公开(公告)号：US20240084376A1

公开(公告)日：2024-03-14

申请号：US18231724

申请日：2023-08-08

Applicant: Illumina, Inc.

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

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

CPC classification number: C12Q1/6869 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  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 (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：US11866777B2

公开(公告)日：2024-01-09

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 ,  C12N15/10 ,  C12Q1/6806 ,  G16B30/10 ,  C12Q1/6855

CPC classification number: C12Q1/6869 ,  C12N15/1065 ,  C12Q1/6806 ,  C12Q1/6855 ,  G16B30/00 ,  G16B30/10 ,  C12Q1/6806 ,  C12Q2525/191 ,  C12Q2535/119 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2565/514 ,  C12Q1/6869 ,  C12Q2525/191 ,  C12Q2535/119 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2565/514 ,  C12N15/1065 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2563/179

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：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：US20180201992A1

公开(公告)日：2018-07-19

申请号：US15863737

申请日：2018-01-05

Applicant: Illumina, Inc.

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

IPC: C12Q1/6869 ,  C12Q1/6855

CPC classification number: 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.