of Change in Control Severance Agreement between Illumina and each of its executive officers

10-K

000-30361

10.34

2/26/2009

+10.4

2000 Employee Stock Purchase Plan, as amended and restated through February 2, 2012

10-K

001-35406

10.4

2/24/2012

+10.5

2005 Stock and Incentive Plan, as amended and restated through May 29, 2013

S-8

333-190322

4.5

8/2/2013

+10.6

Form of Restricted Stock Unit Agreement for Non-Employee Directors under 2005 Stock and Incentive Plan

10-K

001-35406

10.6

2/24/2012

+10.7

Form of Stock Option Agreement for Non-Employee Directors under 2005 Stock and Incentive Plan

10-K

001-35406

10.7

2/24/2012

+10.8

Form of Restricted Stock Unit Agreement for Employees under 2005 Stock and Incentive Plan

10-K

001-35406

10.8

2/24/2012

+10.9

Form of Stock Option Agreement for Employees under 2005 Stock and Incentive Plan

10-K

001-35406

10.9

2/24/2012

+10.10

New Hire Stock and Incentive Plan, as amended and restated through October 28, 2009

10-K

000-30361

10.7

2/26/2010

10.11

License Agreement, effective as of May 6, 1998, between Tufts University and Illumina

10-Q

000-30361

10.5

5/3/2007

~~Table of Contents~~

INDEX TO EXHIBITS — (Continued)
Incorporated by Reference
Exhibit Filing Filed
Number Exhibit Description Form File Number Exhibit Date Herewith
+10.9 Form of Stock Option Agreement for Employees under 2005 Stock and Incentive Plan 10-K 001-35406 10.9
2/24/2012
+10.10 New Hire Stock and Incentive Plan, as amended and restated through October 28, 2009 10-K 000-30361 10.7
2/26/2010
10.11 License Agreement, effective as of May 6, 1998, between Tufts University and Illumina 10-Q 000-30361 10.5
5/3/2007
+10.12 The Solexa Unapproved Company Share Option Plan 8-K 000-30361 99.3
11/26/2007
+10.13 The Solexa Share Option Plan for Consultants 8-K 000-30361 99.4
11/26/2007
+10.14 Solexa Limited Enterprise Management Incentive Plan 8-K 000-30361 99.5
11/26/2007
+10.15 Amended and Restated Solexa 2005 Equity Incentive Plan 10-K 000-30361 10.25
2/26/2009
+10.16 Amended and Restated Solexa 1992 Stock Option Plan 10-K 000-30361 10.26
2/26/2009
10.17 License Agreement, dated June 24, 2002, between Dade Behring Marburg GmbH and Illumina (with certain confidential portions omitted) S-3/A 333-111496 10.23
3/2/2004
10.18 Non-exclusive License Agreement, dated January 24, 2002, between Amersham Biosciences Corp. and Illumina (with certain confidential portions omitted) S-3/A 333-111496 10.24
3/2/2004
10.19 Amended and Restated Lease between BMR-9885 Towne Centre Drive LLC and Illumina for the 9885 Towne Centre Drive property, dated January 26, 2007 10-Q 000-30361 10.41
5/3/2007
10.20 Lease between BMR-9885 Towne Centre Drive LLC and Illumina for the 9865 Towne Centre Drive property, dated January 26, 2007 10-Q 000-30361 10.42
5/3/2007
10.21 Settlement and Release Agreement between Affymetrix, Inc. and Illumina, dated January 9, 2008 10-K 000-30361 10.44
2/26/2008
10.22 Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina 10-Q 001-35406 10.1
5/3/2012
10.23 First Amendment to Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina 10-K 001-35406 10.23
2/18/2015
10.24 Second Amendment to Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina 10-K 001-35406 10.24
2/18/2015
+10.25 Deferred Compensation Plan, effective December 1, 2007 14D-9 005-60457 99(e)(6)
2/7/2012
10.26 Lease between BMR-Lincoln Centre LP and Illumina, dated December 30, 2014 10-K 001-35406 10.26
2/18/2015

INDEX TO EXHIBITS — (Continued)

