Current trend of annotating single nucleotide variation in humans--A case study on SNVrap

Methods. 2015 Jun;79-80:32-40. doi: 10.1016/j.ymeth.2014.10.003. Epub 2014 Oct 13.

Abstract

As high throughput methods, such as whole genome genotyping arrays, whole exome sequencing (WES) and whole genome sequencing (WGS), have detected huge amounts of genetic variants associated with human diseases, function annotation of these variants is an indispensable step in understanding disease etiology. Large-scale functional genomics projects, such as The ENCODE Project and Roadmap Epigenomics Project, provide genome-wide profiling of functional elements across different human cell types and tissues. With the urgent demands for identification of disease-causal variants, comprehensive and easy-to-use annotation tool is highly in demand. Here we review and discuss current progress and trend of the variant annotation field. Furthermore, we introduce a comprehensive web portal for annotating human genetic variants. We use gene-based features and the latest functional genomics datasets to annotate single nucleotide variation (SNVs) in human, at whole genome scale. We further apply several function prediction algorithms to annotate SNVs that might affect different biological processes, including transcriptional gene regulation, alternative splicing, post-transcriptional regulation, translation and post-translational modifications. The SNVrap web portal is freely available at http://jjwanglab.org/snvrap.

Keywords: Functional annotation; Functional prediction; Next generation sequencing; Single nucleotide variation; Web server.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Alternative Splicing
  • Gene Expression Regulation
  • Genetic Variation
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Molecular Sequence Annotation / methods*
  • Molecular Sequence Annotation / trends
  • Polymorphism, Single Nucleotide*