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公开(公告)号：US11475978B2
公开(公告)日：2022-10-18
申请号：US17304940
申请日：2021-06-28
申请人： TEMPUS LABS, INC.
发明人： Ariane Lozac'hmeur , Jason Perera
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.
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2.发明申请公开(公告)号：US20210098078A1
公开(公告)日：2021-04-01
申请号：US16945588
申请日：2020-07-31
申请人： Tempus Labs, Inc.
发明人： Ariane Lozac'hmeur , Aly A. Khan , Jason Perera , Denise Lau , Ashraf Hafez
摘要： Methods, systems, and software are provided for determining a microsatellite instability (MSI) status of a subject. Nucleotide sequences are obtained for cell-free DNA molecules from a liquid biopsy sample of the subject. The nucleotide sequences are used to determine, for each respective microsatellite locus in a plurality of predetermined microsatellite loci, one or more independent corresponding metrics, where each metric in the one or more metrics is determined at least in part by the distribution of the number of repeat units at the respective microsatellite locus. The one or more metrics are input into a classifier trained to distinguish between stable and unstable microsatellite loci, in order to classify the MSI status of the subject. In certain aspects, microsatellite stability metrics are compared against metrics from solid tumor samples and/or normal tissues. In certain aspects, the microsatellite stability metrics are determined relative to a subject-specific standard for microsatellite stability.
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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.
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公开(公告)号：US20210327536A1
公开(公告)日：2021-10-21
申请号：US17304940
申请日：2021-06-28
申请人： TEMPUS LABS, INC.
发明人： Ariane Lozac'hmeur , Jason Perera
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.
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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.
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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.
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公开(公告)号：US20230154563A1
公开(公告)日：2023-05-18
申请号：US17968509
申请日：2022-10-18
申请人： TEMPUS LABS, INC.
发明人： Jason Perera , Ariane Lozac'hmeur
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.
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公开(公告)号：US20230064530A1
公开(公告)日：2023-03-02
申请号：US17816345
申请日：2022-07-29
申请人： TEMPUS LABS, INC.
发明人： Ramit Bharanikumar , Karl Beutner , Jason Perera
摘要： Processes are provided for identifying somatic variants in a human leukocyte antigen (HLA) gene in a subject using analysis of next generation sequencing (NGS) data. The processes include aligning HLA sequence read data for normal samples and the HLA sequence data for a tumor sample to a patient specific HLA reference genome and performing a variant calling process on filtered aligned read data and determining somatic variants of the HLA class. A report may be generated of somatic variants of the HLA gene annotated for functional effect.
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公开(公告)号：US11081210B2
公开(公告)日：2021-08-03
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 , G16B50/30 , G06N3/00
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.
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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.
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