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    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY
    2.
    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
    3.
    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.

    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY
    4.
    发明申请
    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY 审中-公开

    公开(公告)号：US20200273538A1

    公开(公告)日：2020-08-27

    申请号：US16803680

    申请日：2020-02-27

    Applicant: GUARDANT HEALTH, INC.

    Inventor： Catalin BARBACIORU ,  Marcin SIKORA ,  Darya CHUDOVA

    IPC: 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
    5.
    发明公开
    MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA 审中-公开

    公开(公告)号：US20240247319A1

    公开(公告)日：2024-07-25

    申请号：US18500890

    申请日：2023-11-02

    Applicant: GUARDANT HEALTH, INC.

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

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

    CPC classification number: 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.

    MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA
    6.
    发明公开
    MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA 审中-公开

    公开(公告)号：US20230416843A1

    公开(公告)日：2023-12-28

    申请号：US18456362

    申请日：2023-08-25

    Applicant: GUARDANT HEALTH, INC.

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

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

    CPC classification number: C12Q1/6886 ,  G16B30/10 ,  G16B20/20 ,  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.

    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY
    7.
    发明公开
    COMPUTATIONAL MODELING OF LOSS OF FUNCTION BASED ON ALLELIC FREQUENCY 审中-公开

    公开(公告)号：US20230360727A1

    公开(公告)日：2023-11-09

    申请号：US18347986

    申请日：2023-07-06

    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.

    METHODS FOR ANALYZING NUCLEIC ACIDS USING SEQUENCE READ FAMILY SIZE DISTRIBUTION
    8.
    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.

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