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Reliability and utility of single nucleotide polymorphisms for genetic association studies

Part 2. Genomics

2.6. SNPs/Haplotypes

Specialist Review

  1. C. Leigh Pearce1,
  2. Joel N. Hirschhorn2,3,4

Published Online: 15 NOV 2005

DOI: 10.1002/047001153X.g206206

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Pearce, C. L. and Hirschhorn, J. N. 2005. Reliability and utility of single nucleotide polymorphisms for genetic association studies. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2:2.6:69.

Author Information

  1. 1

    USC/Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA, USA

  2. 2

    Children's Hospital, Boston, MA, USA

  3. 3

    Harvard Medical School, Boston, MA, USA

  4. 4

    Broad Institute of Harvard and MIT, Cambridge, MA, USA

Publication History

  1. Published Online: 15 NOV 2005

Abstract

Single-nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the human genome. Significant efforts have been made to attempt to understand their association to common diseases and complex traits. Genetic association studies, however, have been plagued by inconsistent results. The reliability of SNP-based association studies is reviewed in the light of their limited success. The validity, comprehensiveness, and usefulness of the public SNP database (dbSNP) is evaluated, followed by a detailed discussion of why these studies have proven so difficult to replicate. Potential approaches to minimize the inconsistency across studies are considered. We show that while the coverage of the public SNP database is adequate to conduct comprehensive and meaningful association studies, methodological concerns must be taken into account.

Keywords:

  • single-nucleotide polymorphisms;
  • genetic association studies;
  • population substructure;
  • linkage disequilibrium;
  • multiple hypothesis testing