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
=Background=
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit.{{cite journal |vauthors=Bentley DR, Balasubramanian S, Swerdlow HP, etal |title=Accurate whole human genome sequencing using reversible terminator chemistry.|journal=Nature|year=2008|volume=456|pages=53–59|doi=10.1038/nature07517|pmid=18987734|pmc=2581791|issue=7218}} Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium,{{cite journal|vauthors=Need AC, Goldstein DB|title=Next generation disparities in human genomics: concerns and remedies.|journal=Trends in Genetics|year=2009|volume=25|pages=489–494|doi=10.1016/j.tig.2009.09.012|pmid=19836853 }} 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=
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=
SVA is developed on the Java platform.
=Authors=
SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.
References
External links
- [http://www.svaproject.org/ SVA project website]