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    METHOD AND SYSTEM OF MOLECULAR TYPING AND SUBTYING CLASSIFIER FOR IMMUNE-RELATED DISEASES
    4.
    发明申请
    METHOD AND SYSTEM OF MOLECULAR TYPING AND SUBTYING CLASSIFIER FOR IMMUNE-RELATED DISEASES 有权

    公开(公告)号：US20240428955A1

    公开(公告)日：2024-12-26

    申请号：US18705594

    申请日：2022-08-12

    Applicant: HUASHAN HOSPITAL, FUDAN UNIVERSITY

    Inventor： Jie LIU ,  Feifei LUO ,  Shaocong MO ,  Huan SONG

    IPC: G16H50/70 ,  G16B40/30

    Abstract: A method and a system of molecular typing and subtyping classifier for immune-related diseases are provided. The method includes: conducting molecular typing via a clustering algorithm in a training set to obtain a plurality of subtypes stably appearing in the training set and a marker gene for each subtype; conducting enrichment analysis on marker genes for the plurality of subtypes, conducting immune cell infiltration evaluation on the plurality of subtypes, and dividing the plurality of subtypes into a plurality of subtype classes according to results of the analysis and the evaluation; comparing treatment response rates of different subtype classes through a comparison set to determine a subtype class to be identified; constructing a support vector machine model with feature genes screened and an optimal parameter combination; and determining whether immune-related disease data to be classified is the subtype class to be identified.

    Detecting Cross-Contamination in Sequencing Data Using Regression Techniques
    6.
    发明公开
    Detecting Cross-Contamination in Sequencing Data Using Regression Techniques 审中-公开

    公开(公告)号：US20240247306A1

    公开(公告)日：2024-07-25

    申请号：US18627211

    申请日：2024-04-04

    Applicant: GRAIL, LLC

    Inventor： Onur Sakarya ,  Catalin Barbacioru

    IPC: C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B30/20 ,  G16B40/20 ,  G16B40/30

    CPC classification number: C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20 ,  G16B40/30 ,  G16B30/20

    Abstract: Cross-contamination of a test sample used to determine cancer is identified using gene sequencing data. Each test sample includes a number of test sequences that may include a single nucleotide polymorphism (SNP) that can be indicative of cancer. The test sequences are be filtered to remove or negate at least some of the SNPs from the test sequences. Negating the test sequences allows more test sequences to be simultaneously analyzed to determine cross-contamination. Cross-contamination is determined by modeling the variant allele frequency for the test sequences as a function of minor allele frequency, contamination level, and background noise. In some cases, the variant allele frequency is based on a probability function including the minor allele frequency. Cross-contamination of the test sample is determined if the determined contamination level is above a threshold and statistically significant.

    EVALUATION AND IMPROVEMENT OF GENETIC SCREENING TESTS USING RECEIVER OPERATING CHARACTERISTIC CURVES
    7.
    发明公开
    EVALUATION AND IMPROVEMENT OF GENETIC SCREENING TESTS USING RECEIVER OPERATING CHARACTERISTIC CURVES 审中-公开

    公开(公告)号：US20240203521A1

    公开(公告)日：2024-06-20

    申请号：US18592076

    申请日：2024-02-29

    Applicant: MYRIAD WOMEN'S HEALTH, INC.

    Inventor： Kevin R. Haas ,  Kyle A. Beauchamp

    IPC: G16B5/20 ,  G06N7/01 ,  G06N20/00 ,  G16B30/10 ,  G16B40/30

    CPC classification number: G16B5/20 ,  G06N7/01 ,  G06N20/00 ,  G16B30/10 ,  G16B40/30

    Abstract: Described herein are methods for evaluating and improving performance of a genetic screening test for determining a fetal chromosomal abnormality in a test chromosome in a fetus by analyzing a maternal sample of a woman carrying the fetus. The method may include generating simulated maternal samples based on a determined relationship between values of statistical significance and abnormality classifications for the test chromosome of a plurality of reference maternal samples. The method may also include determining specificity values and sensitivity values for a range of abnormality classifier values for the test chromosome based on values of statistical significance and abnormality classifications for the plurality of reference maternal samples and the plurality of simulated maternal samples. A receiver operating characteristic (ROC) curve for the genetic screening test may be generated based on the determined specificity values and sensitivity values.

    Detecting cross-contamination in sequencing data using regression techniques
    9.
    发明授权
    Detecting cross-contamination in sequencing data using regression techniques 有权

    公开(公告)号：US12006533B2

    公开(公告)日：2024-06-11

    申请号：US15900645

    申请日：2018-02-20

    Applicant: Grail, Inc.

    Inventor： Onur Sakarya ,  Catalin Barbacioru

    IPC: C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B30/20 ,  G16B40/20 ,  G16B40/30

    CPC classification number: C12Q1/6827 ,  C12Q1/6809 ,  G16B20/20 ,  G16B30/10 ,  G16B40/20 ,  G16B40/30 ,  G16B30/20

    Abstract: Cross-contamination of a test sample used to determine cancer is identified using gene sequencing data. Each test sample includes a number of test sequences that may include a single nucleotide polymorphism (SNP) that can be indicative of cancer. The test sequences are be filtered to remove or negate at least some of the SNPs from the test sequences. Negating the test sequences allows more test sequences to be simultaneously analyzed to determine cross-contamination. Cross-contamination is determined by modeling the variant allele frequency for the test sequences as a function of minor allele frequency, contamination level, and background noise. In some cases, the variant allele frequency is based on a probability function including the minor allele frequency. Cross-contamination of the test sample is determined if the determined contamination level is above a threshold and statistically significant.

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