公开(公告)号：US11041200B2

公开(公告)日：2021-06-22

申请号：US17076704

申请日：2020-10-21

申请人： Tempus Labs, Inc.

发明人： Richard Blidner

IPC分类号： C12Q1/6874 ,  C12Q1/6883 ,  C40B40/06

摘要： Systems and methods are provided for determining an optimized probe set. The method proceeds by obtaining a set of probes, where each probe has a respective concentration. The set of probes is assayed against a sample library, and at least i) a respective recovery rate for each probe in the set of probes, and ii) a median recovery rate for the set of probes are obtained. Modify the respective concentration of each probe that does not satisfy predetermined recovery rate threshold. Reevaluate the set of probes against the sample library. Repeat the modifying and reevaluation until the respective updated recovery rate for each probe in the updated set of probes satisfies the predetermined recovery rate threshold, thereby providing the optimized set of probes for the sample library.

公开(公告)号：US20210172931A1

公开(公告)日：2021-06-10

申请号：US17114386

申请日：2020-12-07

申请人： Tempus Labs, Inc.

发明人： Brian M. Larsen ,  Michelle M. Stein ,  Luka A. Karginov ,  Ameen Salahudeen ,  Madhavi Kannan ,  Aly A. Khan ,  Verónica Sánchez Freire ,  Yilin Zhang

IPC分类号： G01N33/50 ,  G01N33/58

摘要： Methods, systems, and software are provided for using organoid cultures, e.g., patient-derived tumor organoid cultures, to improve treatment predictions and outcomes.

公开(公告)号：US20210166785A1

公开(公告)日：2021-06-03

申请号：US17139765

申请日：2020-12-31

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 ,  Andrew Westley ,  Ryan Jones ,  Brett Mahon

IPC分类号： G16B30/00 ,  C12Q1/6869 ,  G16B50/30

摘要： A method for qualifying a specimen prepared on one or more hematoxylin and eosin (H&E) slides by assessing an expected yield of nucleic acids for tumor cells and providing associated unstained slides for subsequent nucleic acid analysis is provided.

公开(公告)号：US20200258597A1

公开(公告)日：2020-08-13

申请号：US16789413

申请日：2020-02-12

申请人： TEMPUS LABS, INC.

发明人： Jason Perera

IPC分类号： G16B30/00 ,  C12Q1/6827 ,  G06N3/00 ,  G16B50/30

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.

公开(公告)号：US20240161519A1

公开(公告)日：2024-05-16

申请号：US18511998

申请日：2023-11-16

申请人： TEMPUS LABS, INC.

发明人： Chi-Sing Ho ,  Tianyou Luo ,  Ameen Salahudeen ,  Luca Lonini

IPC分类号： G06V20/69 ,  G06T3/40 ,  G06T7/10 ,  G06V10/46 ,  G16H30/40

CPC分类号： G06V20/698 ,  G06T3/40 ,  G06T7/10 ,  G06V10/46 ,  G06V20/695 ,  G16H30/40 ,  G06T2207/20132

摘要： A computer-implemented method, computing system and computer-readable medium include receiving training data and training a machine learning model to generate a cell expression map. A computer-implemented method, computing system and computer-readable medium includes receiving a histology image and a cell segmentation map and processing them using a trained machine learning model.

公开(公告)号：US20240087747A1

公开(公告)日：2024-03-14

申请号：US18513153

申请日：2023-11-17

申请人： Tempus Labs, Inc.

发明人： Carin Fishel Queen ,  Hailey Lefkofsky ,  Ashraf Hafez ,  Julian Habib ,  Caroline Epstein

IPC分类号： G16H50/20 ,  G16H10/60

CPC分类号： G16H50/20 ,  G16H10/60

摘要： A system and method for analyzing a data store of de-identified patient data to generate one or more dynamic user interfaces usable to predict an expected response of a particular patient population or cohort when provided with a certain treatment. The automated analysis of patterns occurring in patient clinical, molecular, phenotypic, and response data, as facilitated by the various user interfaces, provides an efficient, intuitive way for clinicians to evaluate large data sets to aid in the potential discovery of insights of therapeutic significance.

公开(公告)号：US20240079086A1

公开(公告)日：2024-03-07

申请号：US17902558

申请日：2022-09-02

申请人： TEMPUS LABS, INC.