Incorporated by Reference

Exhibit

Filing

Filed

Number

Exhibit Description

Form

File Number

Exhibit

Date

Herewith

+10.12

The Solexa Unapproved Company Share Option Plan

8-K

000-30361

99.3

11/26/2007

+10.13

The Solexa Share Option Plan for Consultants

8-K

000-30361

99.4

11/26/2007

+10.14

Solexa Limited Enterprise Management Incentive Plan

8-K

000-30361

99.5

11/26/2007

+10.15

Amended and Restated Solexa 2005 Equity Incentive Plan

10-K

000-30361

10.25

2/26/2009

+10.16

Amended and Restated Solexa 1992 Stock Option Plan

10-K

000-30361

10.26

2/26/2009

10,170

Amended and Restated Lease between BMR-9885 Towne Centre Drive LLC and Illumina for the 9885 Towne Centre Drive property, dated January 26, 2007

10-Q

000-30361

10.41

5/3/2007

10.18

Lease between BMR-9885 Towne Centre Drive LLC and Illumina for the 9865 Towne Centre Drive property, dated January 26, 2007

10-Q

000-30361

10.42

5/3/2007

10.19

Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina

10-Q

001-35406

10.1

5/3/2012

10.20

First Amendment to Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina

10-K

001-35406

10.23

2/18/2015

10.21

Second Amendment to Amended and Restated Lease Agreement, dated March 27, 2012, between ARE-SD Region No. 32, LLC and Illumina

10-K

001-35406

10.24

2/18/2015

+10.22

Deferred Compensation Plan, effective December 1, 2007

14D-9

005-60457

99(e)(6)

2/7/2012

10.23

Lease between BMR-Lincoln Centre LP and Illumina, dated December 30, 2014

10-K

001-35406

10.26

2/18/2015

10.24

Pooled Patents Agreement between Illumina and Sequenom, Inc., dated December 2, 2014 (with certain confidential portions omitted)

10-K

001-35406

10.27

2/18/2015

10.25

Agreement for Lease between Granta Park Park Jco 1 Limited and Illumina, dated June 25, 2015

10-Q

001-35406

10.1

7/31/2015

10.26

Third Amendment to Lease between ARE-SD Region No. 32, LLC and Illumina, dated September 2, 2015

10-K

001-35406

10.29

3/2/2016

10.27

First Amendment to Lease between BMR-Lincoln Center LP and Illumina, dated February 23, 2016

10-K

001-35406

10.30

3/2/2016

10.28

Fourth Amendment to Lease between ARE-SD Region No. 32, LLC and Illumina, dated April 14, 2016

10.29

Second Amendment to Lease between BMR-Lincoln Center LP and Illumina dated August 15, 2016

~~Table of Contents~~

INDEX TO EXHIBITS — (Continued)
Incorporated by Reference
Exhibit Filing Filed
Number Exhibit Description Form File Number Exhibit Date Herewith
10.27 Pooled Patents Agreement between Illumina and Sequenom, Inc., dated December 2, 2014 (with certain confidential portions omitted) 10-K 001-35406 10.27
2/18/2015
10.28 Agreement for Lease between Granta Park Park Jco 1 Limited and Illumina, dated June 25, 2015 10-Q 001-35406 10.1
7/31/2015
10.29 Third Amendment to Lease between ARE-SD Region No. 32, LLC and Illumina, dated September 2, 2015 X
10.30 First Amendment to Lease between BMR-Lincoln Center LP and Illumina, dated February 23, 2016 X
21.1 Subsidiaries of Illumina
X
23.1 Consent of Independent Registered Public Accounting Firm
X
24.1 Power of Attorney (included on the signature page)
X
31.1 Certification of Jay T. Flatley pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
X
31.2 Certification of Marc A. Stapley pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
X
32.1 Certification of Jay T. Flatley pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
X
32.2 Certification of Marc A. Stapley pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
X
101.INS XBRL Instance Document X
101.SCH XBRL Taxonomy Extension Schema X
101.CAL XBRL Taxonomy Extension Calculation Linkbase X
101.LAB XBRL Taxonomy Extension Label Linkbase X
101.PRE XBRL Taxonomy Extension Presentation Linkbase X
101.DEF XBRL Taxonomy Extension Definition Linkbase X

