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SequenceVariantAnalyzer

From Wikipedia, the free encyclopedia

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

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Background

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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

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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

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SVA is developed on the Java platform.

Authors

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SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.

References

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  1. ^ 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.
  2. ^ 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.
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