Haplotypes and haplotype-tagging single-nucleotide polymorphism

Presentation Group 8 of Genetic Analysis Workshop 14

Lars Beckmann, Andreas Ziegler, Priya Duggal, Joan E. Bailey-Wilson

Research output: Contribution to journalArticle

Abstract

Moderately dense maps of single-nucleotide polymorphism (SNP) markers across the human genome for both the simulated data set and data from the Collaborative Study of the Genetics of Alcoholism were available at Genetic Analysis Workshop 14 for the first time. This allowed examination of various novel and existing methods for haplotype analyses. Three contributors applied Mantel statistics in different ways for both linkage and association analysis by using the shared length between two haplotypes at a marker locus as a measure of genetic similarity. The results indicate that haplotype-sharing based on Mantel statistics can be a powerful approach and needs further methodological evaluation. Four contributors investigated haplotype-tagging SNP (htSNP) selection procedures, two contributors examined the use of multilocus haplotypes compared to single loci in association tests, and two contributors compared the accuracy of various methods for reconstructing haplotypes and estimating haplotype frequencies for both pedigree data and data from unrelated individuals. For all three different tasks, software packages and procedures gave similar results in regions of high linkage disequilibrium (LD). However, they were not as consistent in regions of moderate to low LD. One coalescence-based approach for estimating haplotype frequencies, coupled with a Markov chain Monte Carlo technique, outperformed the other haplotype frequency estimation methods in regions of low LD. In conclusion, regardless of the task, results were similar in chromosomal regions of high LD. However, based on the differing results observed here, methodological improvements are required for chromosomal regions of low to moderate LD.

Original languageEnglish (US)
JournalGenetic Epidemiology
Volume29
Issue numberSUPPL.
DOIs
StatePublished - 2005
Externally publishedYes

Fingerprint

Haplotypes
Single Nucleotide Polymorphism
Education
Linkage Disequilibrium
Markov Chains
Human Genome
Pedigree
Alcoholism
Software

Keywords

  • Association analysis
  • Genome-wide analysis
  • Haplotype-sharing
  • Haplotype-tagging
  • Linkage analysis
  • Multiple testing
  • Single-nucleotide polymorphism

ASJC Scopus subject areas

  • Genetics(clinical)
  • Epidemiology

Cite this

Haplotypes and haplotype-tagging single-nucleotide polymorphism : Presentation Group 8 of Genetic Analysis Workshop 14. / Beckmann, Lars; Ziegler, Andreas; Duggal, Priya; Bailey-Wilson, Joan E.

In: Genetic Epidemiology, Vol. 29, No. SUPPL., 2005.

Research output: Contribution to journalArticle

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