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    METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES
    1.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES 审中-公开
    用于计算校正的AMPLICON封面的方法，系统和计算机可读介质

    公开(公告)号：WO2016057902A1

    公开(公告)日：2016-04-14

    申请号：PCT/US2015/054910

    申请日：2015-10-09

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： VEITCH, James ,  ZHAN, Yiping

    IPC: G06F19/18 ,  G06F19/20 ,  G06F19/22

    CPC classification number: G06F19/24 ,  C12Q1/6869 ,  G06F19/18 ,  G06F19/22

    Abstract: Methods, systems, and computer-readable media are disclosed for calculating corrected amplicon coverages. One method includes: mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence that includes one or more nucleic acid sequences corresponding to the amplified target regions; calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads; and calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.

    Abstract translation: 公开了用于计算校正的扩增子覆盖物的方法，系统和计算机可读介质。 一种方法包括：基于被怀疑具有一个或多个遗传异常的样本的扩增的目标区域将多个扩增子的多个读取映射到包括与扩增的目标区域相对应的一个或多个核酸序列的参考序列; 计算扩增子覆盖率和总读数，其中扩增子覆盖是映射到扩增子的多个读取，并且总读取是映射读取的数量; 并且通过应用批量效应校正，基于计算的扩增子覆盖率和计算的总读数计算校正的扩增子覆盖率。

    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION
    2.
    发明申请
    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION 审中-公开
    用于确定复制数变化的系统和方法

    公开(公告)号：WO2014138153A1

    公开(公告)日：2014-09-12

    申请号：PCT/US2014/020516

    申请日：2014-03-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： KONVICKA, Karel ,  VEITCH, James

    IPC: G06F19/18

    CPC classification number: G06F19/22 ,  C12Q1/6874 ,  G06F19/18

    Abstract: A method of identifying a copy number variations reads includes mapping reads to a reference genome, computing coverage for a plurality of tiles, and normalizing the coverage for a tile based on a coverage mode across the plurality of tiles. The method further includes determining a score for the plurality of tiles being in a plurality of ploidy states, determining a maximum score path across the tiles and through the ploidy states, and providing a copy number determination based on the maximum score path.

    Abstract translation: 识别拷贝数变化读取的方法包括将读取映射到参考基因组，计算多个瓦片的覆盖范围，以及基于跨越多个瓦片的覆盖模式对瓦片的覆盖进行归一化。 所述方法还包括确定多个倍性状态中的多个瓦片的分数，确定穿过瓦片和穿过倍性状态的最大分数路径，以及基于最大分数路径提供复印件数量确定。

    METHODS AND SYSTEMS TO DETECT LARGE REARRANGEMENTS IN BRCA1/2
    3.
    发明申请
    METHODS AND SYSTEMS TO DETECT LARGE REARRANGEMENTS IN BRCA1/2 审中-公开

    公开(公告)号：WO2018218103A1

    公开(公告)日：2018-11-29

    申请号：PCT/US2018/034564

    申请日：2018-05-25

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： SCAFE, Charles ,  BRINZA, Dumitru ,  VEITCH, James ,  QI, Rongsu ,  HYLAND, Fiona

    IPC: C12Q1/6886 ,  G06F19/18

    Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.

    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION
    6.
    发明公开
    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION 审中-公开

    公开(公告)号：EP4495936A2

    公开(公告)日：2025-01-22

    申请号：EP24210117.8

    申请日：2014-03-05

    Applicant: Life Technologies Corporation

    Inventor： KONVICKA, Karel ,  VEITCH, James

    IPC: G16B20/10

    Abstract: A method of identifying a copy number variations reads includes mapping reads to a reference genome, computing coverage for a plurality of tiles, and normalizing the coverage for a tile based on a coverage mode across the plurality of tiles. The method further includes determining a score for the plurality of tiles being in a plurality of ploidy states, determining a maximum score path across the tiles and through the ploidy states, and providing a copy number determination based on the maximum score path.

    METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES
    7.
    发明公开
    METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES 审中-公开
    用于计算纠正的放大倍数覆盖的方法，系统和计算机可读介质

    公开(公告)号：EP3204882A1

    公开(公告)日：2017-08-16

    申请号：EP15848233.1

    申请日：2015-10-09

    Applicant: Life Technologies Corporation

    Inventor： VEITCH, James ,  ZHAN, Yiping

    IPC: G06F19/18 ,  G06F19/20 ,  G06F19/22

    CPC classification number: G06F19/24 ,  C12Q1/6869 ,  G06F19/18 ,  G06F19/22

    Abstract: Methods, systems, and computer-readable media are disclosed for calculating corrected amplicon coverages. One method includes: mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence that includes one or more nucleic acid sequences corresponding to the amplified target regions; calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads; and calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.

    Abstract translation: 公开了用于计算校正的扩增子覆盖度的方法，系统和计算机可读介质。 一种方法包括：基于怀疑具有一个或多个遗传异常的样品的扩增目标区域将多个扩增子的多个读段映射到参考序列，所述参考序列包括对应于扩增的目标区域的一个或多个核酸序列; 计算扩增子覆盖率和总读数，其中扩增子覆盖度是映射到扩增子的读数的数量，总读数是映射读数的数量; 以及基于计算的扩增子覆盖率和通过应用批量效应校正计算的总读数来计算校正的扩增子覆盖率。

    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION
    9.
    发明公开
    SYSTEMS AND METHODS FOR DETERMINING COPY NUMBER VARIATION 审中-公开
    系统和方法确定拷贝数变异

    公开(公告)号：EP2984598A1

    公开(公告)日：2016-02-17

    申请号：EP14716060.0

    申请日：2014-03-05

    Applicant: Life Technologies Corporation

    Inventor： KONVICKA, Karel ,  VEITCH, James

    IPC: G06F19/18

    CPC classification number: G06F19/22 ,  C12Q1/6874 ,  G06F19/18

    Abstract: A method of identifying a copy number variations reads includes mapping reads to a reference genome, computing coverage for a plurality of tiles, and normalizing the coverage for a tile based on a coverage mode across the plurality of tiles. The method further includes determining a score for the plurality of tiles being in a plurality of ploidy states, determining a maximum score path across the tiles and through the ploidy states, and providing a copy number determination based on the maximum score path.

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