Computer Methods and Programs in Biomedicine
Volume 95, Issue 2 , Pages 181-189, August 2009

SNPit: A federated data integration system for the purpose of functional SNP annotation

  • Terry H. Shen

      Affiliations

    • Department of Biomedical & Health Informatics, University of Washington, Seattle, WA 98195-7240, United States
    • Corresponding Author InformationCorresponding author. Tel.: +1 206 321 2003.
    • ,
  • Christopher S. Carlson

      Affiliations

    • Department of Genome Sciences, University of Washington, Seattle, WA, United States
    • Fred Hutchinson Cancer Research Center, Seattle, WA, United States
    • ,
  • Peter Tarczy-Hornoch

      Affiliations

    • Department of Biomedical & Health Informatics, University of Washington, Seattle, WA 98195-7240, United States
    • Department of Computer Science and Engineering, University of Washington, Seattle, WA, United States
    • Department of Pediatrics, University of Washington, Seattle, WA, United States

Received 8 December 2008; received in revised form 5 February 2009; accepted 23 February 2009.

Abstract 

Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation information on SNPs. We have developed the SNP Integration Tool (SNPit) system to address this need. Built upon a federated data integration system, SNPit provides current information on a comprehensive list of SNP data sources. Additional logical inference analysis was included through an inference engine plug in. The SNPit web servlet is available online for use. SNPit allows users to go to one source for up-to-date information on the functional annotation of SNPs. A tool that can help to integrate and analyze the potential functional significance of SNPs is important for understanding the results from genome wide association studies.

Keywords: Single nucleotide polymorphisms (SNPs), Public health genetics, Biomedical informatics, Data integration, SNP annotation system, SNP integration system

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PII: S0169-2607(09)00080-7

doi:10.1016/j.cmpb.2009.02.010

Computer Methods and Programs in Biomedicine
Volume 95, Issue 2 , Pages 181-189, August 2009

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