SequenceVariantAnalyzer
SequenceVariantAnalyzer (SVA) is a computer program for annotating and analyzing genetic variants called (identified) from a whole genome or exome sequencing study (Shotgun sequencing).
Introduction
[edit]Background
[edit]DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit.[1] Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium,[2] thus, in theory, is more possible to directly identify the genetic variants contributing to biological traits or medical outcomes.
The rapidly evolving high-throughput DNA sequencing technologies have now allowed the rapid generation of large amounts of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is software that analyzes genetic variants identified in such studies.
Functions
[edit]SVA is designed for two specific aims:
(1) To annotate the biological functions of the identified genetic variants and group them, conveniently;
(2) To find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest.
Language
[edit]SVA is developed on the Java platform.
Authors
[edit]SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.
References
[edit]- ^ Bentley DR, Balasubramanian S, Swerdlow HP, et al. (2008). "Accurate whole human genome sequencing using reversible terminator chemistry". Nature. 456 (7218): 53–59. doi:10.1038/nature07517. PMC 2581791. PMID 18987734.
- ^ Need AC, Goldstein DB (2009). "Next generation disparities in human genomics: concerns and remedies". Trends in Genetics. 25: 489–494. doi:10.1016/j.tig.2009.09.012. PMID 19836853.