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    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    2.
    发明申请
    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS 有权

    公开(公告)号：US20210210164A1

    公开(公告)日：2021-07-08

    申请号：US17136800

    申请日：2020-12-29

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Zheng ZHANG ,  Fiona HYLAND ,  Sowmi UTIRAMERUR

    IPC: 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.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EVALUATING VARIANT LIKELIHOOD
    4.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EVALUATING VARIANT LIKELIHOOD 审中-公开

    公开(公告)号：US20180330051A1

    公开(公告)日：2018-11-15

    申请号：US15974976

    申请日：2018-05-09

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Earl HUBBELL ,  Sowmi UTIRAMERUR

    IPC: G06F19/22 ,  C12Q1/6874 ,  G06F19/24

    CPC classification number: G06F19/22 ,  C12Q1/6874 ,  G06F19/24

    Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.

    SYSTEMS AND METHODS FOR PAIRED END SEQUENCING
    5.
    发明申请
    SYSTEMS AND METHODS FOR PAIRED END SEQUENCING 审中-公开
    配对终端序列的系统和方法

    公开(公告)号：US20130288902A1

    公开(公告)日：2013-10-31

    申请号：US13787221

    申请日：2013-03-06

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Sowmi UTIRAMERUR ,  Simon CAWLEY ,  Yongming SUN ,  Fiona HYLAND

    IPC: C12Q1/68

    CPC classification number: C12Q1/6869 ,  G16B30/00

    Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.

    Abstract translation: 用于分析重叠序列信息的系统和方法可以获得多核苷酸的第一和第二重叠序列信息，对齐第一和第二序列信息，确定沿着多核苷酸的位置的第一和第二序列信息之间的一致程度，并确定 基地电话和位置的质量值。

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EVALUATING VARIANT LIKELIHOOD
    6.
    发明公开
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EVALUATING VARIANT LIKELIHOOD 审中-公开

    公开(公告)号：US20230360726A1

    公开(公告)日：2023-11-09

    申请号：US18130134

    申请日：2023-04-03

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Earl HUBBELL ,  Sowmi UTIRAMERUR

    IPC: C12Q1/6874 ,  C12Q1/6869 ,  G16B20/20 ,  G16B30/00 ,  G16B40/00

    CPC classification number: G16B20/20 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B40/00

    Abstract: A method comprises receiving an ensemble of sequencing reads based on measurements from a plurality of microwells of a sensor array; assigning measured values to the ensemble of sequencing reads; calculating model-predicted values utilizing a predictive model of nucleotide incorporations resulting from flows of nucleotide species according to a predetermined order; modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands, the modifying based on variations between model-predicted values for different hypothesized sequences obtained using the predictive model of nucleotide incorporations resulting from the flows of nucleotide species according to the predetermined order; calculating a measurement confidence value for each read in the ensemble of sequencing reads, the confidence value representing variations between the measured values and the modified model-predicted values; and identifying a plurality of reads in the ensemble as corresponding to a variant sequence.

    SYSTEMS AND METHODS FOR MAPPING SEQUENCE READS
    8.
    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
    9.
    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 Detecting Homopolymer Insertions/Deletions
    10.
    发明申请
    Systems and Methods for Detecting Homopolymer Insertions/Deletions 审中-公开
    用于检测均聚物插入/缺失的系统和方法

    公开(公告)号：US20140052381A1

    公开(公告)日：2014-02-20

    申请号：US13966378

    申请日：2013-08-14

    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.

    Abstract translation: 用于确定变体的系统和方法可以接收映射读取并且从均聚物区域的多次读取确定匹配滤波器残差分布的分布。 匹配滤波器残差的分布可以适用于单模和双模态模型。 基于最适合匹配滤波器残差分布的模型，可以确定样品的杂合度和均聚物中插入/缺失的不存在或不存在。

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