INDEX TO EXHIBITS — (Continued)

Incorporated by Reference

Exhibit

Filing

Filed

Number

Exhibit Description

Form

File Number

Exhibit

Date

Herewith

10.30

Deed of Variation to the Agreement for Lease between Granta Park Jco 1 Limited and Illumina dated October 24, 2016

10.31

Separation Agreement and General Release of All Claims between Illumina and Christian Henry

21.1

Subsidiaries of Illumina

23.1

Consent of Independent Registered Public Accounting Firm

24.1

Power of Attorney (included on the signature page)

31.1

Certification of Francis A. deSouza pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

31.2

Certification of Sam A. Samad pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

32.1

Certification of Frances A. deSouza pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

32.2

Certification of Sam A. Samad pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

101.INS

XBRL Instance Document

101.SCH

XBRL Taxonomy Extension Schema

101.CAL

XBRL Taxonomy Extension Calculation Linkbase

101.LAB

XBRL Taxonomy Extension Label Linkbase

101.PRE

XBRL Taxonomy Extension Presentation Linkbase

101.DEF

XBRL Taxonomy Extension Definition Linkbase



+		Management contract or corporate plan or arrangement

Supplemental Information

No Annual Report to stockholders or proxy materials has been sent to stockholders as of the date of this report. The Annual Report to stockholders and proxy material will be furnished to our stockholders subsequent to the filing of this Annual Report on Form 10-K and we will furnish such material to the SEC at that time.

~~Table of Contents~~

SIGNATURES

Pursuant to the requirements of the Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized, on ~~March 2, 2016.~~February 13, 2017.



	ILLUMINA, INC.

	By	/s/ JFAYRANCIS ~~T. F~~A. ~~LATLEY~~DESOUZA
		~~Jay T. Flatley~~Francis A. deSouza President and Chief Executive Officer ~~and Chairman of the Board of Directors~~

~~Table of Contents~~

~~March 2, 2016~~February 13, 2017

POWER OF ATTORNEY

KNOW ALL PERSONS BY THESE PRESENT, that each person whose signature appears below constitutes and appoints ~~Jay T. Flatley~~Francis A. deSouza and ~~Marc~~Sam A. ~~Stapley,~~Samad, and each or any one of them, his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him and in his or her name, place and stead, in any and all capacities, to sign any and all amendments to this Annual Report on Form 10-K, and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or their, his, or her substitutes or substitute, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.



/s/ JFAYRANCIS ~~T. F~~A.~~LATLEY~~ DESOUZA	President, Chief Executive Officer, and ~~Chairman of the Board of Directors~~Director (Principal Executive Officer)	~~March 2, 2016~~February 13, 2017
~~Jay T. Flatley~~Francis A. deSouza

/s/ MS~~ARC~~AM A. S~~TAPLEY~~AMAD	~~Executive~~Senior Vice President ~~Chief Administrative Officer~~ and Chief Financial Officer (Principal Financial Officer)	~~March 2, 2016~~February 13, 2017
~~Marc~~Sam A. ~~Stapley~~Samad

/s/ MICHEL BOUCHARD	Vice President and Chief Accounting Officer (Principal Accounting Officer)	~~March 2, 2016~~February 13, 2017
Michel Bouchard

/s/ JAY T. F~~RANCIS~~ ~~A. DESOUZA~~LATLEY	~~President and Director~~Executive Chairman of the Board of Directors	~~March 2, 2016~~February 13, 2017
~~Francis A. deSouza~~Jay T. Flatley

/s/ ~~FRANCES ARNOLD~~FRANCESARNOLD	Director	~~March 2, 2016~~February 13, 2017
Frances Arnold

/s/ A. BLAINE BOWMAN	Director	~~March 2, 2016~~February 13, 2017
A. Blaine Bowman

/s/ DANIEL M. BRADBURY	Director	~~March 2, 2016~~February 13, 2017
Daniel M. Bradbury

