Integrative DNA copy number detection and genotyping from sequencing and array-based platforms

Motivation: Copy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large‐scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous single‐nucleotide polymorphism (SNP)‐array data are available. An integrated cross‐platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele‐specific reads. Results: We propose a statistical framework, integrated CNV (iCNV) detection algorithm, which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform‐specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP‐array data by a hidden Markov model. We compare integrated two‐platform CNV detection using iCNV to naïve intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only and show that the utilization of allele‐specific reads improve CNV detection accuracy compared to existing methods. Availability and implementation: https://github.com/zhouzilu/iCNV Supplementary information: Supplementary data are available at Bioinformatics online.