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：US20210355533A1

公开(公告)日：2021-11-18

申请号：US17302030

申请日：2021-04-21

申请人： Tempus Labs, Inc.

发明人： Jason Perera ,  Taylor Harding ,  Brittany Mineo ,  Aly A. Khan ,  Richard Blidner ,  Jenna L. Malinauskas

IPC分类号： C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6806

摘要： This present disclosure relates to systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. The present disclosure also relates to systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.

公开(公告)号：US20210115511A1

公开(公告)日：2021-04-22

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

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：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：US20240209417A1

公开(公告)日：2024-06-27

申请号：US18556838

申请日：2022-04-21

申请人： Tempus Labs, Inc.

发明人： Richard Blidner ,  Hala Samir Kuttab-Boulos

IPC分类号： C12Q1/6811 ,  C12Q1/6874

CPC分类号： C12Q1/6811 ,  C12Q1/6874

摘要： Systems and methods are provided for balancing a probe set for enriching a plurality of genomic loci. A nucleic acid probe set containing pools of nucleic acid probe species is obtained. Each probe species aligns to a different subsequence of a respective locus and includes proportions of a capture moiety conjugated version and a capture moiety-free version. Each probe species in a pool aligns to a portion of the genome that is at least 100 nucleotides away from any other probe species in the pool. Each pool in the probe set is separately analyzed against reference nucleic acid samples to obtain recovery rates and identify probe species that do not satisfy a minimum or a maximum recovery rate threshold. An adjusted version of a final design for the probe set is established by adjusting proportions of capture moiety conjugated and capture moiety-free versions for the identified probe species.

公开(公告)号：US20230121729A1

公开(公告)日：2023-04-20

申请号：US17886769

申请日：2022-08-12

申请人： Tempus Labs, Inc.

发明人： Jason Perera ,  Taylor Harding ,  Brittany Mineo ,  Aly A. Khan ,  Richard Blidner ,  Jenna L. Malinauskas

IPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6876 ,  C07K14/725 ,  C12Q1/6881

摘要： This present disclosure relates to systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. The present disclosure also relates to systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.

公开(公告)号：US11414700B2

公开(公告)日：2022-08-16

申请号：US17302030

申请日：2021-04-21

申请人： Tempus Labs, Inc.

发明人： Jason Perera ,  Taylor Harding ,  Brittany Mineo ,  Aly A. Khan ,  Richard Blidner ,  Jenna L. Malinauskas

IPC分类号： C12P19/34 ,  C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6876 ,  C07K14/725 ,  C12Q1/6881

摘要： Disclosed herein are systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. In certain embodiments, the methods include enriching a sample for TCR/BCR RNA sequences, and determining the TCR/BCR profile of a subject using five different oligonucleotide pools. Also disclosed herein are systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.

公开(公告)号：US20210269878A1

公开(公告)日：2021-09-02

申请号：US17323986

申请日：2021-05-18

申请人： Tempus Labs, Inc.

发明人： Richard Blidner

IPC分类号： C12Q1/6874 ,  C12Q1/6883

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.