Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3

Marsha A. Wilcox, Elizabeth W. Pugh, Heping Zhang, Xiaoyun Zhong, Douglas F. Levinson, Giulia C. Kennedy, Ellen M. Wijsman

Research output: Contribution to journalArticle

Abstract

The papers in presentation groups 1-3 of Generic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was ∼1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use.

Original languageEnglish (US)
Pages (from-to)S7-S28
JournalGenetic epidemiology
Volume29
Issue numberSUPPL.
DOIs
StatePublished - 2005

Keywords

  • Error rate
  • GAW
  • Genome scan
  • Haplotype block
  • Information content
  • Linkage disequilibrium
  • Population structure
  • Power
  • SNP
  • STRP
  • Support interval

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

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