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公开(公告)号：US11242569B2
公开(公告)日：2022-02-08
申请号：US16737819
申请日：2020-01-08
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：US20220025469A1
公开(公告)日：2022-01-27
申请号：US17367245
申请日：2021-07-02
IPC分类号： C12Q1/6886 , G16B20/20 , C12Q1/6806 , G16B30/10 , C12Q1/6869
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：US20210398610A1
公开(公告)日：2021-12-23
申请号：US17162897
申请日：2021-01-29
发明人： Aliaksandr ARTSIOMENKA , Aaron Isaac HARDIN , Stephen FAIRCLOUGH , Marcin SIKORA , Catalin BARBACIORU
摘要： Provided herein are methods of making negative predictions. In some aspects, methods of determining that a first target nucleic acid variant is absent at a first genetic locus in a cell-free nucleic acid (cfNA) sample obtained from a subject having a given cancer type at least partially using a computer are provided. Certain of these methods include determining that the first target nucleic acid variant is not detected in the cfNA sample obtained from the subject, generating, by the computer, at least one tumor fraction based value; generating, by the computer, at least one mutual exclusivity value; and determining that the first target nucleic acid variant is absent at the first genetic locus in the cfNA sample using the tumor fraction based value and/or the mutual exclusivity value. Additional methods and related systems and computer readable media are also provided.
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公开(公告)号：US20210395816A1
公开(公告)日：2021-12-23
申请号：US17210202
申请日：2021-03-23
IPC分类号： C12Q1/6874
摘要： Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease. However, the value of such information can be compromised by errors introduced by or before the sequencing process including preparing nucleic acids for sequencing. Blunting single-stranded overhangs on nucleic acids in a sample can introduce deamination-induced sequencing errors. The disclosure provides methods of identifying and correcting for such deamination-induced sequencing errors and distinguishing them from real sequence variations.
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公开(公告)号：US11193175B2
公开(公告)日：2021-12-07
申请号：US16866229
申请日：2020-05-04
发明人： Darya Chudova
IPC分类号： G16B20/00 , G16H50/30 , G16B20/20 , C12Q1/6886
摘要： Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample. Such analysis can provide an indication where the tumor mutation burden of a test sample lies on a distribution of tumor mutation burdens in a control population, and thus, whether the individual providing the test sample is likely to be amenable to immunotherapy to treat cancer.
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公开(公告)号：US20210371912A1
公开(公告)日：2021-12-02
申请号：US17396097
申请日：2021-08-06
IPC分类号： C12Q1/6827 , C12Q1/6806 , G16B30/00
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：US20210358567A1
公开(公告)日：2021-11-18
申请号：US17383385
申请日：2021-07-22
发明人： Marcin SIKORA
IPC分类号： G16B30/00 , G16B5/00 , G16B40/30 , C12Q1/6806 , G16B25/10
摘要： Systems and methods are provided for improving accuracy of detecting an insertion or deletion (indel) from a plurality of sequence reads derived from cell-free deoxyribonucleic acid (cfDNA). For each of the plurality of sequence reads associated with cfDNA molecules, a candidate indel may be identified. Each candidate indel may then be classified as either a true indel or an introduced indel, using a combination of predetermined expectations of (i) an indel being detected in one or more sequence reads, (ii) that a detected indel is a true indel present in a given cfDNA molecule, given that an indel has been detected in the one or more of the sequence reads, and/or (iii) that a detected indel is introduced by non-biological error, given that an indel has been detected in the one or more of the sequence reads, in conjunction with one or more model parameters to perform a hypothesis test.
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公开(公告)号：US11149307B2
公开(公告)日：2021-10-19
申请号：US17167974
申请日：2021-02-04
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：US11118221B2
公开(公告)日：2021-09-14
申请号：US16672267
申请日：2020-01-07
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：US11091797B2
公开(公告)日：2021-08-17
申请号：US17070843
申请日：2020-10-14
IPC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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