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：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：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：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：US20210130885A1

公开(公告)日：2021-05-06

申请号：US17145846

申请日：2021-01-11

Applicant: ILLUMINA, INC.

Inventor： Alex So ,  Li Liu ,  Min-Jui Richard Shen ,  Neeraj Salathia ,  Kathryn M. Stephens ,  Anne Jager ,  Timothy Wilson ,  Justin Fullerton ,  Sean M. Ramirez ,  Shannon Kaplan ,  Rigo Pantoja ,  Bala Murali Venkatesan ,  Steven Modiano

IPC: C12Q1/6837 ,  C12Q1/6874 ,  C12Q1/6816 ,  C12Q1/6855

Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

公开(公告)号：US20210108262A1

公开(公告)日：2021-04-15

申请号：US17076715

申请日：2020-10-21

Applicant: Illumina, Inc.

Inventor： Sante Gnerre ,  Byoungsok Jung ,  Emrah Kostem ,  Alex Aravanis ,  Alex So ,  Xuyu Cai ,  Zhihong Zhang ,  Frank J. Steemers

IPC: C12Q1/6869 ,  G16B30/00 ,  C12Q1/6806 ,  C12N15/10 ,  C12Q1/6855

Abstract: 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. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

公开(公告)号：US20210254170A1

公开(公告)日：2021-08-19

申请号：US17172380

申请日：2021-02-10

Applicant: ILLUMINA, INC.

Inventor： Mahdi Golkaram ,  Shile Zhang ,  Li Liu ,  Aaron Wise ,  Joyee Yao ,  Shannon Kaplan ,  Alex So ,  Michael Salmans ,  Raakhee Vijayaraghavan

IPC: C12Q1/6886

Abstract: A potential prognostic biomarker is based on a combination of a composite score generated by sequence analysis of global human endogenous retrovirus (hERV)/retro-transposon transactivation and a cell signature generated using deconvolution of immune cells within a tumor sample for predicting the efficacy of chemotherapeutic agents and immune checkpoint inhibitors. Correlation analysis of the composite score with cell signature within a tumor sample enables survival analysis in individuals receiving chemotherapeutic agents and immune checkpoint inhibitors.

公开(公告)号：US10913975B2

公开(公告)日：2021-02-09

申请号：US15747670

申请日：2016-07-21

Applicant: ILLUMINA, INC.

Inventor： Alex So ,  Li Liu ,  Min-Jui Richard Shen ,  Neeraj Salathia ,  Kathryn M. Stephens ,  Anne Jager ,  Timothy Wilson ,  Justin Fullerton ,  Sean M. Ramirez ,  Shannon Kaplan ,  Rigo Pantoja ,  Bala Murali Venkatesan ,  Steven Modiano

IPC: C12Q1/68 ,  C12Q1/6837 ,  C12Q1/6874 ,  C12Q1/6816 ,  C12Q1/6855

Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

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.

公开(公告)号：US20160319345A1

公开(公告)日：2016-11-03

申请号：US15130668

申请日：2016-04-15

Applicant: Illumina, Inc.

Inventor： Sante Gnerre ,  Byoungsok Jung ,  Emrah Kostem ,  Alex Aravanis ,  Alex So ,  Xuyu Cai ,  Zhihong Zhang

IPC: C12Q1/68 ,  C12N15/10 ,  G06F19/22

CPC classification number: C12Q1/6869 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  G16B30/00 ,  C12Q2525/191 ,  C12Q2535/119 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2565/514

Abstract: 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. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract translation: 所公开的实施例涉及使用与单个多核苷酸片段唯一相关联的独特分子指数（UMI）序列确定感兴趣序列的方法，装置，系统和计算机程序产品，包括具有低等位基因频率和长序列长度的序列。 在一些实现中，UMI包括物理UMI和虚拟UMI。 在一些实施方案中，独特的分子索引序列包括非随机序列。 还提供了系统，装置和计算机程序产品，用于确定实现所公开方法的感兴趣的顺序。