Systems and methods for identifying and quantifying gene copy number variations

A system for identifying and quantifying copy number variations in a gene of interest from a genomic DNA sample, the system comprising:

• (1) a next generation sequencing device that:
• (i) fragments a genomic DNA sample having an unknown copy number for regions of a target gene to produce a plurality of polynucleotide fragments;
• (ii) isolates a plurality of target polynucleotide from the plurality of polynucleotide fragments by using a plurality of breakpoint probes to isolate target polynucleotide fragments comprising one or more breakpoint regions, each of the plurality of target polynucleotide fragments including at least a portion of the target gene, wherein the plurality of breakpoint probes target a chromosome region where one or more breakpoints in structural variation are selected from the group consisting of:
• duplication, deletion, insertion, translocation, interchange, fusion, and inversion that have been observed in one or more other samples;
• and
• (iii) sequences the plurality of target polynucleotide fragments to obtain a plurality of fragment sequences;
• (2) an alignment module, stored in memory, that aligns fragment sequences of the plurality of fragment sequences to a reference sequence;
• (3) a read depth module, stored in memory, that:
• (i) calculates read depths for base positions of the plurality of target polynucleotide fragments relative to each base position of the reference sequence;
• and
• (ii) calculates copy number likelihoods for each base position of the reference sequence based on the read depths to make a call on at least one copy number variation in the target gene;
• (4) a breakpoint module, stored in memory, that performs a breakpoint analysis on a set of fragment sequences of the plurality of fragment sequences to:
• (i) identify at least one sequence variation located between selected breakpoint regions of the target gene, wherein the selected breakpoint regions comprise sequence regions that include a breakpoint between adjacent base pairs that result in the at least one sequence variation, and wherein the breakpoint comprises a point in a sequencing read located between a region of the target gene that matches the reference sequence and a region of the target gene that differs from the reference sequence;
• and
• (ii) calculate modified copy number likelihoods for base positions of the reference sequence based on the at least one sequence variation, the modified copy number likelihoods each including a modification to a respective copy number likelihood indicating an increase or decrease in evidence for a copy number variation in the target gene at the corresponding base position of the reference sequence;
• (5) a copy number module, stored in memory, that corrects, based on the modified copy number likelihoods for the base positions of the reference sequence, the call on the at least one copy number variation in the target gene when the modified copy number likelihoods breach a threshold probability;
• and
• (6) at least one physical processor that executes the alignment module, the read depth module, the breakpoint module, and the copy number module.