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The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.

Publication ,  Journal Article
Saul, R; Lutz, MW; Burns, DK; Roses, AD; Chiba-Falek, O
Published in: Hum Mutat
September 2016

Short structural variants (SSVs) are short genomic variants (<50 bp) other than SNPs. It has been suggested that SSVs contribute to many human complex traits. However, high-throughput analysis of SSVs presents numerous technical challenges. In order to facilitate the discovery and assessment of SSVs, we have developed a prototype bioinformatics tool, "SSV evaluation system," which is a searchable, annotated database of SSVs in the human genome, with associated customizable scoring software that is used to evaluate and prioritize SSVs that are most likely to have significant biological effects and impact on disease risk. This new bioinformatics tool is a component in a larger strategy that we have been using to discover potentially important SSVs within candidate genomic regions that have been identified in genome-wide association studies, with the goal to prioritize potential functional/causal SSVs and focus the follow-up experiments on a relatively small list of strong candidate SSVs. We describe our strategy and discuss how we have used the SSV evaluation system to discover candidate causal variants related to complex neurodegenerative diseases. We present the SSV evaluation system as a powerful tool to guide genetic investigations aiming to uncover SSVs that underlie human complex diseases including neurodegenerative diseases in aging.

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Published In

Hum Mutat

DOI

EISSN

1098-1004

Publication Date

September 2016

Volume

37

Issue

9

Start / End Page

877 / 883

Location

United States

Related Subject Headings

  • Software
  • Humans
  • Genomics
  • Genome-Wide Association Study
  • Genetics & Heredity
  • Genetic Variation
  • Genetic Predisposition to Disease
  • Computational Biology
  • 3202 Clinical sciences
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
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Saul, R., Lutz, M. W., Burns, D. K., Roses, A. D., & Chiba-Falek, O. (2016). The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants. Hum Mutat, 37(9), 877–883. https://doi.org/10.1002/humu.23023
Saul, Robert, Michael W. Lutz, Daniel K. Burns, Allen D. Roses, and Ornit Chiba-Falek. “The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.Hum Mutat 37, no. 9 (September 2016): 877–83. https://doi.org/10.1002/humu.23023.
Saul R, Lutz MW, Burns DK, Roses AD, Chiba-Falek O. The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants. Hum Mutat. 2016 Sep;37(9):877–83.
Saul, Robert, et al. “The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants.Hum Mutat, vol. 37, no. 9, Sept. 2016, pp. 877–83. Pubmed, doi:10.1002/humu.23023.
Saul R, Lutz MW, Burns DK, Roses AD, Chiba-Falek O. The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants. Hum Mutat. 2016 Sep;37(9):877–883.
Journal cover image

Published In

Hum Mutat

DOI

EISSN

1098-1004

Publication Date

September 2016

Volume

37

Issue

9

Start / End Page

877 / 883

Location

United States

Related Subject Headings

  • Software
  • Humans
  • Genomics
  • Genome-Wide Association Study
  • Genetics & Heredity
  • Genetic Variation
  • Genetic Predisposition to Disease
  • Computational Biology
  • 3202 Clinical sciences
  • 3105 Genetics