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：US20210217491A1

公开(公告)日：2021-07-15

申请号：US17248083

申请日：2021-01-08

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G16B30/00 ,  G16B20/20

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

公开(公告)号：US20190385698A1

公开(公告)日：2019-12-19

申请号：US16445477

申请日：2019-06-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland

IPC: G16B30/00

Abstract: Systems and method for identifying gene fusions can obtain sequencing information for a plurality of amplicons from a nucleic acid sample. The sequencing information can include a plurality of reads that are initially partially mapped to a reference sequence. Fragments may be generated by splitting the partially mapped reads into mapped and unmapped fragments, and the fragments may be remapped to the reference sequence. Gene fusions can be identified based on reads where the first fragment maps to a first gene and the second fragment maps to a second gene.

公开(公告)号：US20180268103A1

公开(公告)日：2018-09-20

申请号：US15866578

申请日：2018-01-10

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Fiona Hyland ,  Rajesh Gottimukkala

IPC: G06F19/22 ,  C12Q1/6809 ,  G06F19/18

CPC classification number: G16B30/00 ,  C12Q1/6809 ,  G16B20/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine.

公开(公告)号：US20180068061A1

公开(公告)日：2018-03-08

申请号：US15672865

申请日：2017-08-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

公开(公告)号：US20140051154A1

公开(公告)日：2014-02-20

申请号：US13965944

申请日：2013-08-13

Applicant: Life Technologies Corporation

Inventor： Fiona Hyland ,  Rajesh Gottimukkala

IPC: G06F19/22

CPC classification number: G16B30/00 ,  C12Q1/6809 ,  G16B20/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc.

Abstract translation: 一方面，公开了一种用于实现副本号变更分析方法的系统。 该系统可以包括与核酸测序仪通信的核酸测序仪和计算设备。 核酸测序仪可配置成询问样品以产生含有多个核酸序列读数的核酸序列数据文件。 在各种实施例中，计算设备可以是工作站，大型计算机，个人计算机，移动设备等。