41 - Detection of Exon-Centric Copy Number Changes and Mutations with Customizable Target Enrichment

Abstract

Although targeted exome sequencing is a cost-effective method for identifying mutations in exons, high read depths from several neighboring regions away from exons are often required to provide confident copy number determination. There are significant limitations in exome sequencing to identify accurate aberration boundaries associated with potentially important regulatory regions outside of exons such as in introns or promoters. To enable higher resolution copy number calls in and around genes/exons of interest, we have augmented exonic tiling with custom target enrichment probes designed specifically to improve copy number variation (CNV) detection in these regions while maintaining exonic coverage of single nucleotide polymorphisms (SNPs), and insertions and deletions (INDELs). Herein we describe custom OneSeq, enabling higher resolution, exon-centric CNV detection in any genes of interest. When deployed in conjunction with existing exonic probes, they improve detection of biologically relevant CNVs in and near exons, while simultaneously detecting exonic SNPs and INDELs. The targeted CNV regions can be customized to address only a subset of genes, thus maximizing sequencing efficiency. We demonstrate that our approach improves detection of copy number changes with resolution often spanning just one or a few exons. Additionally, we identify aberrations in samples with either SNP/INDEL or CNV at a particular locus, and in some cases, compound heterozygotes with different aberrations in both alleles of the same locus. The addition of customizable, exon-centric OneSeq probes provides a means to detect exonic, intronic and intergenic CNVs, together with SNPs/ INDELs in a single assay. Conflict of Interest: All authors are employees of Agilent Technologies.