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    METHODS FOR PARTNER AGNOSTIC GENE FUSION DETECTION
    1.
    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.

    METHODS FOR DETECTION OF FUSIONS USING COMPRESSED MOLECULAR TAGGED NUCLEIC ACID SEQUENCE DATA
    2.
    发明申请
    METHODS FOR DETECTION OF FUSIONS USING COMPRESSED MOLECULAR TAGGED NUCLEIC ACID SEQUENCE DATA 审中-公开

    公开(公告)号：US20190087539A1

    公开(公告)日：2019-03-21

    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: G06F19/22 ,  C12Q1/6853

    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.

    Systems and Methods for Detecting Homopolymer Insertions/Deletions
    4.
    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。

    COMPOSITIONS AND METHODS FOR ASSESSING MICROBIAL POPULATIONS
    5.
    发明申请
    COMPOSITIONS AND METHODS FOR ASSESSING MICROBIAL POPULATIONS 有权

    公开(公告)号：US20220251669A1

    公开(公告)日：2022-08-11

    申请号：US17658493

    申请日：2022-04-08

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Shrutii SARDA ,  Anna MCGEACHY ,  Rajesh GOTTIMUKKALA ,  David MERRILL ,  Heesun SHIN ,  Aren EWING ,  Wing LEE ,  Birgit DREWS ,  Fiona HYLAND ,  Janice AU-YOUNG

    IPC: C12Q1/6888 ,  C12Q1/6874 ,  C12Q1/686 ,  G16B30/10

    Abstract: The present disclosure provides compositions and methods, as well as combinations, kits, and systems that include the compositions and methods, for amplification, detection, characterization, assessment, profiling and/or measurement of nucleic acids in samples, particularly biological samples. Compositions and methods provided herein include combinations of microbial species target-specific nucleic acid primers for selective amplification and/or combinations of primers for amplification of nucleic acids from a large group of taxonomically related microorganisms. In one aspect, amplified nucleic acids obtained using the compositions and methods can be used in various processes including nucleic acid sequencing and used to detect the presence of microbial species and assess microbial populations in a variety of samples. In accordance with the teachings and principles, new methods, systems and non-transitory machine-readable storage medium are provided to compress reference sequence databases used in mapping sequence reads for analysis and profiling of microbial populations.

    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION
    7.
    发明申请
    SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION 审中-公开
    用于识别序列变异的系统和方法

    公开(公告)号：US20130345066A1

    公开(公告)日：2013-12-26

    申请号：US13890923

    申请日：2013-05-09

    Applicant: Life Technologies Corporation

    Inventor： Dumitru BRINZA ,  Zheng ZHANG ,  Fiona HYLAND ,  Rajesh GOTTIMUKKALA

    IPC: C12Q1/68 ,  G06F19/12

    CPC classification number: C12Q1/6874 ,  G16B5/00 ,  G16B30/00

    Abstract: Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.

    Abstract translation: 用于确定变体的系统和方法可以接收映射读取，将流空间信息对准参考的对应部分的流空间表示。 可以以上下文特定的方式评估跨越具有潜在变体的位置的读数。 可以提供可能的变体列表。

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