SYSTEMS AND METHODS FOR IDENTIFYING AND QUANTIFYING GENE COPY NUMBER VARIATIONS

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.