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    METHODS AND SYSTEMS FOR ACCURATE GENOTYPING OF REPEAT POLYMORPHISMS
    4.
    发明公开
    METHODS AND SYSTEMS FOR ACCURATE GENOTYPING OF REPEAT POLYMORPHISMS 审中-公开

    公开(公告)号：US20230162815A1

    公开(公告)日：2023-05-25

    申请号：US17981212

    申请日：2022-11-04

    申请人： Tempus Labs, Inc.

    发明人： Gene Selkov ,  Kurt Oliver Gaastra ,  Sean Allistair Irvine ,  Leonard Eric Trigg ,  Francisco Miguel De La Vega

    IPC分类号： G16B20/20 ,  G16B30/10 ,  C12Q1/6827

    CPC分类号： G16B20/20 ,  G16B30/10 ,  C12Q1/6827 ,  C12Q2600/156

    摘要： Methods, systems, and software are provided for determining a genotype for a genomic locus comprising a tandem repeat having contiguous repeat units. Sequence reads that encompass and map to the tandem repeat are obtained. A repeat count distribution for the number of repeat units in the reads is determined. Sets of adjustment factors are obtained, each set (i) corresponding to a different allele having a different repeat unit count and (ii) including corresponding adjustment factors for a range of repeat unit counts. Candidate genotypes correspond to combinations of two alleles in a plurality of candidate alleles. Each candidate genotype is assigned a likelihood based at least in part on, for each allele in the candidate genotype: (i) a proportion of sequence reads having the repeat count corresponding to the allele and (ii) an adjustment factor from the corresponding set. The candidate genotype having the highest likelihood is selected.

    Artificial Intelligence Based Cardiac Event Predictor Systems and Methods
    6.
    发明申请
    Artificial Intelligence Based Cardiac Event Predictor Systems and Methods 有权

    公开(公告)号：US20220378379A1

    公开(公告)日：2022-12-01

    申请号：US17829356

    申请日：2022-05-31

    申请人： Tempus Labs, Inc.

    发明人： Noah Zimmerman

    IPC分类号： A61B5/00 ,  A61B5/318 ,  G16H50/30 ,  G16H50/20

    摘要： A method and system for predicting the likelihood that a patient will suffer from a cardiac event is provided. The method includes receiving electrocardiogram data associated with the patient, providing at least a portion of the electrocardiogram data to a trained model, receiving a risk score indicative of the likelihood the patient will suffer from the cardiac event within a predetermined period of time from when the electrocardiogram data was generated, and outputting the risk score to at least one of a memory or a display for viewing by a medical practitioner or healthcare administrator. The system includes at least one processor executing instructions to carry out the steps of the method.

    METHODS AND SYSTEMS FOR REFINING COPY NUMBER VARIATION IN A LIQUID BIOPSY ASSAY
    7.
    发明申请
    METHODS AND SYSTEMS FOR REFINING COPY NUMBER VARIATION IN A LIQUID BIOPSY ASSAY 有权

    公开(公告)号：US20220336046A1

    公开(公告)日：2022-10-20

    申请号：US17527657

    申请日：2021-11-16

    申请人： Tempus Labs, Inc.

    发明人： Wei Zhu ,  Robert Tell ,  Terri M. Driessen

    IPC分类号： G16B20/10 ,  G16B40/30 ,  G16B40/20 ,  G16B30/10

    摘要： Methods, systems, and software are provided for validating a copy number variation in a test subject. A first dataset is obtained comprising bin-level sequence ratios, segment-level sequence ratios and segment-level measures of dispersion. Bins representing regions of a human reference genome are determined from sequencing cell-free nucleic acids in a liquid biopsy sample and reference samples. Segments encompass subsets of adjacent bins, where segment-level sequence ratios and measures of dispersion are determined using bin-level sequence ratios. A copy number status annotation for a segment is validated by applying the first dataset to a plurality of filters comprising a measure of central tendency bin-level sequence ratio filter, a confidence filter, and a measure of central tendency-plus-deviation bin-level sequence ratio filter. When a filter is fired, the copy number status annotation of the segment is rejected; and when no filter is fired, the copy number status annotation of the segment is validated.

    Methods and systems for dynamic variant thresholding in a liquid biopsy assay
    8.
    发明授权
    Methods and systems for dynamic variant thresholding in a liquid biopsy assay 有权

    公开(公告)号：US11475981B2

    公开(公告)日：2022-10-18

    申请号：US17179086

    申请日：2021-02-18

    申请人： Tempus Labs, Inc.

    发明人： Robert Tell ,  Wei Zhu ,  Justin David Finkle ,  Christine Lo ,  Terri M. Driessen

    IPC分类号： G16B30/10 ,  G16B20/40 ,  G16B20/20

    摘要： Methods, systems, and software are provided for validating a somatic sequence variant in a subject having a cancer condition. Sequence reads are obtained from sequencing cell-free DNA fragments in a liquid biopsy sample of the subject. Sequence reads are aligned to a reference sequence. A variant allele fragment count and locus fragment count are identified for a candidate variant that maps to a locus in the reference sequence. The variant allele fragment count is compared against a dynamic variant count threshold for the locus. The threshold is based on a pre-test odds of a positive variant call for the locus, based on the prevalence of variants in a genomic region including the locus in a cohort of subjects having the cancer condition. The somatic sequence variant in the subject is validated, or rejected, when the variant allele fragment count for the candidate variant satisfies, or does not satisfy, the threshold.

    Detection of human leukocyte antigen loss of heterozygosity
    9.
    发明授权
    Detection of human leukocyte antigen loss of heterozygosity 有权

    公开(公告)号：US11475978B2

    公开(公告)日：2022-10-18

    申请号：US17304940

    申请日：2021-06-28

    申请人： TEMPUS LABS, INC.

    发明人： Ariane Lozac'hmeur ,  Jason Perera

    IPC分类号： G16B20/10 ,  G16B30/10 ,  G16B40/00

    摘要： Processes are provided for detecting loss of heterozygosity of Human Leukocyte Antigen (HLA) in a subject using analysis of next generation sequencing (NGS) data. The processes include aligning NGS data and identifying unmapped and mapped reads, updating reference data, and feeding one or more sequence reads to an HLA typing process for identifying candidate HLA alleles and feeding HLA type data to a loss of heterozygosity (LOH) modeling process for determining a LOH status for each HLA allele. A report may be generated of the LOH statuses for each of HLA allele.

    GANs for Latent Space Visualizations
    10.
    发明申请
    GANs for Latent Space Visualizations 有权

    公开(公告)号：US20220319675A1

    公开(公告)日：2022-10-06

    申请号：US17648936

    申请日：2022-01-25

    申请人： Tempus Labs, Inc.

    发明人： Ryan Mork

    IPC分类号： G16H30/40 ,  G06T7/00 ,  G06N3/12

    摘要： The disclosure provides a method of analyzing a patient. The method includes receiving a plurality of latent space representations of patient data including genetic data associated with a plurality of patients, providing each of the plurality of latent space representations to a trained model, receiving a plurality of images from the trained model, each image included in the plurality of images being associated with a patient included in the plurality of patients, grouping at least a portion of the plurality of images into a plurality of groups, and displaying the plurality of groups to at least one user.