公开(公告)号：US20240304280A1

公开(公告)日：2024-09-12

申请号：US18664975

申请日：2024-05-15

Applicant: ILLUMINA, INC.

Inventor： Tingting Jiang ,  Chen Zhao

IPC: G16B20/20 ,  G16B30/00 ,  G16B40/00

CPC classification number: G16B20/20 ,  G16B30/00 ,  G16B40/00

Abstract: Presented herein are techniques for identifying and/or validating sequence variants in genomic sequence data. The techniques include generating an error rate reflective of sequence errors present in the genomic sequence data. The error rate may be used to validate potential sequence variants. The error rate may be based on errors identified during consensus sequence confirmation for sequence reads associated with individual unique molecular identifiers.

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：US11688489B2

公开(公告)日：2023-06-27

申请号：US16667642

申请日：2019-10-29

Applicant: Illumina, Inc.

Inventor： Chen Zhao ,  Kevin Eric Wu ,  Sven Bilke

IPC: G01N33/48 ,  G16B30/10 ,  G06F16/22 ,  G06F16/2457 ,  G16B30/20

CPC classification number: G16B30/10 ,  G06F16/2255 ,  G06F16/24578 ,  G16B30/20

Abstract: Disclosed herein are systems and methods for collapsing sequencing reads and identifying similar sequencing reads. In one example, a method includes generating a plurality of first identifier subsequences from a first identifier sequence of each nucleotide sequencing read and generating a first signature for the nucleotide sequencing read by applying hashing to the plurality of first identifier subsequences. The method may include assigning the nucleotide sequencing read to a first particular bin of a first data structure based on the first signature and determining a nucleotide sequence for each first particular bin of the first data structure with one or more nucleotide sequencing reads assigned.

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：US12040047B2

公开(公告)日：2024-07-16

申请号：US16206552

申请日：2018-11-30

Applicant: ILLUMINA, INC.

Inventor： Tingting Jiang ,  Chen Zhao

IPC: G16B20/20 ,  G16B30/00 ,  G16B40/00

CPC classification number: G16B20/20 ,  G16B30/00 ,  G16B40/00

Abstract: Presented herein are techniques for identifying and/or validating sequence variants in genomic sequence data. The techniques include generating an error rate reflective of sequence errors present in the genomic sequence data. The error rate may be used to validate potential sequence variants. The error rate may be based on errors identified during consensus sequence confirmation for sequence reads associated with individual unique molecular identifiers.

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：US20190206510A1

公开(公告)日：2019-07-04

申请号：US16206552

申请日：2018-11-30

Applicant: ILLUMINA, INC.

Inventor： Tingting Jiang ,  Chen Zhao

IPC: G16B20/20 ,  G16B30/00

CPC classification number: G16B20/20 ,  G16B30/00 ,  G16B40/00

Abstract: Presented herein are techniques for identifying and/or validating sequence variants in genomic sequence data. The techniques include generating an error rate reflective of sequence errors present in the genomic sequence data. The error rate may be used to validate potential sequence variants. The error rate may be based on errors identified during consensus sequence confirmation for sequence reads associated with individual unique molecular identifiers.