Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping

PeerJ. 2021 Jul 26;9:e11724. doi: 10.7717/peerj.11724. eCollection 2021.

Abstract

Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.

Keywords: Annotation; Bioinformatics; Genomics; Genotyping; Pipelines; Prediction; Tools; Variants; WES; WGS.

Grant support

This work was supported by the Institute for Health, Health Care Policy and Aging Research, and Robert Wood Johnson Medical School, at Rutgers, The State University of New Jersey. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.