Abstract
The recent advancement of the next generation sequencing technology has enabled the fast and low-cost detection of all genetic variants spreading across the entire human genome, making the application of whole-genome sequencing a tendency in the study of disease-causing genetic variants. Nevertheless, there still lacks a repository that collects predictions of functionally damaging effects of human genetic variants, though it has been well recognized that such predictions play a central role in the analysis of whole-genome sequencing data. To fill this gap, we developed a database named dbWGFP (a database and web server of human whole-genome single nucleotide variants and their functional predictions) that contains functional predictions and annotations of nearly 8.58 billion possible human whole-genome single nucleotide variants. Specifically, this database integrates 48 functional predictions calculated by 17 popular computational methods and 44 valuable annotations obtained from various data sources. Standalone software, user-friendly query services and free downloads of this database are available at http://bioinfo.au.tsinghua.edu.cn/dbwgfp. dbWGFP provides a valuable resource for the analysis of whole-genome sequencing, exome sequencing and SNP array data, thereby complementing existing data sources and computational resources in deciphering genetic bases of human inherited diseases.
Highlights
The identification of genetic variants responsible for human inherited diseases is one of the major tasks in medical and human genetics [1]
We have introduced dbWGFP, a database and web server of human whole-genome single nucleotide variants and their functional predictions
This database collects nearly 8.58 billion possible SNVs across the whole human genome, with each SNV described by 48 functional prediction scores and 44 valuable annotations
Summary
The identification of genetic variants responsible for human inherited diseases is one of the major tasks in medical and human genetics [1]. A majority of SNVs in whole-genome sequencing studies occur in non-coding regions, and there still lacks a repository that collects functional predictions and annotations of such variants. These facts have greatly restricted the scope of functional analysis of whole-genome sequencing data. A more comprehensive way for assessing functional implications of SNVs is to use prediction results of multiple methods to make more reliable inference With this understanding, we developed dbWGFP, a database of whole-genome single nucleotide variants and their functional predictions. We further compiled a cross-platform program to enable ultrafast search of this database and offered user-friendly web services and free downloads at http://bioinfo.au.tsinghua. edu.cn/dbwgfp
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