LOHA Comprehensive Assay for Single Nucleotide Polymorphism, Copy Number Variants and Loss of Heterozygosity Using SureSelect Target Enrichment

Genetic variation in the mammalian genome spans a size extreme that includes cytogenetically recognizable elements and single-nucleotide polymorphisms. Copy number variations (CNVs) are an important intermediate size class of structural variations that involve unbalanced arrangements that increase or decrease the DNA content in mammalian genomes. CNVs are responsible for a continuous spectrum of phenotypic effects ranging from adaptive traits to embryonic lethality. The technology platforms available to identify CNVs include fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and more recently next generation sequencing. More mature platforms such as FISH and aCGH suffer from low resolution of genomic regions. The rapid development of low cost short-read sequencing technologies has paved the way to detect mutations and high resolution structural variation detection in a single experiment. Here we describe a comprehensive assay that enables researchers to identify SNP, INDEL, CNV, and LOH using SureSelect target enrichment. This design can be employed as a standalone entity or in concert with other bait designs for SNP and INDEL detection. We also describe methods for data analysis and visualization.