ILMN Illumina

Illumina Inc.
Company
Patents are sorted by USPTO publication date, most recent first
APP
Utility
Methods and Compositions for Whole Genome Amplification and Genotyping
26 Nov 20
This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments.
Kevin L. Gunderson, Frank J. Steemers
Filed: 5 Aug 20
APP
Utility
Flexible Seed Extension for Hash Table Genomic Mapping
26 Nov 20
Methods, systems, and apparatuses, including computer programs for generating and using a hash table configured to improve mapping of reads are disclosed that include obtaining a first seed of K nucleotides from a reference sequence, generating a seed extension tree having a nodes, wherein each node of the nodes corresponds to (i) an extended seed that is an extension of the first seed and has a nucleotide length of K* and (ii) one or more locations, in a seed extension table, that include data describing reference sequence locations that match the extended seed, and for each node: storing interval information at a location of the hash table that corresponds to an index key for the extended seed, wherein the interval information references one or more locations in the seed extension table that include reference sequence locations that match the extended seed associated with the node.
Michael Ruehle
Filed: 22 May 20
APP
Utility
Sensors Having an Active Surface
26 Nov 20
Disclosed in one example is an apparatus including a substrate, a sensor over the substrate including an active surface and a sensor bond pad, a molding layer over the substrate and covering sides of the sensor, the molding layer having a molding height relative to a top surface of the substrate that is greater than a height of the active surface of the sensor relative to the top surface of the substrate, and a lidding layer over the molding layer and over the active surface.
Arvin Emadi, Arnaud Rival, Ali Agah
Filed: 20 May 20
GRANT
Utility
Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)
24 Nov 20
The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length.
Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers
Filed: 15 Apr 16
GRANT
Utility
Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
24 Nov 20
The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length.
Kevin Wu, Chen Zhao, Han-Yu Chuang, Alex So, Stephen Tanner, Stephen M. Gross
Filed: 5 Jan 18
GRANT
Utility
Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
24 Nov 20
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects.
Pieter van Rooyen, Robert J. McMillen, Michael Ruehle, Rami Mehio
Filed: 11 Jan 17
APP
Utility
Modified Polymerases for Improved Incorporation of Nucleotide Analogues
19 Nov 20
Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same.
Erin Bomati, Michael Previte, Matthew William Kellinger, Cheng-Yao Chen, Molly He
Filed: 22 May 20
APP
Utility
Systems and Devices for Characterization and Performance Analysis of Pixel-Based Sequencing
19 Nov 20
In one embodiment, a method of determining tag signals from measured intensities, the measured intensities collected by light sensors in a sensor array directed to a sample surface, the sample surface including pixel areas and holding a plurality of clusters during a sequence of sampling events, each light sensor directed to and measuring intensity from one of the pixel areas during each sampling period includes adjustments for background intensity and crosstalk and taking into account signal decay and phasing/pre-phasing.
Emrah KOSTEM
Filed: 14 May 20
APP
Utility
Linear Peristaltic Pumps For Use With Fluidic Cartridges
19 Nov 20
Linear peristaltic pumps for use with fluidic cartridges.
Cameron Mar, Wesley A. Cox-Muranami, Steven Hendrix, Cyril Delattre
Filed: 15 May 20
APP
Utility
Base Calling Using Convolutions
19 Nov 20
We propose a neural network-based base caller that detects and accounts for stationary, kinetic, and mechanistic properties of the sequencing process, mapping what is observed at each sequence cycle in the assay data to the underlying sequence of nucleotides.
Emrah KOSTEM
Filed: 14 May 20
GRANT
Utility
Non-invasive prenatal diagnosis of fetal genetic condition using cellular DNA and cell free DNA
17 Nov 20
Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother.
Anupama Srinivasan, Darya I. Chudova, Richard P. Rava
Filed: 9 Aug 18
GRANT
Utility
Conformational probes and methods for sequencing nucleic acids
17 Nov 20
This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template.
Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
Filed: 13 Mar 19
GRANT
Utility
Photonic superlattice-based devices and compositions for use in luminescent imaging, and methods of using the same
17 Nov 20
Under one aspect, a device is provided for use in luminescent imaging.
Dietrich Dehlinger, Cheng Frank Zhong, Juraj Topolancik
Filed: 17 Oct 19
GRANT
Utility
Multiplex nucleic acid reactions
17 Nov 20
A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.
Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
Filed: 30 Nov 17
APP
Utility
Methods for Determining Tumor Microsatellite Instability
12 Nov 20
Presented herein are methods and compositions for determining MSI status and LS screening in a single test of colorectal cancer tissue.
Li Liu, Shile Zhang, Mahdi Golkaram, Shannon Kaplan, Jie Ren
Filed: 7 May 20
GRANT
Utility
Optical cleaning cartridge
10 Nov 20
An optical cleaning cartridge for automated cleaning of optical components of analysis instruments is disclosed.
Ashish Kumar, Peter Clarke Newman
Filed: 2 Apr 19
GRANT
Utility
Methods and compositions for single cell genomics
10 Nov 20
Presented are methods and compositions for obtaining sequence information from one or more individual cells.
Jian-Bing Fan, Kun Zhang
Filed: 17 Jun 15
GRANT
Utility
Solid inspection apparatus and method of use
10 Nov 20
An inspection apparatus is provided that comprises an optical target including a solid host material and a fluorescing material embedded in the solid host material.
John Gerhardt Earney, Joseph Francis Pinto, M. Shane Bowen, Michael S. Graige, Arthur Pitera, Bala Murali K. Venkatesan, Dajun Yuan
Filed: 1 Mar 19
GRANT
Utility
Detection apparatus having a microfluorometer, a fluidic system, and a flow cell latch clamp module
10 Nov 20
Detection apparatus includes a microfluorometer having an objective, an excitation radiation source, and a detector.
Beng Keong Ang, Heng Kuang Cheng, John M. Beierle, Bradley Kent Drews, David Kaplan
Filed: 26 Mar 18
GRANT
Utility
Reagent mixing system and methods
10 Nov 20
A method includes, under control of control circuitry implementing a mixing protocol, aspirating reagents from multiple different reagent reservoirs into a cache channel.
Johanna L. Whitacre, Steven S. Phelps, Bradley Kent Drews, Debra Sue Bryan, II, Michael A. Niziolek, Joshua A. Darland, Umberto Ulmanella, Michael Dai Wang, Michelle L. Alvarez, Stephen Wayne Clark
Filed: 19 Dec 17