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    SYSTEMS AND METHODS FOR AUTOMATING RNA EXPRESSION CALLS IN A CANCER PREDICTION PIPELINE
    1.
    发明申请
    SYSTEMS AND METHODS FOR AUTOMATING RNA EXPRESSION CALLS IN A CANCER PREDICTION PIPELINE 有权

    公开(公告)号：US20210272649A1

    公开(公告)日：2021-09-02

    申请号：US17324949

    申请日：2021-05-19

    申请人： Tempus Labs, Inc.

    发明人： Joshua SK Bell ,  Catherine Igartua ,  Joshua Drews

    IPC分类号： G16B25/10 ,  G16B50/30 ,  C12Q1/6886 ,  G16B5/00

    摘要： Systems and methods are provided for performing quality control analysis. The method obtains, in electronic form, a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs one or more global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.

    METHODS AND SYSTEMS FOR DETECTING ALTERNATIVE SPLICING IN SEQUENCING DATA
    4.
    发明公开
    METHODS AND SYSTEMS FOR DETECTING ALTERNATIVE SPLICING IN SEQUENCING DATA 审中-公开

    公开(公告)号：US20230144221A1

    公开(公告)日：2023-05-11

    申请号：US17963969

    申请日：2022-10-11

    申请人： Tempus Labs, Inc.

    发明人： Alessandra Breschi ,  Joshua SK Bell ,  Joshua Drews ,  Benjamin Leibowitz ,  Jackson Michuda

    IPC分类号： G16B20/20 ,  G16B30/10

    CPC分类号： G16B20/20 ,  G16B30/10

    摘要： The disclosure provides methods and systems for detecting alternative splicing variants in a patient sample. The methods involve comparison of splice junction data from RNA sequencing with principal splicing isoforms and identifying those sequences, identifying those sequences that do not match the principal splicing isoform. These sequences are categorized into alternative splicing events and documented. Optionally, previously identified target sequences can be utilized in the comparison where the method seeks sequences which do match. Other methods and systems of the present disclosure include those for building a splice profile of alternative splicing variants for a patient sample and those for developing a companion diagnostic test for a treatment method of a disease based on the presence or absence of alternative splicing variants in a patient sample.

    Systems and methods for automating RNA expression calls in a cancer prediction pipeline
    6.
    发明授权
    Systems and methods for automating RNA expression calls in a cancer prediction pipeline 有权

    公开(公告)号：US11043283B1

    公开(公告)日：2021-06-22

    申请号：US17112877

    申请日：2020-12-04

    申请人： Tempus Labs, Inc.

    发明人： Joshua S K Bell ,  Catherine Igartua ,  Joshua Drews

    IPC分类号： G16B25/10 ,  G16B50/30 ,  G16B5/00 ,  C12Q1/6886

    摘要： Systems and methods are provided for performing quality control analysis. The method obtains, in electronic form, a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs one or more global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.

    SYSTEMS AND METHODS FOR AUTOMATING RNA EXPRESSION CALLS IN A CANCER PREDICTION PIPELINE
    7.
    发明申请
    SYSTEMS AND METHODS FOR AUTOMATING RNA EXPRESSION CALLS IN A CANCER PREDICTION PIPELINE 有权

    公开(公告)号：US20210174898A1

    公开(公告)日：2021-06-10

    申请号：US17112877

    申请日：2020-12-04

    申请人： Tempus Labs, Inc.

    发明人： Joshua SK Bell ,  Catherine Igartua ,  Joshua Drews

    IPC分类号： G16B25/10 ,  C12Q1/6886 ,  G16B5/00 ,  G16B50/30

    摘要： Systems and methods are provided for performing quality control analysis. The method obtains, in electronic form, a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs one or more global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.