title: Current trend of annotating single nucleotide variation in humans--A case study on SNVrap.
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.
authors.affiliation: Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.
authors.forename: Mulin Jun
authors.initials: MJ
authors.lastname: Li
authors.affiliation: Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China. Electronic address: junwen@hku.hk.
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D005786:Gene Expression Regulation; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods* / Q000639:trends; D020641:Polymorphism, Single Nucleotide
keywords: Functional annotation; Functional prediction; Next generation sequencing; Single nucleotide variation; Web server