公开(公告)号：US11887699B2

公开(公告)日：2024-01-30

申请号：US17932706

申请日：2022-09-16

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai

IPC: G06F7/00 ,  G16B50/50 ,  H03M7/30 ,  G16B50/00 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B40/10 ,  G16B20/20 ,  G16B20/40 ,  C12Q1/6869 ,  G16B30/10

CPC classification number: G16B50/50 ,  G16B20/00 ,  G16B20/20 ,  G16B20/40 ,  G16B30/00 ,  G16B40/00 ,  G16B40/10 ,  G16B50/00 ,  H03M7/70 ,  C12Q1/6869 ,  G16B30/10 ,  C12Q1/6869 ,  C12Q2537/165

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US20230410943A1

公开(公告)日：2023-12-21

申请号：US18143828

申请日：2023-05-05

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai ,  Eugene Ingerman ,  Chao Wang ,  Alison Lai ,  Werner Puschitz

IPC: G16B20/20 ,  G06N3/0464 ,  G06N3/09 ,  G16B30/00 ,  G16B40/20

CPC classification number: G16B20/20 ,  G06N3/0464 ,  G06N3/09 ,  G16B30/00 ,  G16B40/20

Abstract: A method for labeling sequence reads includes retrieving a sequence read having an associated flow measurement and an associated flow order; matching a sequence selected from a plurality of sequences with the sequence read, the sequence having a position within the sequence that has more than one acceptable variants; determining which variant of the more than one acceptable variants matches the sequence; generating a predicted flow measurement based on the matched sequence, the variant, and a flow order; and labeling the sequence read and associated flow measurement with the predicted flow measurement.

公开(公告)号：US20230083776A1

公开(公告)日：2023-03-16

申请号：US17932706

申请日：2022-09-16

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai

IPC: G16B50/50 ,  H03M7/30 ,  G16B50/00 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B40/10 ,  G16B20/20 ,  G16B20/40

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US20210202044A1

公开(公告)日：2021-07-01

申请号：US17135196

申请日：2020-12-28

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai

IPC: G16B50/00 ,  H03M7/30 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B50/50

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US20180336316A1

公开(公告)日：2018-11-22

申请号：US15979804

申请日：2018-05-15

Applicant: Life Technologies Corporation

Inventor： Cheng-Zong Bai

IPC: G06F19/28 ,  G06F19/22 ,  G06F19/24 ,  H03M7/30

CPC classification number: C12Q1/6869 ,  G06F19/18 ,  G06F19/22 ,  C12Q2537/165

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US12243626B2

公开(公告)日：2025-03-04

申请号：US18392060

申请日：2023-12-21

Applicant: Life Technologies Corporation

Inventor： Cheng-Zong Bai

IPC: G06F17/00 ,  G06F7/00 ,  G16B20/00 ,  G16B20/20 ,  G16B20/40 ,  G16B30/00 ,  G16B40/00 ,  G16B40/10 ,  G16B50/00 ,  G16B50/50 ,  H03M7/30 ,  C12Q1/6869 ,  G16B30/10

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US20240203525A1

公开(公告)日：2024-06-20

申请号：US18531920

申请日：2023-12-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Cheng-Zong Bai ,  Dumitru Brinza ,  Jeoffrey Schageman ,  Varun Bagai

IPC: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

CPC classification number: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.

公开(公告)号：US11894105B2

公开(公告)日：2024-02-06

申请号：US16136463

申请日：2018-09-20

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Cheng-Zong Bai ,  Dumitru Brinza ,  Jeoffrey Schageman ,  Varun Bagai

IPC: G16B30/00 ,  C12Q1/6853 ,  G16B30/10 ,  G16B20/20 ,  G16B50/50

CPC classification number: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.

公开(公告)号：US11468972B2

公开(公告)日：2022-10-11

申请号：US17135196

申请日：2020-12-28

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai

IPC: G06F7/00 ,  G16B50/50 ,  H03M7/30 ,  G16B50/00 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B40/10 ,  G16B20/20 ,  G16B20/40 ,  C12Q1/6869 ,  G16B30/10

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

公开(公告)号：US10892037B2

公开(公告)日：2021-01-12

申请号：US15979804

申请日：2018-05-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Cheng-Zong Bai

IPC: G06F17/00 ,  G06F7/00 ,  G16B50/00 ,  H03M7/30 ,  G16B30/00 ,  G16B40/00 ,  G16B20/00 ,  G16B50/50 ,  C12Q1/6869 ,  G16B30/10

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.