发明人： Charles Jaros ,  Nayeem Qadir ,  Isaiah Simpson ,  Marc Wielansky

IPC分类号： G16B20/00 ,  G16B40/20

CPC分类号： G16B20/00 ,  G16B40/20 ,  G16H50/30

摘要： The following relates generally to determining genomic biomarkers from biological data (e.g., a read of a nucleic acid, or an image, such as an image of a slide). In some embodiments, a transform orchestrator: (i) receives an order to transform biological data to one or more genomic biomarkers; (ii) selects a transform for deriving each of the received one or more genomic biomarkers; (iii) associates each selected transform with a cloud computing platform; (iv) executes instructions for each selected transform; (v) communicates an operational status of each selected transform; (vi) stores the genomic biomarker output from each selected transform; and (vii) provides a notification of a final operational status of each selected transform.

公开(公告)号：US20240076744A1

公开(公告)日：2024-03-07

申请号：US18261985

申请日：2022-01-21

申请人： Tempus Labs, Inc.

发明人： Richard Blidner ,  Eric Leon Harness

IPC分类号： C12Q1/6886 ,  G06N20/10 ,  G16B20/20 ,  G16B25/10 ,  G16B40/20 ,  G16H20/00 ,  G16H50/20

CPC分类号： C12Q1/6886 ,  G06N20/10 ,  G16B20/20 ,  G16B25/10 ,  G16B40/20 ,  G16H20/00 ,  G16H50/20 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/156

摘要： Methods, systems, and software are provided for detecting gene fusions in a subject with a cancer condition through mRNA boundary analysis of next generation sequencing of a transcriptome or relevant part thereof. Methods, systems, and software are provided for detecting splice variants in a subject with a cancer condition through mRNA boundary analysis of next generation sequencing of a transcriptome or relevant part thereof. Methods, systems, and software are provided for evaluating the complexity of an RNA-seq sequencing reaction through mRNA boundary analysis. Generally, the methods described herein include obtaining sequences of mRNA molecules for a plurality of genes in a sample of a subject. For each gene, an RNA boundary distribution including relative abundance value for each respective RNA boundary sub-sequence of the gene is determined from the plurality of sequences. These abundance values are evaluated using one or more models to provide the analyses described herein.

公开(公告)号：US11848107B2

公开(公告)日：2023-12-19

申请号：US17558479

申请日：2021-12-21

申请人： Tempus Labs, Inc.

发明人： Ashraf Hafez ,  Martin Christian Stumpe ,  Nike Beaubier ,  Daniel Neems ,  Caroline Epstein ,  Adrian William George Lange

IPC分类号： G16H50/30 ,  G16H10/60 ,  G16H50/20 ,  G16H20/00 ,  G16B20/00 ,  G16B30/00 ,  G16B25/10

CPC分类号： G16H50/30 ,  G16B20/00 ,  G16B25/10 ,  G16B30/00 ,  G16H10/60 ,  G16H20/00 ,  G16H50/20

摘要： Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

公开(公告)号：US20230272489A1

公开(公告)日：2023-08-31

申请号：US18300253

申请日：2023-04-13

申请人： Tempus Labs, Inc.

发明人： Ameen Salahudeen ,  Verónica Sánchez Freire ,  Brandon L. Mapes

IPC分类号： C12Q1/6886 ,  C12N5/071 ,  G16H50/30 ,  C12M1/32 ,  G01N33/50 ,  G16B20/20 ,  C12N5/09 ,  C12Q1/02 ,  C12Q1/6806 ,  C12Q1/6816

CPC分类号： C12Q1/6886 ,  C12N5/0691 ,  G16H50/30 ,  C12M23/12 ,  G01N33/5091 ,  G16B20/20 ,  C12N5/0693 ,  C12Q1/025 ,  C12Q1/6806 ,  C12Q1/6816 ,  C12N2500/25 ,  C12N2527/00 ,  C12N2521/10 ,  C12N2509/10 ,  C12N2501/117 ,  C12N2501/11 ,  C12N2501/119 ,  C12N2501/999 ,  C12N2501/998 ,  C12N2533/54 ,  C12N2533/52 ,  C12N2533/90 ,  C12N2501/33 ,  C12Q1/6844

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).