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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.

    Methods for detecting mutation load from a tumor sample
    3.
    发明授权
    Methods for detecting mutation load from a tumor sample 有权

    公开(公告)号：US11101019B2

    公开(公告)日：2021-08-24

    申请号：US15834520

    申请日：2017-12-07

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Ruchi Chaudhary ,  Fiona Hyland

    IPC: G16B20/00 ,  G16B30/00

    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.

    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE
    4.
    发明申请
    METHODS FOR DETECTING MUTATION LOAD FROM A TUMOR SAMPLE 审中-公开

    公开(公告)号：US20180165410A1

    公开(公告)日：2018-06-14

    申请号：US15834520

    申请日：2017-12-07

    Applicant: Life Technologies Corporation

    Inventor： Ruchi Chaudhary ,  Fiona Hyland

    IPC: G06F19/18

    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, including 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.

    METHODS FOR CONTEXT BASED COMPRESSION OF GENOMIC DATA FOR IMMUNO-ONCOLOGY BIOMARKERS
    5.
    发明申请
    METHODS FOR CONTEXT BASED COMPRESSION OF GENOMIC DATA FOR IMMUNO-ONCOLOGY BIOMARKERS 有权

    公开(公告)号：US20240428885A1

    公开(公告)日：2024-12-26

    申请号：US18748533

    申请日：2024-06-20

    Applicant: Life Technologies Corporation

    Inventor： Fiona Hyland ,  Asha Kamat ,  Timothy Looney

    IPC: G16B20/20 ,  G06F16/2457 ,  G06F16/248 ,  G06N3/126

    Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

    Systems and methods for identifying somatic mutations
    7.
    发明授权
    Systems and methods for identifying somatic mutations 有权

    公开(公告)号：US11468968B2

    公开(公告)日：2022-10-11

    申请号：US16434709

    申请日：2019-06-07

    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 CONTEXT BASED COMPRESSION OF GENOMIC DATA FOR IMMUNO-ONCOLOGY BIOMARKERS
    8.
    发明申请
    METHODS FOR CONTEXT BASED COMPRESSION OF GENOMIC DATA FOR IMMUNO-ONCOLOGY BIOMARKERS 审中-公开

    公开(公告)号：US20200335176A1

    公开(公告)日：2020-10-22

    申请号：US16851472

    申请日：2020-04-17

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Fiona Hyland ,  Asha KAMAT ,  Timothy LOONEY

    IPC: G16B20/20 ,  G06N3/12 ,  G06F16/2457 ,  G06F16/248

    Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

    SYSTEMS AND METHODS FOR VALIDATION OF SEQUENCING RESULTS
    10.
    发明申请
    SYSTEMS AND METHODS FOR VALIDATION OF SEQUENCING RESULTS 审中-公开

    公开(公告)号：US20180298424A1

    公开(公告)日：2018-10-18

    申请号：US15952463

    申请日：2018-04-13

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Dumitru Brinza ,  Fiona Hyland

    IPC: C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6858 ,  G06F19/22

    Abstract: Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence.

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