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公开(公告)号：US20240344115A1
公开(公告)日：2024-10-17
申请号：US18470187
申请日：2023-09-19
发明人： Yupeng HE , Ariel JAIMOVICH , Andrew KENNEDY , William J. GREENLEAF , Meromit SINGER , Emily Katherine TSANG
IPC分类号： C12Q1/6827 , C12Q1/6806 , C12Q1/6886
CPC分类号： C12Q1/6827 , C12Q1/6806 , C12Q1/6886 , C12Q2600/154
摘要： Provided herein is a DNA analysis method for detecting and quantifying immune cell types from which the DNA originated. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
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公开(公告)号：US12110560B2
公开(公告)日：2024-10-08
申请号：US18594336
申请日：2024-03-04
发明人： AmirAli Talasaz
IPC分类号： C12Q1/68 , C12N15/10 , C12Q1/6806 , C12Q1/6869 , C12Q1/6874 , C12Q1/6886 , G16B30/00 , G16B30/10
CPC分类号： C12Q1/6886 , C12N15/1065 , C12Q1/6806 , C12Q1/6869 , C12Q1/6874 , G16B30/00 , G16B30/10 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , C12Q1/6869 , C12Q2537/165 , C12Q2545/114
摘要： The present disclosure provides a method for monitoring residual disease in a subject. Generally, the method comprises determining a frequency of cancer mutations from a first sample obtained from a tumor biopsy from the subject; determining a frequency of the cancer mutations discovered in the first sample from a second sample comprising cell-free deoxyribonucleic acid (cfDNA) molecules that is obtained from the subject after the subject has undergone a course of treatment for cancer; and determining a presence or absence of cancer in the subject based on an analysis of the frequency of the cancer mutations from sequence data from the second sample.
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公开(公告)号：US12098421B2
公开(公告)日：2024-09-24
申请号：US18317550
申请日：2023-05-15
IPC分类号： C12P19/34 , C12Q1/6869 , C12Q1/6886 , G16B15/00
CPC分类号： C12Q1/6869 , C12Q1/6886 , C12Q2535/122 , C12Q2600/158 , G16B15/00
摘要： Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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公开(公告)号：US20240263241A1
公开(公告)日：2024-08-08
申请号：US18506858
申请日：2023-11-10
发明人： Andrew KENNEDY
IPC分类号： C12Q1/6886 , C12Q1/6855 , C12Q1/6869
CPC分类号： C12Q1/6886 , C12Q1/6855 , C12Q1/6869 , C12Q2600/154
摘要： Provided herein are methods of analyzing nucleic acids for detecting DNA comprising cell or tissue type-specific epigenetically variable regions, such as differentially methylated regions, that are also copy number variants. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
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公开(公告)号：US20240233868A9
公开(公告)日：2024-07-11
申请号：US18482779
申请日：2023-10-06
IPC分类号： G16B30/00 , C12Q1/6806 , C12Q1/6827 , G16B5/00 , G16B25/10 , G16B40/30
CPC分类号： G16B30/00 , C12Q1/6806 , C12Q1/6827 , G16B5/00 , G16B25/10 , G16B40/30 , C12Q2535/122 , C12Q2537/159
摘要： The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
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公开(公告)号：US20240200123A1
公开(公告)日：2024-06-20
申请号：US18535812
申请日：2023-12-11
IPC分类号： C12Q1/6827 , C12Q1/6806 , C12Q1/6869 , G16B30/00
CPC分类号： C12Q1/6827 , C12Q1/6806 , G16B30/00 , C12Q1/6869
摘要： The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
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公开(公告)号：US20240182977A1
公开(公告)日：2024-06-06
申请号：US18436821
申请日：2024-02-08
IPC分类号： C12Q1/6886 , C12M1/00 , C12M1/34 , C12Q1/6806 , C12Q1/6855 , C12Q1/6869 , G01N33/574 , G16B20/20 , G16B30/10 , G16H50/20 , G16H50/30
CPC分类号： C12Q1/6886 , C12M1/00 , C12M1/34 , C12Q1/6806 , C12Q1/6855 , C12Q1/6869 , G01N33/57407 , G16B20/20 , G16B30/10 , G16H50/20 , G16H50/30 , C12Q2600/118 , C12Q2600/154 , C12Q2600/156 , C12Q2600/158 , C12Q2600/166
摘要： Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
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公开(公告)号：US11959139B2
公开(公告)日：2024-04-16
申请号：US18316864
申请日：2023-05-12
IPC分类号： C12P19/34 , C12Q1/6869 , C12Q1/6886 , G16B15/00
CPC分类号： C12Q1/6869 , C12Q1/6886 , C12Q2535/122 , C12Q2600/158 , G16B15/00
摘要： Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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9.发明授权公开(公告)号：US11946106B2
公开(公告)日：2024-04-02
申请号：US18087724
申请日：2022-12-22
IPC分类号： C12Q1/6886 , C12N9/22 , C12N15/10 , C12Q1/6809 , C12Q1/683
CPC分类号： C12Q1/6886 , C12N9/22 , C12N15/1065 , C12Q1/6809 , C12Q1/683 , C12N2800/80 , C12Q2600/112 , C12Q2600/154 , C12Q2600/156 , C12Q2600/166
摘要： In an aspect, the present disclosure provides a method for determining a methylation status comprises: providing a biological sample of nucleic acid molecules; partitioning at least a subset of the nucleic acid molecules in the biological sample based on the methylation status of the nucleic acid molecules into a plurality of partitioned sets; digesting at least a subset of the one or more partitioned sets in the plurality of partitioned sets with at least one methylation sensitive restriction enzyme; enriching at least a subset of the nucleic acid molecules in the plurality of partitioned sets for genomic regions of interest, wherein the at least a subset of the nucleic acid molecules comprises digested nucleic acid molecules in the one or more partitioned sets; and determining methylation status at one or more genetic loci of the nucleic acid molecules in at least one of the partitioned sets.
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公开(公告)号：US20240102101A1
公开(公告)日：2024-03-28
申请号：US18185683
申请日：2023-03-17
发明人： AmirAli TALASAZ
IPC分类号： C12Q1/6886 , C12N15/10 , C12Q1/6869 , C12Q1/6883 , G16B30/00 , G16B30/10
CPC分类号： C12Q1/6886 , C12N15/1072 , C12Q1/6869 , C12Q1/6883 , G16B30/00 , G16B30/10 , C12Q2600/118 , C12Q2600/156
摘要： The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
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