公开(公告)号：US20240011087A1

公开(公告)日：2024-01-11

申请号：US18230114

申请日：2023-08-03

Applicant: Illumina, Inc.

Inventor： Kevin Wu ,  Chen Zhao ,  Han-Yu Chuang ,  Alex So ,  Stephen Tanner ,  Stephen M. Gross

IPC: C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B30/00 ,  G16B30/10 ,  G16B25/20

CPC classification number: C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B30/00 ,  G16B30/10 ,  G16B25/20

Abstract: 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. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

公开(公告)号：US11624084B2

公开(公告)日：2023-04-11

申请号：US16782833

申请日：2020-02-05

Applicant: ILLUMINA, INC.

Inventor： Li Teng ,  Chia-Ling Hsieh ,  Charles Lin ,  Han-Yu Chuang

IPC: C12Q1/6806

Abstract: Presented herein are methods and compositions for enhancing specific enrichment of target sequences in a nucleic acid library. Off-target hybridization probes may be used to reduce binding and/or capture of off-target regions of a nucleic acid library in a targeted sequencing workflow. The off-target hybridization probes may be specific for locations known to generate off-target sequencing reads for a particular set of hybridization probes.

公开(公告)号：US20210079462A1

公开(公告)日：2021-03-18

申请号：US17073074

申请日：2020-10-16

Applicant: Illumina, Inc.

Inventor： Kevin Wu ,  Chen Zhao ,  Han-Yu Chuang ,  Alex So ,  Stephen Tanner ,  Stephen M. Gross

IPC: C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B30/00

Abstract: 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. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

公开(公告)号：US20200172960A1

公开(公告)日：2020-06-04

申请号：US16782833

申请日：2020-02-05

Applicant: ILLUMINA, INC.

Inventor： Teng Li ,  Chia-Ling Hsieh ,  Charles Lin ,  Han-Yu Chuang

IPC: C12Q1/6806

Abstract: Presented herein are methods and compositions for enhancing specific enrichment of target sequences in a nucleic acid library. Off-target hybridization probes may be used to reduce binding and/or capture of off-target regions of a nucleic acid library in a targeted sequencing workflow. The off-target hybridization probes may be specific for locations known to generate off-target sequencing reads for a particular set of hybridization probes.

公开(公告)号：US20170101676A1

公开(公告)日：2017-04-13

申请号：US15286374

申请日：2016-10-05

Applicant: ILLUMINA, INC.

Inventor： Li Teng ,  Chia-Ling Hsieh ,  Charles Lin ,  Han-Yu Chuang

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q2535/122 ,  C12Q2537/159 ,  C12Q2537/163 ,  C12Q2563/131

Abstract: Presented herein are methods and compositions for enhancing specific enrichment of target sequences in a nucleic acid library. Off-target hybridization probes may be used to reduce binding and/or capture of off-target regions of a nucleic acid library in a targeted sequencing workflow. The off-target hybridization probes may be specific for locations known to generate off-target sequencing reads for a particular set of hybridization probes.

公开(公告)号：US20240026348A1

公开(公告)日：2024-01-25

申请号：US18476719

申请日：2023-09-28

Applicant: Illumina, Inc. ,  Illumina Cambridge Limited

Inventor： Susan C. Verity ,  Robert Scott Kuersten ,  Niall Anthony Gormley ,  Andrew B. Kennedy ,  Sarah E. Shultzaberger ,  Andrew Slatter ,  Emma Bell ,  Sebastien Georg Gabriel Ricoult ,  Grace DeSantis ,  Fiona Kaper ,  Han-Yu Chuang ,  Oliver Jon Miller ,  Jason Richard Betley ,  Stephen M. Gross ,  Mats Ekstrand

IPC: C12N15/10

CPC classification number: C12N15/1065 ,  C12N15/1068

Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.

公开(公告)号：US11761035B2

公开(公告)日：2023-09-19

申请号：US17073074

申请日：2020-10-16

Applicant: Illumina, Inc.

Inventor： Kevin Wu ,  Chen Zhao ,  Han-Yu Chuang ,  Alex So ,  Stephen Tanner ,  Stephen M. Gross

IPC: G01N33/48 ,  G01N33/50 ,  C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B30/00 ,  G16B30/10 ,  G16B25/20

CPC classification number: C12Q1/6869 ,  C12Q1/6855 ,  G16B25/00 ,  G16B25/20 ,  G16B30/00 ,  G16B30/10

Abstract: 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. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

公开(公告)号：US20230242977A1

公开(公告)日：2023-08-03

申请号：US17890208

申请日：2022-08-17

Applicant: Illumina, Inc.

Inventor： Chen Zhao ,  Kevin Wu ,  Han-Yu Chuang ,  Jennifer Lococo ,  Alex So ,  Dwight Baker ,  Tatjana Singer

IPC: C12Q1/6855 ,  G16B20/20 ,  G16B35/10 ,  G16B30/10 ,  G16B25/20 ,  G16B40/00 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6876

CPC classification number: C12Q1/6855 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6876 ,  G16B20/00 ,  G16B20/20 ,  G16B25/20 ,  G16B30/00 ,  G16B30/10 ,  G16B35/10 ,  G16B40/00 ,  C12Q2525/191 ,  C12Q2525/197 ,  C12Q2600/16 ,  C12Q2600/166

Abstract: The disclosed embodiments concern methods, systems and computer program products for determining sequences of interest using unique molecular indexes (UMIs) that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies or long sequence length. In some implementations, the UMIs include variable-length nonrandom UMIs (vNRUMIs). Methods and systems for making and using sequencing adapters comprising vNRUMIs are also provided.

公开(公告)号：US11447818B2

公开(公告)日：2022-09-20

申请号：US16129099

申请日：2018-09-12

Applicant: Illumina, Inc.

Inventor： Chen Zhao ,  Kevin Wu ,  Han-Yu Chuang ,  Jennifer Lococo ,  Alex So ,  Dwight Baker ,  Tatjana Singer

IPC: C12P19/34 ,  C12Q1/6855 ,  G16B20/20 ,  G16B35/10 ,  G16B30/10 ,  G16B25/20 ,  G16B40/00 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6876

Abstract: The disclosed embodiments concern methods, systems and computer program products for determining sequences of interest using unique molecular indexes (UMIs) that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies or long sequence length. In some implementations, the UMIs include variable-length nonrandom UMIs (vNRUMIs). Methods and systems for making and using sequencing adapters comprising vNRUMIs are also provided.

公开(公告)号：US20200090784A1

公开(公告)日：2020-03-19

申请号：US16467228

申请日：2018-01-16

Applicant: ILLUMINA, INC.

Inventor： June Snedecor ,  Han-Yu Chuang ,  Gwenn Berry ,  Xiao Chen

IPC: G16B20/20 ,  G16B30/10 ,  C12N15/10 ,  C12Q1/6809 ,  C12Q1/6886

Abstract: Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events.