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    Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage
    2.
    发明授权
    Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage 有权

    公开(公告)号：US11118234B2

    公开(公告)日：2021-09-14

    申请号：US16917582

    申请日：2020-06-30

    申请人： GUARDANT HEALTH, INC.

    发明人： Katie Julia Quinn ,  Elena Helman ,  Darya Chudova

    IPC分类号： G16B20/40 ,  G16B20/20 ,  G16B20/10 ,  C12Q1/6886

    摘要： Provided herein are methods for detecting tumor mutational burden (TMB) in subjects. In one aspect, the methods include determining observed mutational counts from sequence information obtained from nucleic acids in samples from the subjects and determining a tumor fraction and/or a coverage of the nucleic acids to generate sequencing parameters. The methods also include determining an expected mutational fraction and/or an expected distribution of the expected mutational fraction given the sequencing parameters to generate an expected result, and adjusting the observed mutational count given the expected result to generate an adjusted result, thereby detecting the TMB in the subject. Other aspects are directed to methods of selecting customized therapies for treating cancer in subjects, and methods of treating cancer in subjects. Yet other aspects include related systems and computer readable media used to detect TMB in subjects.

    Microsatellite instability detection in cell-free DNA
    4.
    发明授权
    Microsatellite instability detection in cell-free DNA 有权

    公开(公告)号：US11773451B2

    公开(公告)日：2023-10-03

    申请号：US16907034

    申请日：2020-06-19

    申请人： GUARDANT HEALTH, INC.

    发明人： Aliaksandr Artsiomenka ,  Marcin Sikora ,  Catalin Barbacioru ,  Darya Chudova ,  Martina I. Lefterova

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

    CPC分类号： C12Q1/6886 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20

    摘要： 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.

    Normalizing tumor mutation burden
    6.
    发明授权
    Normalizing tumor mutation burden 有权

    公开(公告)号：US11193175B2

    公开(公告)日：2021-12-07

    申请号：US16866229

    申请日：2020-05-04

    申请人： GUARDANT HEALTH, INC.

    发明人： Darya Chudova

    IPC分类号： G16B20/00 ,  G16H50/30 ,  G16B20/20 ,  C12Q1/6886

    摘要： 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.