Systems and methods for using density of single nucleotide variations for the verification of copy number variations in human embryos

A non-transitory computer-readable medium storing computer instruction for verifying a genomic variant region in an embryo, comprising:

• receiving, by one or more processors, embryo sequencing data;
• aligning, by the one or more processors, the received embryo sequencing data to a reference genome;
• identifying, by the one or more processors, a genomic variant region in the aligned embryo sequencing data;
• counting, by the one or more processors, a number of single nucleotide variants (SNVs) in the identified genomic variant region;
• normalizing, by the one or more processors, the counted number of SNVs in the identified genomic variant region against a baseline count of SNVs for a reference region corresponding to the identified genomic variant region to generate a normalized SNV density for the genomic variant region;
• and
• verifying, by the one or more processors, the identified genomic variant region, if the normalized SNV density in the identified genomic variant region satisfies a tolerance criterion.

A system for verifying a genomic variant region in an embryo, comprising:

• a data store for storing embryo sequencing data;
• a computing device communicatively connected to the data store, comprising,
• an alignment engine configured to receive and align the embryo sequencing data against a reference genome,
• a genomic variant caller configured to identify a genomic variant region in the aligned embryo sequencing data, and
• a verification engine configured to:
• count a number of single nucleotide variants (SNVs) in the identified genomic variant region and normalize the SNVs count in the identified genomic variant region against a baseline count of SNVs for a reference region corresponding to the identified genomic variant region to generate a normalized SNV density for the identified genomic variant region, and
• verify the identified genomic variant region if the normalized SNV density in the identified genomic variant region satisfies a tolerance criterion;
• and
• a display communicatively connected to the computing device and configured to display a report containing genomic variant region results from the verification engine.