/s/ CAROLINE D. DORSA	Director	February 13, 2017
Caroline D. Dorsa

/s/ KARIN EASTHAM	Director	~~March 2, 2016~~February 13, 2017
Karin Eastham

/s/ ROBERT S. EPSTEIN	Director	~~March 2, 2016~~February 13, 2017
Robert S. Epstein

/s/ DP~~AVID~~HILIP ~~R. W~~W. S~~ALT~~CHILLER	Director	~~March 2, 2016~~February 13, 2017
~~David R. Walt~~Philip W. Schiller

/s/ ROY WHITFIELD	Director	~~March 2, 2016~~February 13, 2017
Roy Whitfield

8788



Delaware		33-0804655
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)
5200 Illumina Way San Diego, California		92122
(Address of principal executive offices)		(Zip Code)



Title of each class		Name of each exchange on which registered
Common Stock, $0.01 par value		The NASDAQ Global Select Market



Large accelerated filer þ	Accelerated filer o	Non-accelerated filer o	Smaller reporting company o
		(Do not check if a smaller reporting company)


	Payments Due by Period(1)										Payments Due by Period(1)
			Less Than						More Than				Less Than						More Than
Contractual Obligation	Total		1 Year		1 – 3 Years		3 – 5 Years		5 Years		Total		1 Year		1 – 3 Years		3 – 5 Years		5 Years
Debt obligations(2)	$	1,239,873	$	78,229	$	5,175	$	637,675	$	518,794	$	1,161,644	$	2,588	$	637,675	$	521,381	$	—
Leases	905,436		40,410		96,052		108,338		660,636
Operating leases											661,931		42,759		91,981		91,586		435,605
Build-to-suit leases											376,857		12,244		53,297		56,488		254,828
License agreements	91,295		12,380		31,865		47,050		—		77,225		12,920		41,155		23,150		—
Purchase obligations	23,142		12,172		8,048		2,922		—		22,458		18,503		3,955		—		—
Amounts due under executive deferred compensation plan	24,925		24,925		—		—		—		29,223		29,223		—		—		—
Contingent consideration payments related to acquisitions	35,000		35,000		—		—		—		4,139		—		4,139		—		—
Total	$	2,319,671	$	203,116	$	141,140	$	795,985	$	1,179,430	$	2,333,477	$	118,237	$	832,202	$	692,605	$	690,433


	January 3, 2016		December 28, 2014		January 1, 2017		January 3, 2016
Raw materials	$	97,740	$	73,179	$	101,999	$	97,740
Work in process	138,322		94,102		161,087		138,322
Finished goods	34,715		23,863		37,084		34,715
Total inventory	$	270,777	$	191,144	$	300,170	$	270,777



þ		ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934



o		TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
		For the transition period from to



		Page
PART I
Item 1	Business	4
Item 1A	Risk Factors	11
Item 1B	Unresolved Staff Comments	22
Item 2	Properties	2223
Item 3	Legal Proceedings	23
Item 4	Mine Safety Disclosures	23

PART II
Item 5	Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities	24
Item 6	Selected Financial Data	26
Item 7	Management’s Discussion and Analysis of Financial Condition and Results of Operations	26
Item 7A	Quantitative and Qualitative Disclosures About Market Risk	40
Item 8	Financial Statements and Supplementary Data	41
Item 9	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure	78
Item 9A	Controls and Procedures	78
Item 9B	Other Information	8081

PART III
Item 10	Directors, Executive Officers and Corporate Governance	8081
Item 11	Executive Compensation	8081
Item 12	Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters	8081
Item 13	Certain Relationships and Related Transactions, and Director Independence	8081
Item 14	Principal Accountant Fees and Services	8182

PART IV
Item 15	Exhibits and Financial Statement Schedule	8182
Signatures		8687



	January 3, 2016		December 28, 2014
Balance at beginning of period	$	724,904	$	723,061
Current period acquisition	27,725		3,338
Purchase price allocation adjustments related to prior year acquisitions	—		(1,495		)
Balance at end of period	$	752,629	$	724,904



