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公开(公告)号：US20220351805A1
公开(公告)日：2022-11-03
申请号：US17750055
申请日：2022-05-20
申请人： Tempus Labs, Inc.
发明人： Nike T. Beaubier , Joshua SK Bell , Catherine Igartua , Hailey B. Lefkofsky , Lee F. Langer , Joshua Drews
摘要： Disclosed herein are systems, methods, and compositions useful for determining cellular pathway disruption comprising the use of RNA expression level information. This determined level of disruption can assist in the identification of genetic variants that alter pathway activity, to correlate these variants with disease state and disease progression, and to identify those therapeutics most likely to be effective and which should be avoided.
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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.
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公开(公告)号：US20200098448A1
公开(公告)日：2020-03-26
申请号：US16581706
申请日：2019-09-24
申请人： TEMPUS LABS, INC.
发明人： Kaanan Shah , Ashraf Hafez , Catherine Igartua , Jackson Michuda
IPC分类号： G16B30/00 , G16B5/00 , G06F16/215
摘要： A platform to perform normalization and correction on gene expression datasets and combines different datasets into a standard dataset using a framework configured to continuously incorporate new gene expression data. The framework determines a series of conversion factors that are used to on-board new gene expression datasets, such as unpaired datasets, where these conversion factors are able to correct for variations in data type, variations in gene expressions, and variations in collection systems.
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4.发明授权公开(公告)号：US11164655B2
公开(公告)日：2021-11-02
申请号：US17118227
申请日：2020-12-10
申请人： Tempus Labs, Inc.
摘要： Methods, systems, and software are provided for an ensemble model trained to distinguish between cancers with homologous recombination pathway deficiencies (HRD positive cancers) and cancers without homologous recombination pathway deficiencies (HRD negative cancers) based on nucleic acid sequencing data, e.g., both RNA and DNA sequencing data, generated from a cancerous tissue sample of the subject.
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5.发明申请公开(公告)号：US20210172024A1
公开(公告)日：2021-06-10
申请号：US17118227
申请日：2020-12-10
申请人： Tempus Labs, Inc.
IPC分类号： C12Q1/6886
摘要： Methods, systems, and software are provided for an ensemble model trained to distinguish between cancers with homologous recombination pathway deficiencies (HRD positive cancers) and cancers without homologous recombination pathway deficiencies (HRD negative cancers) based on nucleic acid sequencing data, e.g., both RNA and DNA sequencing data, generated from a cancerous tissue sample of the subject.
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公开(公告)号：US20200210852A1
公开(公告)日：2020-07-02
申请号：US16732229
申请日：2019-12-31
申请人： TEMPUS LABS, INC.
发明人： Catherine Igartua , Kaanan Shah , Mathew Barber
摘要： A platform for transcriptome deconvolution of gene expression data is provided and may be used in assessing metastatic cancer samples. The deconvolution is performed using an unsupervised clustering technique, such as grade of membership, that allows for samples to be assigned to multiple clusters during a training process. A deconvolution gene expression model is generated as a result and is used for accurate assess of metastases in subsequent samples.
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公开(公告)号：US20230187070A1
公开(公告)日：2023-06-15
申请号：US17982399
申请日：2022-11-07
申请人： Tempus Labs, Inc.
发明人： Jackson Michuda , Kyle Ashley Beauchamp , Joshuah Kapilivsky , Calvin McCarter , Nike Tsiapera Beaubier , Martin Christian Stumpe , Catherine Igartua , Joshua SK Bell , Timothy Taxter , Raphael Pelossof
摘要： Systems and methods are provided for identifying a diagnosis of a cancer condition for a somatic tumor specimen of a subject. The method receives sequencing information comprising analysis of a plurality of nucleic acids derived from the somatic tumor specimen. The method identifies a plurality of features from the sequencing information, including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as inputs to a first classifier and a second classifier, respectively. The method generates, from two or more classifiers, two or more predictions of cancer condition based at least in part on the identified plurality of features. The method combines, at a final classifier, the two or more predictions to identify the diagnosis of the cancer condition for the somatic tumor specimen of the subject.
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公开(公告)号：US11527323B2
公开(公告)日：2022-12-13
申请号：US15930234
申请日：2020-05-12
申请人： Tempus Labs, Inc.
发明人： Jackson Michuda , Kyle Ashley Beauchamp , Joshuah Kapilivsky , Calvin McCarter , Nike Beaubier , Martin Christian Stumpe , Catherine Igartua , Joshua S K Bell , Timothy Taxter , Raphael Pelossof
摘要： Systems and methods are provided for identifying a diagnosis of a cancer condition for a somatic tumor specimen of a subject. The method receives sequencing information comprising analysis of a plurality of nucleic acids derived from the somatic tumor specimen. The method identifies a plurality of features from the sequencing information, including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as inputs to a first classifier and a second classifier, respectively. The method generates, from two or more classifiers, two or more predictions of cancer condition based at least in part on the identified plurality of features. The method combines, at a final classifier, the two or more predictions to identify the diagnosis of the cancer condition for the somatic tumor specimen of the subject.
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公开(公告)号：US10975445B2
公开(公告)日：2021-04-13
申请号：US16789363
申请日：2020-02-12
申请人： Tempus Labs, Inc.
发明人： Aarti Venkat , Jerod Parsons , Joshua S K Bell , Catherine Igartua , Yilin Zhang , Ameen Salahudeen , Verónica Sánchez Freire , Robert Tell
摘要： Methods, systems, and software are provided for determining a homologous recombination pathway status of a cancer in a test subject, e.g., to improve cancer treatment predictions and outcomes. In some embodiments, classifiers using one or more of (i) a heterozygosity status for DNA damage repair genes in a cancerous tissue, (ii) a measure of the loss of heterozygosity across the genome of the cancerous tissue, (iii) a measure of variant alleles detected in a second plurality of DNA damage repair genes in the genome of the cancerous tissue, (iv) a measure of variant alleles detected in the second plurality of DNA damage repair genes in the genome of a non-cancerous tissue, and (v) tumor sample purity are provided.
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公开(公告)号：US20230253070A1
公开(公告)日：2023-08-10
申请号：US18176476
申请日：2023-02-28
申请人： Tempus Labs, Inc.
发明人： Joshua Drews , Bonnie Dougherty , Lee Langer , Catherine Igartua , Andrew J. Sedgwick , Justin Guinney
摘要： Disclosed herein are systems, methods, and compositions useful for determining cellular pathway disruption comprising the use of RNA expression level information. This determined level of disruption can assist in the identification of genetic variants that alter pathway activity, to correlate these variants with disease state and disease progression, and to identify those therapeutics most likely to be effective and which should be avoided.
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