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公开(公告)号：US20240363195A1
公开(公告)日：2024-10-31
申请号：US18765053
申请日：2024-07-05
摘要： A computer-implemented method for inferring genetic ancestry from low-coverage genomic data may include (i) generating a reference matrix representing a genetic reference panel in terms of dosages for given reference samples at given loci, (ii) decomposing the reference matrix via non-negative matrix factorization into an ancestral genotype matrix and an ancestral attribution matrix, (iii) resampling the reference matrix, (iv) deriving an ancestral alternate reads matrix that, when multiplied with the ancestral attribution matrix, approximates the resampled reference matrix, (v) deriving an ancestral attribution vector that, when multiplied with the ancestral alternate reads matrix, approximates a vector representing the test sample, and (vi) determining the genetic ancestry of the subject based on the ancestral attribution vector. Various other methods, systems, and computer-readable media are also disclosed.
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公开(公告)号：US20240294990A1
公开(公告)日：2024-09-05
申请号：US18665479
申请日：2024-05-15
IPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874
CPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874
摘要： The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.
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公开(公告)号：US12080383B2
公开(公告)日：2024-09-03
申请号：US16659449
申请日：2019-10-21
发明人： A. Scott Patterson , Imran S. Haque , Eric A. Evans , Clement Chu
摘要： The present disclosure relates to processes for determining the number of nucleic acid repeats in a DNA fragment comprising a nucleic acid repeat region. One example method may include receiving DNA size and abundance data generated by resolving DNA amplification products. A set of low-pass data may be generated by applying a low-pass filter to the DNA size and abundance data and a set of band-pass data may be generated by applying a band-pass filter to the DNA size and abundance data. A peak of the DNA size and abundance data representative of a number of nucleic acid repeats in the DNA may be identified based on peaks identified from the low-pass data and the band-pass data.
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公开(公告)号：US20240271224A1
公开(公告)日：2024-08-15
申请号：US18633462
申请日：2024-04-11
IPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874
CPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874
摘要： The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.
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公开(公告)号：US20230170046A1
公开(公告)日：2023-06-01
申请号：US18075387
申请日：2022-12-05
摘要： A computer-implemented method for Error! Reference source not found. may include (i) generating a reference matrix representing a genetic reference panel in terms of dosages for given reference samples at given loci, (ii) decomposing the reference matrix via non-negative matrix factorization into an ancestral genotype matrix and an ancestral attribution matrix, (iii) resampling the reference matrix, (iv) deriving an ancestral alternate reads matrix that, when multiplied with the ancestral attribution matrix, approximates the resampled reference matrix, (v) deriving an ancestral attribution vector that, when multiplied with the ancestral alternate reads matrix, approximates a vector representing the test sample, and (vi) determining the genetic ancestry of the subject based on the ancestral attribution vector. Various other methods, systems, and computer-readable media are also disclosed.
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公开(公告)号：US20220267837A1
公开(公告)日：2022-08-25
申请号：US17694443
申请日：2022-03-14
IPC分类号： C12Q1/6827
摘要： Disclosed is a method of determining whether a human subject is not a carrier of spinal muscular atrophy (SMA). This method includes the steps of (i) collecting a genomic deoxyribonucleic acid (DNA) sample from a human subject; (ii) screening the genomic DNA sample to determine the human subject's copy number of survival of motor neuron 1 (SMN1) gene and whether one of the copies of the SMN1 gene is positive for a polymorphism associated with non-carriers of SMA having two copies of the SMN1 gene; and (iii) determining the human subject as not a carrier of SMA if the human subject includes two copies of the SMN1 gene with one of those copies being positive for the polymorphism. Also disclosed is a method of determining whether an individual has a decreased risk of being a carrier of spinal muscular atrophy (SMA), where the individual is identified to have a decreased risk of being a carrier of SMA when the individual has two copies of the SMN1 gene with one of those copies being positive for the polymorphism.
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公开(公告)号：US20210180050A1
公开(公告)日：2021-06-17
申请号：US17187211
申请日：2021-02-26
发明人： Henry H. Lai , Clement S. Chu
IPC分类号： C12N15/10 , C12Q1/6806 , C12Q1/686 , C12Q1/6855
摘要： High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.
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公开(公告)号：US20240352511A1
公开(公告)日：2024-10-24
申请号：US18638528
申请日：2024-04-17
IPC分类号： C12Q1/6858 , C12Q1/6869 , G16B20/10 , G16B30/10
CPC分类号： C12Q1/6858 , C12Q1/6869 , G16B20/10 , G16B30/10
摘要： A method of identifying and quantifying copy number variations in a gene of interest for a genomic DNA sample includes (i) fragmenting a genomic DNA sample to produce a plurality of polynucleotide fragments, (ii) isolating a plurality of target polynucleotide fragments, (iii) sequencing the plurality of target polynucleotide fragments, (iv) aligning fragment sequences to a reference sequence, (v) calculating read depths for base positions of the plurality of target polynucleotide fragments, (vi) calculating copy number likelihoods for each base position of the reference sequence, (vii) performing a breakpoint analysis on a set of fragment sequences to identify at least one sequence variation located between selected breakpoint regions of the target gene and calculate modified copy number likelihoods for base positions of the reference sequence based on the at least one sequence variation, and (viii) determining whether the target gene includes at least one copy number variation.
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公开(公告)号：US12024749B2
公开(公告)日：2024-07-02
申请号：US16784761
申请日：2020-02-07
IPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874
CPC分类号： C12Q1/6886 , C12Q1/6818 , C12Q1/6874 , C12Q1/6818 , C12Q2521/113 , C12Q2521/327 , C12Q2531/113
摘要： The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.
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公开(公告)号：US11854666B2
公开(公告)日：2023-12-26
申请号：US15720351
申请日：2017-09-29
IPC分类号： G16B20/10 , G16B20/00 , G16B30/00 , G16B40/00 , G16B30/10 , G16B40/30 , G16B20/20 , C12Q1/6869 , C12Q1/6883 , C12Q1/6809
CPC分类号： G16B20/10 , C12Q1/6869 , C12Q1/6883 , G16B20/00 , G16B30/00 , G16B30/10 , G16B40/00 , G16B40/30 , C12Q1/6809 , G16B20/20 , C12Q1/6869 , C12Q2535/122 , C12Q2537/165
摘要： Fetal maternal samples taken from pregnant women include both maternal cell-free DNA and fetal cell-free DNA. Described herein are methods for determining a chromosomal abnormality of a test chromosome or a portion thereof in a fetus by analyzing a test maternal sample of a woman carrying said fetus, wherein the test maternal sample comprises fetal cell-free DNA and maternal cell-free DNA. The chromosomal abnormality can be, for example, aneuploidy or the presence of a microdeletion. In some embodiments, the chromosomal abnormality is determined by measuring a dosage of the test chromosome or portion thereof in the test maternal sample, measuring a fetal fraction of cell-free DNA in the test maternal sample, and determining an initial value of likelihood that the test chromosome or the portion thereof in the fetal cell-free DNA is abnormal based on the measured dosage, an expected dosage of the test chromosome or portion thereof, and the measured fetal fraction.
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