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公开(公告)号：US20220356527A1
公开(公告)日：2022-11-10
申请号：US17552728
申请日：2021-12-16
发明人： Helmy Eltoukhy , AmirAli Talasaz , Darya Chudova , Diana Abdueva
IPC分类号： C12Q1/6886 , G16B30/00 , C12Q1/6809 , G16B99/00 , G16B30/10 , G16B20/10 , C12Q1/6874
摘要： Methods are provided herein to improve automatic detection of copy number variation in nucleic acid samples. These methods provide improved approaches for determining baseline copy number of genetic loci within a sample, reduce variation due to features of genetic loci, sample preparation, and probe exhaustion.
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公开(公告)号：US11434531B2
公开(公告)日：2022-09-06
申请号：US17410903
申请日：2021-08-24
发明人： AmirAli Talasaz , Helmy Eltoukhy
IPC分类号： C12P19/34 , C12Q1/6869 , C12Q1/6886 , 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：US20210265013A1
公开(公告)日：2021-08-26
申请号：US17178102
申请日：2021-02-17
摘要： Systems and methods are disclosed to detect single-nucleotide variations (SNVs) from somatic sources in a cell-free biological sample of a subject by generating training data with class labels; in computer memory, generating a machine learning unit comprising one output for each of adenine (A), cytosine (C), guanine (G), and thymine (T) calls; training the machine learning unit; and applying the machine learning unit to detect the SNVs from somatic sources in the cell-free biological sample of the subject, wherein the cell-free biological sample comprises a mixture of nucleic acid molecules from somatic and germline sources.
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公开(公告)号：US10883139B2
公开(公告)日：2021-01-05
申请号：US15892178
申请日：2018-02-08
IPC分类号： C12P19/34 , C12Q1/6869 , C12Q1/6886 , 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：US09850523B1
公开(公告)日：2017-12-26
申请号：US15426668
申请日：2017-02-07
CPC分类号： C12Q1/6806 , C12Q1/6827 , C12Q1/6869 , G06F19/20 , C12Q2527/143 , C12Q2537/143
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：US11359248B2
公开(公告)日：2022-06-14
申请号：US17507109
申请日：2021-10-21
IPC分类号： C12Q1/6886 , G01N33/574 , G16B30/10 , G16B20/20 , C12Q1/6806 , C12Q1/6869 , C12M1/34 , C12M1/00 , G16H50/30 , G16H50/20
摘要： Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.
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公开(公告)号：US11345968B2
公开(公告)日：2022-05-31
申请号：US17367245
申请日：2021-07-02
IPC分类号： C12Q1/6886 , C12M1/34 , C12M1/00 , G01N33/574 , G16B30/10 , G16B20/20 , C12Q1/6806 , C12Q1/6869 , G16H50/30 , G16H50/20
摘要： Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease.
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公开(公告)号：US11335463B2
公开(公告)日：2022-05-17
申请号：US16075105
申请日：2017-02-02
发明人： Helmy Eltoukhy , AmirAli Talasaz
摘要： The present disclosure provides methods for determining a probability that after any of a number of therapeutic interventions, an initial state of a subject, such as somatic cell mutational status of a subject with cancer, will develop a subsequent state. Such probabilities can be used to inform a health care provider as to particular courses of treatment to maximize probability of a desired outcome for the subject.
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公开(公告)号：US11149306B2
公开(公告)日：2021-10-19
申请号：US16945124
申请日：2020-07-31
IPC分类号： C12P19/34 , C12Q1/6869 , C12Q1/6886 , 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：US20180171415A1
公开(公告)日：2018-06-21
申请号：US15828099
申请日：2017-11-30
发明人： AmirAli Talasaz , Helmy Eltoukhy
IPC分类号： C12Q1/6886 , C12Q1/6874 , C12Q1/6869 , C12N15/10 , C12Q1/6806 , G06F19/22
CPC分类号： C12Q1/6886 , C12N15/1065 , C12Q1/6806 , C12Q1/6869 , C12Q1/6874 , C12Q2600/118 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , G16B30/00 , C12Q2537/165 , C12Q2545/114
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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