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    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE
    2.
    发明申请
    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE 有权

    公开(公告)号：US20210343367A1

    公开(公告)日：2021-11-04

    申请号：US17371378

    申请日：2021-07-09

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Ruchi Chaudhary ,  Fiona HYLAND

    IPC: G16B20/20 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10

    Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.

    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    4.
    发明申请
    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 审中-公开

    公开(公告)号：US20180089366A1

    公开(公告)日：2018-03-29

    申请号：US15679261

    申请日：2017-08-17

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Fiona HYLAND ,  Sowmi UTIRAMERUR

    IPC: G06F19/22

    CPC classification number: G16B30/00

    Abstract: Systems, methods, and computer program products for aligning a fragment sequence to a target sequencing. The alignment is allowed at most one gap, such as an insertion or a deletion. In some embodiments, both a gapped alignment and an ungapped alignment can be produced. A selection can be made between the gapped alignment and the ungapped alignment based on a quality value for each alignment.

    Systems and Methods for Sequence Data Alignment Quality Assessment
    6.
    发明申请
    Systems and Methods for Sequence Data Alignment Quality Assessment 审中-公开
    序列数据对齐质量评估的系统和方法

    公开(公告)号：US20160140291A1

    公开(公告)日：2016-05-19

    申请号：US15001389

    申请日：2016-01-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Sowmi UTIRAMERUR ,  Fiona HYLAND

    IPC: G06F19/24 ,  G06N7/00 ,  G06N3/12 ,  G06F19/22

    CPC classification number: G16B40/00 ,  G06N3/126 ,  G06N7/005 ,  G16B30/00

    Abstract: A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.

    Abstract translation: 公开了用于分类配对核酸序列读数的计算机实现的方法。 接收多个配对的核酸序列读取，其中每个读取包括由插入区域分隔的第一标签和第二标签。 确定每个读取到参考序列的第一和第二标签的潜在对准，其中所述电位对准满足最小阈值失配约束。 识别每个读取的第一和第二标签的潜在配对比对，其中每个潜在配对对准的第一和第二标签之间的距离在估计的插入尺寸范围内。 基于第一和第二标签之间的距离和每个标签的总失配数，针对每个潜在配对对齐计算对准分数。

    SYSTEMS AND METHODS FOR IDENTIFYING SOMATIC MUTATIONS
    8.
    发明申请
    SYSTEMS AND METHODS FOR IDENTIFYING SOMATIC MUTATIONS 有权

    公开(公告)号：US20230083827A1

    公开(公告)日：2023-03-16

    申请号：US17932712

    申请日：2022-09-16

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Alexander Joyner ,  Fiona HYLAND ,  Heinz BREU

    IPC: G16B20/20 ,  G16B30/00 ,  G16B30/10

    Abstract: Systems and method for identifying somatic mutations can receive first and second sequence information, determine if a variant present in the first sequencing information is also present in the second sequence information, and identify variants present in the first sequence information are somatic mutations when the variant is either not present in the second sequence information or the presence of the variant in the second sequence information is likely due to a sequencing error.

    METHODS FOR PARTNER AGNOSTIC GENE FUSION DETECTION
    9.
    发明申请
    METHODS FOR PARTNER AGNOSTIC GENE FUSION DETECTION 审中-公开

    公开(公告)号：US20200318175A1

    公开(公告)日：2020-10-08

    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: C12Q1/6851 ,  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 IDENTIFYING SEQUENCE VARIATION ASSOCIATED WITH GENETIC DISEASES
    10.
    发明申请
    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION ASSOCIATED WITH GENETIC DISEASES 审中-公开

    公开(公告)号：US20200027525A1

    公开(公告)日：2020-01-23

    申请号：US16434677

    申请日：2019-06-07

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Fiona HYLAND ,  Heinz BREU

    IPC: G16B20/00

    Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.

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