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公开(公告)号：US11773451B2
公开(公告)日：2023-10-03
申请号：US16907034
申请日：2020-06-19
发明人： Aliaksandr Artsiomenka , Marcin Sikora , Catalin Barbacioru , Darya Chudova , Martina I. Lefterova
IPC分类号： C12Q1/6886 , G16B30/10 , G16B20/20 , G16B40/20
CPC分类号： C12Q1/6886 , G16B20/20 , G16B30/10 , G16B40/20
摘要： Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.
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公开(公告)号：US12106825B2
公开(公告)日：2024-10-01
申请号：US18469130
申请日：2023-09-18
发明人： Catalin Barbacioru , Marcin Sikora , Darya Chudova
IPC分类号： G16B20/20 , C12Q1/6809 , G16H50/20
CPC分类号： G16B20/20 , G16H50/20 , C12Q1/6809 , C12Q2600/156
摘要： The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.
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公开(公告)号：US11718873B2
公开(公告)日：2023-08-08
申请号：US17210202
申请日：2021-03-23
IPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869
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：US20230335219A1
公开(公告)日：2023-10-19
申请号：US18339887
申请日：2023-06-22
摘要： Methods and systems for improving callings of insertions and/or deletions by identifying genetic sequence reads having identical molecular barcodes and sequences among sequence reads from a nucleic acid sequencer, grouping the genetic reads into a family, and processing families comprising split reads to detect the insertion and/or deletion in a sample of polynucleotide molecules.
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公开(公告)号：US11008616B2
公开(公告)日：2021-05-18
申请号：US16866252
申请日：2020-05-04
IPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869
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：US20240006022A1
公开(公告)日：2024-01-04
申请号：US18469290
申请日：2023-09-18
摘要： Methods and systems for improving callings of insertions and/or deletions by identifying genetic sequence reads having identical molecular barcodes and sequences among sequence reads from a nucleic acid sequencer, grouping the genetic reads into a family, and processing families comprising split reads to detect the insertion and/or deletion in a sample of polynucleotide molecules.
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