wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders

Abstract

With the rapid advances in high-throughput sequencing technologies, exome sequencing and targeted region sequencing have become routine approaches for identifying mutations of inherited disorders in both genetics research and molecular diagnosis. There is an imminent need for comprehensive and easy-to-use downstream analysis tools to isolate causal mutations in exome sequencing studies. We have developed a user-friendly online framework, wKGGSeq, to provide systematic annotation, filtration, prioritization, and visualization functions for characterizing causal mutation(s) in exome sequencing studies of inherited disorders. wKGGSeq provides: (1) a novel strategy-based procedure for downstream analysis of a large amount of exome sequencing data and (2) a disease-targeted analysis procedure to facilitate clinical diagnosis of well-studied genetic diseases. In addition, it is also equipped with abundant online annotation functions for sequence variants. We demonstrate that wKGGSeq either outperforms or is comparable to two popular tools in several real exome sequencing samples. This tool will greatly facilitate the downstream analysis of exome sequencing data and can play a useful role for researchers and clinicians in identifying causal mutations of inherited disorders. The wKGGSeq is freely available at http://statgenpro.psychiatry.hku.hk/wkggseq or http://jjwanglab.org/wkggseq, and will be updated frequently. © 2015 WILEY PERIODICALS, INC.