	Redeemable Noncontrolling Interests
Balance as of December 28, 2014	$	—
Cash contributions	56,875
Amount held in escrow by third party	(24,747		)
Vested portion of stock units	418
Net loss attributable to noncontrolling interests	(4,169		)
Adjustment to the redemption value	4,169
Balance as of January 3, 2016	$	32,546



	Weighted-Average Useful Lives (in years)	Gross Carrying Amount
Core technologies	5.0	$	3,698
Customer relationships	10.0	8,076
License agreements	4.6	400
Trade name	3.0	679
Total intangible asset additions		$	12,853


	Estimated Annual Amortization		Estimated Annual Amortization
2016	$	49,608
2017	45,137		$	47,360
2018	35,652		37,967
2019	32,249		34,532
2020	24,533		26,795
2021			22,768
Thereafter	86,442		67,930
Total	$	273,621	$	237,352


	Contingent Consideration Liability (Level 3 Measurement)			Contingent Consideration Liability (Level 3 Measurement)
Balance as of December 30, 2012	$	12,519
Additional liability recorded for current period acquisitions	60,184
Change in estimated fair value, recorded in acquisition related gain, net	(18,784		)
Cash payments	(4,439		)
Balance as of December 29, 2013	49,480			$	49,480
Change in estimated fair value, recorded in acquisition related gain, net	(5,356		)	(5,356		)
Balance as of December 28, 2014	44,124			44,124
Change in estimated fair value, recorded in acquisition related gain, net	(6,124		)	(6,124		)
Cash payments	(3,000		)	(3,000		)
Balance as of January 3, 2016	$	35,000		35,000
Additional liability recorded as a result of a current period acquisition				5,300
Change in estimated fair value, recorded in selling, general and administrative expenses				(1,161		)
Cash payments				(35,000		)
Balance as of January 1, 2017				$	4,139


	2016 Notes		2016 Notes
Cash paid for principal of notes converted	$	244,480	$	75,543
Conversion value over principal amount paid in shares of common stock	$	345,829	$	63,753
Number of shares of common stock issued upon conversion	1,721		409
Loss on extinguishment of debt	$	4,062
Effective interest rate used to measure fair value of converted notes upon conversion	1.1% - 1.4%



	Operating Leases		Sublease Income			Net Operating Leases
2016	$	39,397	$	(3,252	)	$	36,145
2017	37,909		(3,113		)	34,796
2018	39,853		(3,206		)	36,647
2019	43,027		(3,303		)	39,724
2020	43,656		(3,291		)	40,365
Thereafter	488,127		(8,878		)	479,249
Total minimum lease payments	$	691,969	$	(25,043	)	$	666,926


	Facility Exit Obligation			Facility Exit Obligation
Balance as of December 30, 2012	$	45,352
Adjustment to facility exit obligation	(114		)
Accretion of interest expense	2,738
Cash payments	(9,758		)
Balance as of December 29, 2013	38,218			$	38,218
Adjustment to facility exit obligation	2,555			2,555
Accretion of interest expense	2,638			2,638
Cash payments	(5,711		)	(5,711		)
Balance as of December 28, 2014	37,700			37,700
Adjustment to facility exit obligation	(5,303		)	(5,303		)
Accretion of interest expense	2,294			2,294
Cash payments	(12,531		)	(12,531		)
Balance as of January 3, 2016	$	22,160		22,160
Adjustment to facility exit obligation				190
Accretion of interest expense				1,296
Cash payments				(4,723		)
Balance as of January 1, 2017				$	18,923


	Minimum Payments		Minimum Payments
2016	$	12,380
2017	13,410		$	12,920
2018	18,455		18,055
2019	23,500		23,100
2020	23,550		23,150
Total minimum royalty payments	$	91,295	$	77,225


	Warranty Reserve			Warranty Reserve
Balance as of December 30, 2012	$	10,136
Additions charged to cost of revenue	15,674
Repairs and replacements	(15,403		)
Balance as of December 29, 2013	10,407			$	10,407
Additions charged to cost of revenue	24,150			24,150
Repairs and replacements	(18,941		)	(18,941		)
Balance as of December 28, 2014	15,616			15,616
Additions charged to cost of revenue	27,574			27,574
Repairs and replacements	(26,473		)	(26,473		)
Balance as of January 3, 2016	$	16,717		16,717
Additions charged to cost of revenue				21,243
Repairs and replacements				(24,721		)
Balance as of January 1, 2017				$	13,239


