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公开(公告)号：WO2018144228A1
公开(公告)日：2018-08-09
申请号：PCT/US2018/014163
申请日：2018-01-18
申请人： COUNSYL, INC.
发明人： WANG, Xin , DAVISON, Daniel , HAAS, Kevin R. , EVANS, Eric A.
CPC分类号： G16B20/10 , C12Q1/686 , G16B40/00 , C12Q2537/165 , C12Q2545/101 , C12Q2561/113
摘要： A method of quantitatively determining a copy number of a gene of interest in a genomic DNA sample may include (i) determining a cycle threshold value for a target gene having an unknown copy number and a cycle threshold value for a reference gene in each of a plurality of wells of an assay plate, (ii) calculating a delta cycle threshold value for each of the plurality of wells, (iii) fitting a Gaussian mixture model to the delta cycle threshold values, (iv) generating a modified Gaussian mixture model by performing an iterative expectation-maximization routine on the Gaussian mixture model, and (v) determining the target gene copy number in each of the plurality of genomic DNA samples based on the modified Gaussian mixture model. Various other methods and systems are also disclosed.
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公开(公告)号：WO2018144449A1
公开(公告)日：2018-08-09
申请号：PCT/US2018/015934
申请日：2018-01-30
申请人： COUNSYL, INC.
CPC分类号： C12Q1/6858 , C12Q1/6869 , G16B20/10 , C12Q2537/16
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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