An approach for determination of copy number variation using short-read next-generation sequencing

Contributors

Kaajal Reeves^a , Mafalda Bourbon^b,c, Sandra Kachhia^a , Douglas Hurd^a , James Reid^a , Duarte Molha^a , Darren Houniet^a and John Cousin^a

^aOxford Gene Technology (OGT); ^bUnidade de I&D; ^cBioISI-Biosystems & Integrative Sciences Institute

Introduction

The ability to determine Copy Number Variation (CNV) from short-read Next Generation Sequencing (NGS) data would enable laboratories to determine both CNV and Single Nucleotide Variation (SNV) simultaneously in one assay. To date, most NGS CNV analysis approaches have been designed for whole genome/exome sequencing and besides being less robust than standard array comparative genomic hybridisation (aCGH), they are not suitable for small targeted NGS panels. In this study, we describe a method for detecting exonic CNVs using targeted NGS panels and a bioinformatics approach. This is demonstrated with the LDLR gene, involved in Familial Hypercholesterolaemia (FH) which is thought to have a prevalence between 1/500 and 1/200¹ ; and the DMD gene on the X chromosome, involved in Duchenne muscular dystrophy (DMD) which has an estimated prevalence of 1/3500 of male births².