公开(公告)号：US20190156922A1

公开(公告)日：2019-05-23

申请号：US16191142

申请日：2018-11-14

Applicant: ILLUMINA, INC.

Inventor： Shile Zhang ,  Alex S. So ,  Shannon Kaplan ,  Kristina M. Kruglyak ,  Sven Bilke

IPC: G16H10/60 ,  C12Q1/6886 ,  G01N33/50 ,  G16B30/20 ,  G06F9/30

Abstract: Presented herein are techniques for determining microsatellite instability. The techniques include generating a reference sample dataset representative of or mimicking a hypothetical matched sample for an individual sample of interest. The reference sample dataset may be generated from a set of reference normal samples that are not matched to the sample of interest. For samples of interest lacking a matched sample, the reference sample dataset may be used to determine microsatellite instability and to provide an indication of a presence, absence, or degree of microsatellite instability of the sample of interest. The reference sample dataset may be generated such that individual microsatelliate regions associated with a high degree of variability between ethnic groups are filtered out, masked, or otherwise not considered.

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：US20210350873A1

公开(公告)日：2021-11-11

申请号：US17314513

申请日：2021-05-07

Applicant: ILLUMINA, INC.

Inventor： Sven Bilke ,  Johann Felix Wilhelm Schlesinger

IPC: G16B30/00 ,  G16B20/20

Abstract: A nucleic acid sequencing technique is described. Sequence data, e.g., generated by a sequencing device, may be analyzed to scan k-mers of a fixed size n in individual reads in the sequence data. Exact matches of the k-mers in the sequence data with reference k-mers are identified. The number of exact matches, their distribution in a reference genome, and/or a number of sequence reads in the sequence data that map to different target regions can be used to determine a characteristic of a sample. In one example, the characteristic is a presence of a pathogen in the sample.

公开(公告)号：US12230365B2

公开(公告)日：2025-02-18

申请号：US18316939

申请日：2023-05-12

Applicant: Illumina, Inc.

Inventor： Chen Zhao ,  Kevin Eric Wu ,  Sven Bilke

IPC: G01N33/48 ,  G06F16/22 ,  G06F16/2457 ,  G16B30/10 ,  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：US12154664B2

公开(公告)日：2024-11-26

申请号：US16191142

申请日：2018-11-14

Applicant: ILLUMINA, INC.

Inventor： Shile Zhang ,  Alex S. So ,  Shannon Kaplan ,  Kristina M. Kruglyak ,  Sven Bilke

IPC: G16H10/60 ,  C12Q1/6869 ,  C12Q1/6886 ,  G01N33/50 ,  G06F9/30 ,  G16B20/20 ,  G16B30/20

Abstract: Presented herein are techniques for determining microsatellite instability. The techniques include generating a reference sample dataset representative of or mimicking a hypothetical matched sample for an individual sample of interest. The reference sample dataset may be generated from a set of reference normal samples that are not matched to the sample of interest. For samples of interest lacking a matched sample, the reference sample dataset may be used to determine microsatellite instability and to provide an indication of a presence, absence, or degree of microsatellite instability of the sample of interest. The reference sample dataset may be generated such that individual microsatelliate regions associated with a high degree of variability between ethnic groups are filtered out, masked, or otherwise not considered.

公开(公告)号：US20250069714A1

公开(公告)日：2025-02-27

申请号：US18919011

申请日：2024-10-17

Applicant: ILLUMINA, INC.

Inventor： Shile Zhang ,  Alex S. So ,  Shannon Kaplan ,  Kristina M. Kruglyak ,  Sven Bilke

IPC: G16H10/60 ,  C12Q1/6869 ,  C12Q1/6886 ,  G01N33/50 ,  G06F9/30 ,  G16B20/20 ,  G16B30/20

Abstract: Presented herein are techniques for determining microsatellite instability. The techniques include generating a reference sample dataset representative of or mimicing a hypothetical matched sample for an individual sample of interest. The reference sample dataset may be generated from a set of reference normal samples that are not matched to the sample of interest. For samples of interest lacking a matched sample, the reference sample dataset may be used to determine microsatellite instability and to provide an indication of a presence, absence, or degree of microsatellite instability of the sample of interest. The reference sample dataset may be generated such that individual microsatelliate regions associated with a high degree of variability between ethnic groups are filtered out, masked, or otherwise not considered.

公开(公告)号：US20230282309A1

公开(公告)日：2023-09-07

申请号：US18316939

申请日：2023-05-12

Applicant: Illumina, Inc.

Inventor： Chen Zhao ,  Kevin Eric Wu ,  Sven Bilke

IPC: 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：US20230207059A1

公开(公告)日：2023-06-29

申请号：US17997633

申请日：2021-05-07

Applicant: ILLUMINA, INC.

Inventor： Sven Bilke ,  Johann Felix Wilhelm Schlesinger

IPC: G16B30/00 ,  G16B20/20

CPC classification number: G16B30/00 ,  G16B20/20

Abstract: A nucleic acid sequencing technique is described. Sequence data, e.g., generated by a sequencing device, may be analyzed to scan k-mers of a fixed size n in individual reads in the sequence data. Exact matches of the k-mers in the sequence data with reference k-mers are identified. K-mer matching may be used to identify alternative alleles in sequence data with anomalous distribution associated with contamination or other quality issues and to determine a quality metric in real-time.