公开(公告)号：US20240271199A1

公开(公告)日：2024-08-15

申请号：US18397836

申请日：2023-12-27

Applicant: Illumina, Inc.

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

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

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：US12087401B2

公开(公告)日：2024-09-10

申请号：US17724951

申请日：2022-04-20

Applicant: Illumina, Inc.

Inventor： Tingting Jiang ,  Chen Zhao ,  Han-Yu Chuang

IPC: G01N33/48 ,  G01N33/50 ,  G06N3/047 ,  G06N3/126 ,  G16B20/00 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B40/00 ,  G16B35/00 ,  G16C20/60

CPC classification number: G16B20/20 ,  G06N3/047 ,  G06N3/126 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  G16B40/00 ,  G16B35/00 ,  G16C20/60

Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.

公开(公告)号：US11898198B2

公开(公告)日：2024-02-13

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: C12P19/34 ,  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 ,  C12Q1/6869 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q1/6869 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2563/179

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：US20230193357A1

公开(公告)日：2023-06-22

申请号：US18165153

申请日：2023-02-06

Applicant: ILLUMINA, INC.

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

IPC: C12Q1/6806

CPC classification number: 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：US20220246234A1

公开(公告)日：2022-08-04

申请号：US17724951

申请日：2022-04-20

Applicant: Illumina, Inc.

Inventor： Tingting Jiang ,  Chen Zhao ,  Han-Yu Chuang

IPC: G16B20/20 ,  G06N3/04 ,  G06N3/12 ,  G16B40/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10

Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.

公开(公告)号：US20250046394A1

公开(公告)日：2025-02-06

申请号：US18798594

申请日：2024-08-08

Applicant: Illumina, Inc.

Inventor： Tingting Jiang ,  Chen Zhao ,  Han-Yu Chuang

IPC: G16B20/20 ,  G06N3/047 ,  G06N3/126 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  G16B35/00 ,  G16B40/00 ,  G16C20/60

Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.

公开(公告)号：US20230207048A1

公开(公告)日：2023-06-29

申请号：US16333933

申请日：2017-09-21

Applicant: ILLUMINA, INC.

Inventor： Han-Yu Chuang ,  Chen Zhao

IPC: G16B20/10 ,  G16B20/20 ,  G16B30/10

CPC classification number: G16B20/10 ,  G16B20/20 ,  G16B30/10

Abstract: Presented herein are techniques for assessing copy number variation. The techniques include generating a baseline representative of or mimicing a hypothetical matched sample for an individual biological sample from a set of baseline samples that are not matched to the biological sample. Normalized sequencing data from the set of baseline samples that includes at least one copy number baseline for a region of interest is provided to a user.

公开(公告)号：US11342047B2

公开(公告)日：2022-05-24

申请号：US15957622

申请日：2018-04-19

Applicant: Illumina, Inc.

Inventor： Tingting Jiang ,  Chen Zhao ,  Han-Yu Chuang

IPC: G01N33/48 ,  G01N33/50 ,  G16B20/20 ,  G06N3/04 ,  G06N3/12 ,  G16B40/00 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10 ,  G16B35/00 ,  G16C20/60

Abstract: Methods and systems are provided for determining a variant of interest by analyzing sizes and sequences of cfDNA fragments obtained from a test sample. The methods and systems provided herein implement processes that synergistically combine size and sequence information, thereby improving specificity and sensitivity of assays over conventional methods.

公开(公告)号：US10577643B2

公开(公告)日：2020-03-03

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 ,  C07H21/00 ,  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：US20190085384A1

公开(公告)日：2019-03-21

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: C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6876 ,  G06F19/22 ,  G06F19/18 ,  G06F19/24 ,  C12Q1/686

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.