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    NORMALIZING TUMOR MUTATION BURDEN
    11.
    发明申请
    NORMALIZING TUMOR MUTATION BURDEN 审中-公开

    公开(公告)号：US20200263260A1

    公开(公告)日：2020-08-20

    申请号：US16866229

    申请日：2020-05-04

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Darya CHUDOVA

    IPC: C12Q1/6886 ,  G16B20/00

    Abstract: Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample. Such analysis can provide an indication where the tumor mutation burden of a test sample lies on a distribution of tumor mutation burdens in a control population, and thus, whether the individual providing the test sample is likely to be amenable to immunotherapy to treat cancer.

    METHODS FOR ANALYZING NUCLEIC ACIDS USING SEQUENCE READ FAMILY SIZE DISTRIBUTION
    13.
    发明申请
    METHODS FOR ANALYZING NUCLEIC ACIDS USING SEQUENCE READ FAMILY SIZE DISTRIBUTION 有权

    公开(公告)号：US20250084469A1

    公开(公告)日：2025-03-13

    申请号：US18883708

    申请日：2024-09-12

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Darya CHUDOVA ,  Tingting JIANG ,  Catalin BARBACIORU ,  Marcin Pawel SIKORA

    IPC: C12Q1/6851 ,  C12Q1/6855 ,  G16B20/10 ,  G16B20/20 ,  G16B30/10

    Abstract: The present invention provides a method for determining a quantitative measure indicative of the number of nucleic acids in a sample that map to a specific genomic region. The method involves: (a) providing a sample containing parent nucleic acids; (b) amplifying these parent nucleic acids to generate progeny nucleic acids; (c) sequencing the progeny nucleic acids to produce sequence reads; (d) grouping the sequence reads into families, where each family corresponds to sequence reads derived from the same parent nucleic acid; and (e) utilizing both the number of families mapping to the genomic region and the family size distribution of these families to calculate a quantitative measure indicative of the number of nucleic acids in the sample that map to the genomic region. This method enhances the accuracy of quantifying nucleic acids within a genomic region, particularly in complex or low-abundance samples.

    CORRECTING FOR DEAMINATION-INDUCED SEQUENCE ERRORS
    19.
    发明申请
    CORRECTING FOR DEAMINATION-INDUCED SEQUENCE ERRORS 有权

    公开(公告)号：US20210395816A1

    公开(公告)日：2021-12-23

    申请号：US17210202

    申请日：2021-03-23

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Marcin SIKORA ,  Andrew KENNEDY ,  Ariel JAIMOVICH ,  Darya CHUDOVA ,  Stephen FAIRCLOUGH

    IPC: C12Q1/6874

    Abstract: Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease. However, the value of such information can be compromised by errors introduced by or before the sequencing process including preparing nucleic acids for sequencing. Blunting single-stranded overhangs on nucleic acids in a sample can introduce deamination-induced sequencing errors. The disclosure provides methods of identifying and correcting for such deamination-induced sequencing errors and distinguishing them from real sequence variations.

    METHODS AND SYSTEMS FOR DETECTING CONTAMINATION BETWEEN SAMPLES
    20.
    发明申请
    METHODS AND SYSTEMS FOR DETECTING CONTAMINATION BETWEEN SAMPLES 审中-公开

    公开(公告)号：US20200071754A1

    公开(公告)日：2020-03-05

    申请号：US16557931

    申请日：2019-08-30

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Darya CHUDOVA ,  Helmy ELTOUKHY ,  Stephen FAIRCLOUGH ,  Narsi RAJAGOPALAN ,  Marcin SIKORA

    IPC: C12Q1/6869 ,  G16B30/10 ,  G16B20/00

    Abstract: Provided herein are various methods and related systems for detecting the presence/absence of contamination of a first sample with a second sample. In some embodiments, for example, the methods include (a) sequencing a set of polynucleotides to produce a plurality of sequencing reads, (b) aligning the plurality of sequencing reads to a reference sequence, (c) grouping the plurality of sequencing reads into a plurality of families, (d) generating family identifiers for the plurality of families, (e) screening for a set of shared family identifiers, (f) determining a quantitative measure of the set of shared family identifiers, and (g) classifying the first sample as being contaminated or not contaminated with the second sample based on the quantitative measure of the shared family identifiers.

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