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

An integrated approach for copy number variation discovery in parent-offspring trios

Whole-genome sequencing (WGS) of parent-offspring trios has become widely used to identify causal copy number variations (CNVs) in rare and complex diseases. Existing CNV detection approaches usually do not make effective use of Mendelian inheritance in parent-offspring trios and yield low accuracy. In this study, we propose a novel integrated approach, TrioCNV2, for jointly detecting CNVs from WGS data of the parent-offspring trio. TrioCNV2 first makes use of the read depth and discordant read pairs to infer approximate locations of CNVs and then employs the split read and local de novo assembly approaches to refine the breakpoints. We use the real WGS data of two parent-offspring trios to demonstrate TrioCNV2's performance and compare it with other CNV detection approaches. The software TrioCNV2 is implemented using a combination of Java and R and is freely available from the website at https://github.com/yongzhuang/TrioCNV2.

Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios

Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.