Detection of de novo copy number deletions from targeted sequencing of trios.

Abstract

De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms. We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. MDTS is freely available as open source software from the Bioconductor repository. Supplementary data are available at Bioinformatics online.