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    METHODS AND SYSTEMS FOR DIFFERENTIATING SOMATIC AND GERMLINE VARIANTS
    3.
    发明申请
    METHODS AND SYSTEMS FOR DIFFERENTIATING SOMATIC AND GERMLINE VARIANTS 审中-公开

    公开(公告)号：US20200327954A1

    公开(公告)日：2020-10-15

    申请号：US16823937

    申请日：2020-03-19

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Tracy NANCE ,  Elena HELMAN ,  Darya CHUDOVA

    IPC: G16B5/00 ,  G06F17/18 ,  C12P19/34 ,  C12Q1/6869

    Abstract: In an aspect, a method of identifying a somatic or germline origin of a nucleic acid variant from a sample of nucleic acid molecules comprises: determining quantitative measures for the nucleic acid variant comprising total allele count and minor allele count for the nucleic acid variant; identifying an associated variable of the nucleic acid variant; determining quantitative value for the associated variable; generating a statistical model for expected germline mutant allele counts at a genomic locus of the nucleic acid variant; generating a probability value (p-value) for the nucleic acid variant based at least in part on the statistical model, the quantitative value, and at least one of the quantitative measures; and classifying the nucleic acid variant as (i) being of somatic origin when the p-value is below a predetermined threshold value, or as (ii) being of germline origin when the p-value is at or above the predetermined threshold value.

    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY
    8.
    发明公开
    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY 审中-公开

    公开(公告)号：US20240029890A1

    公开(公告)日：2024-01-25

    申请号：US18469130

    申请日：2023-09-18

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Catalin BARBACIORU ,  Marcin SIKORA ,  Darya CHUDOVA

    IPC: G16B20/20

    CPC classification number: G16B20/20

    Abstract: The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.

    MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA
    10.
    发明申请
    MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA 有权

    公开(公告)号：US20210363586A1

    公开(公告)日：2021-11-25

    申请号：US16907034

    申请日：2019-08-30

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Aliaksandr ARTSIOMENKA ,  Marcin SIKORA ,  Catalin BARBACIORU ,  Darya CHUDOVA ,  Martina I. LEFTEROVA

    IPC: C12Q1/6886 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20

    Abstract: Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.

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