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公开(公告)号：US20210233238A1
公开(公告)日：2021-07-29
申请号：US17192383
申请日：2021-03-04
申请人： TEMPUS LABS, INC.
发明人： Stephen Yip , Irvin Ho , Lingdao Sha , Boleslaw Osinski , Aly Azeem Khan , Andrew J. Kruger , Michael Carlson , Abel Greenwald , Caleb Willis
摘要： A generalizable and interpretable deep learning model for predicting biomarker status and biomarker metrics from histopathology slide images is provided.
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162.发明授权公开(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.
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163.发明申请公开(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.
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公开(公告)号：US20210155989A1
公开(公告)日：2021-05-27
申请号：US16693117
申请日：2019-11-22
申请人： Tempus Labs, Inc.
摘要： Provided herein are novel organoid culture media, organoid culture systems, and methods of culturing tumor organoids using the subject organoid culture media. Also provided herein are tumor organoids developed using such organoid culture systems, methods for assessing the clonal diversity of the tumor organoids, and methods for using such tumor organoids, for example, for tumor modelling and drug development applications. In particular embodiments, the tumor organoid culture media provided herein is substantially free of R-spondins (e.g., R-spondin1).
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公开(公告)号：US20210142904A1
公开(公告)日：2021-05-13
申请号：US17150992
申请日：2021-01-15
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 SK Bell , Timothy Taxter , Raphael Pelossof
摘要： Systems and methods are provided for determining a cancer type of a somatic tissue in a subject. A first plurality of sequence reads is obtained from a plurality of RNA molecules in a biopsy of the subject. A first set of sequence features comprising relative miRNA abundance values of genes is determined from the first plurality of sequence reads. Sequence features are applied to a classification model trained to distinguish between each cancer type in a set of at least 50 cancer types, thus determining the cancer type of the somatic tissue in the subject. The classification model provides an indication that the somatic tissue is or is not a respective cancer type, and the set of cancer types includes at least two cancer types from one or more classes of cancer selected from the group consisting of hematological cancers, squamous cancers, endometrial cancers, sarcoma cancers, and neuroendocrine cancers.
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公开(公告)号：US20210057042A1
公开(公告)日：2021-02-25
申请号：US16994315
申请日：2020-08-14
申请人： Tempus Labs, Inc.
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：US20200005461A1
公开(公告)日：2020-01-02
申请号：US16460975
申请日：2019-07-02
申请人： TEMPUS LABS, INC.
发明人： Stephen Yip
摘要： A platform is provided for generating 3D models of a tumor segmented from a series of 2D medical images and for identifying from these 3D models, radiomic features that may be used for diagnostic, prognostic, and treatment response assessment of the tumor. The radiomic features may be shape-based features, intensity-based features, textural features, and filter-based features. The radiomic features are compared to remove sufficiently redundant features, thereby producing a reduced set of radiomic features, which is then compared to separate genomic data and/or outcome data to identify clinically and biologically significant radiomic features for diagnostic, prognostic, and treatment response assessment, other applications.
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