	Restricted Stock Awards (RSA)		Restricted Stock Units (RSU)			Performance Stock Units (PSU)(1)		Weighted-Average Grant-Date Fair Value per Share							Restricted Stock Awards (RSA)		Restricted Stock Units (RSU)			Performance Stock Units (PSU)(1)		Weighted-Average Grant-Date Fair Value per Share
	Restricted Stock Awards (RSA)				RSA			RSU		PSU				RSA			Restricted Stock Units (RSU)		RSU			PSU
Outstanding at December 30, 2012	465		Restricted Stock Units (RSU)		3,660	Performance Stock Units (PSU)(1)			587	$	53.84	$	45.49		Restricted Stock Awards (RSA)		$	49.64		Performance Stock Units (PSU)(1)
Awarded	—		1,532			584		—		$	77.53	$	59.16
Vested	(217	)	(1,308	)		—		$	54.27	$	42.97	—
Cancelled	—		(256	)		(70	)	—		$	49.24	$	50.42
Outstanding at December 29, 2013	248		3,628			1,101		$	53.46	$	59.66	$	54.64		248		3,628			1,101		$	53.46	$	59.66	$	54.64
Awarded	—		780			968		—		$	172.53	$	104.52		—		780			968		—		$	172.53	$	104.52
Vested	(140	)	(1,383	)		(753	)	$	47.90	$	55.44	$	49.52		(140	)	(1,383	)		(753	)	$	47.90	$	55.44	$	49.52
Cancelled	—		(184	)		(59	)	—		$	65.09	$	52.87		—		(184	)		(59	)	—		$	65.09	$	52.87
Outstanding at December 28, 2014	108		2,841			1,257		$	56.62	$	92.35	$	96.21		108		2,841			1,257		$	56.62	$	92.35	$	96.21
Awarded	—		756			194		—		$	184.10	$	183.29		—		756			194		—		$	184.10	$	183.29
Vested	(87	)	(1,138	)		(741	)	$	58.72	$	75.29	$	60.80		(87	)	(1,138	)		(741	)	$	58.72	$	75.29	$	60.80
Cancelled	—		(253	)		(127	)	—		$	99.50	$	99.30		—		(253	)		(127	)	—		$	99.50	$	99.30
Outstanding at January 3, 2016	21		2,206			583		$	47.93	$	131.80	$	169.41		21		2,206			583		$	47.93	$	131.80	$	169.41
Awarded															22		1,245			172		$	179.00	$	132.47	$	113.56
Vested															(11	)	(928	)		(199	)	$	47.93	$	105.49	$	148.99
Cancelled															—		(230	)		(96	)	—		$	139.74	$	163.05
Outstanding at January 1, 2017															32		2,293			460		$	136.30	$	141.80	$	158.66


(1)	The number of units reflect the estimated number of shares to be issued at the end of the performance period.


	Options (in thousands)		Weighted- Average Exercise Price		Options (in thousands)		Weighted- Average Exercise Price
Outstanding at December 30, 2012	8,351		$	32.10
Granted	512		$	14.74
Exercised	(3,006	)	$	27.70
Cancelled	(133	)	$	41.80
Outstanding at December 29, 2013	5,724		$	32.64	5,724		$	32.64
Exercised	(2,478	)	$	29.93	(2,478	)	$	29.93
Cancelled	(35	)	$	31.73	(35	)	$	31.73
Outstanding at December 28, 2014	3,211		$	34.74	3,211		$	34.74
Exercised	(1,529	)	$	28.54	(1,529	)	$	28.54
Cancelled	(83	)	$	10.31	(83	)	$	10.31
Outstanding at January 3, 2016	1,599		$	41.95	1,599		$	41.95
Exercised					(552	)	$	29.41
Cancelled					(2	)	$	46.35
Outstanding at January 1, 2017					1,045		$	48.56


12.	Segment Information, Geographic Data, and Significant Customers