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    SYSTEMS AND METHODS TO DETECT COPY NUMBER VARIATION
    2.
    发明申请
    SYSTEMS AND METHODS TO DETECT COPY NUMBER VARIATION 有权

    公开(公告)号：US20210292831A1

    公开(公告)日：2021-09-23

    申请号：US17225833

    申请日：2021-04-08

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Fiona Hyland ,  Rajesh Gottimukkala

    IPC: C12Q1/6869 ,  G16B30/10 ,  G16B20/10

    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.

    Systems and Methods for Detecting Structural Variants
    3.
    发明申请
    Systems and Methods for Detecting Structural Variants 有权
    检测结构变体的系统和方法

    公开(公告)号：US20150094212A1

    公开(公告)日：2015-04-02

    申请号：US14503461

    申请日：2014-10-01

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Rajesh Gottimukkala ,  Fiona Hyland ,  Sowmi Utiramerur ,  Jeoffrey Schageman ,  Susan Magdaleno

    IPC: C12Q1/68 ,  G06F19/18

    CPC classification number: G06F19/18 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q2535/101 ,  C12Q2537/143 ,  C12Q2539/105

    Abstract: Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant.

    Abstract translation: 用于识别长缺失的系统和方法可以获得核酸样品的潜在区域内和周围的多个扩增子的测序信息。 排序信息可以包括可以映射到参考序列的多个读取。 使用诸如读数映射到扩增子的参考序列和相对丰度的信息的信息，可以鉴定结构变体，并且如果核酸样品对于结构变体是纯合的或杂合的，则可以进行确定。

    METHODS FOR PARTNER AGNOSTIC GENE FUSION DETECTION
    4.
    发明申请
    METHODS FOR PARTNER AGNOSTIC GENE FUSION DETECTION 有权

    公开(公告)号：US20250084470A1

    公开(公告)日：2025-03-13

    申请号：US18896256

    申请日：2024-09-25

    Applicant: Life Technologies Corporation

    Inventor： Rajesh Gottimukkala ,  Amir Marcovitz ,  Jeoffrey Schageman ,  Varun Bagai ,  Jian Gu ,  James Veitch ,  Kelli Bramlett ,  Scott Myrand ,  Fiona Hyland ,  Seth Sadis ,  Paul Williams

    IPC: C12Q1/6851 ,  G06F17/18 ,  G16B25/10

    Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

    SYSTEMS AND METHODS FOR DETECTING STRUCTURAL VARIANTS
    6.
    发明申请
    SYSTEMS AND METHODS FOR DETECTING STRUCTURAL VARIANTS 有权

    公开(公告)号：US20250037797A1

    公开(公告)日：2025-01-30

    申请号：US18786945

    申请日：2024-07-29

    Applicant: Life Technologies Corporation

    Inventor： Rajesh Gottimukkala ,  Fiona Hyland

    IPC: G16B30/10 ,  C12Q1/6869 ,  G16B20/20 ,  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.

    Methods for partner agnostic gene fusion detection
    10.
    发明授权
    Methods for partner agnostic gene fusion detection 有权

    公开(公告)号：US12139753B2

    公开(公告)日：2024-11-12

    申请号：US16825238

    申请日：2020-03-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Rajesh Gottimukkala ,  Amir Marcovitz ,  Jeoffrey Schageman ,  Varun Bagai ,  Jian Gu ,  James Veitch ,  Kelli Bramlett ,  Scott Myrand ,  Fiona Hyland ,  Seth Sadis ,  Paul Williams

    IPC: C12Q1/68 ,  C12Q1/6851 ,  G06F17/18 ,  G16B25/10

    Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

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