Searching for epistasis and linkage heterogeneity by correlations of pedigree-specific linkage scores

Daniel J Schaid, Shannon K. McDonnell, Erin E. Carlson, Stephen N Thibodeau, Janet L. Stanford, Elaine A. Ostrander

Research output: Contribution to journalArticle

Abstract

Recognizing that multiple genes are likely responsible for common complex traits, statistical methods are needed to rapidly screen for either interacting genes or locus heterogeneity in genetic linkage data. To achieve this, some investigators have proposed examining the correlation of pedigree linkage scores between pairs of chromosomal regions, because large positive correlations suggest interacting loci and large negative correlations suggest locus heterogeneity (Cox et al. [1999]; Maclean et al. [1993]). However, the statistical significance of these extreme correlations has been difficult to determine due to the autocorrelation of linkage scores along chromosomes. In this study, we provide novel solutions to this problem by using results from random field theory, combined with simulations to determine the null correlation for syntenic loci. Simulations illustrate that our new methods control the Type-I error rates, so that one can avoid the extremely conservative Bonferroni correction, as well as the extremely time-consuming permutational method to compute P-values for non-syntenic loci. Application of these methods to prostate cancer linkage studies illustrates interpretation of results and provides insights into the impact of marker information content on the resulting statistical correlations, and ultimately the asymptotic P-values.

Original languageEnglish (US)
Pages (from-to)464-475
Number of pages12
JournalGenetic Epidemiology
Volume32
Issue number5
DOIs
StatePublished - Jul 2008

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Pedigree
Genetic Linkage
Genes
Prostatic Neoplasms
Chromosomes
Research Personnel

Keywords

  • Epistasis
  • Extreme values
  • Gene-gene interaction
  • Locus heterogeneity

ASJC Scopus subject areas

  • Genetics(clinical)
  • Epidemiology

Cite this

Searching for epistasis and linkage heterogeneity by correlations of pedigree-specific linkage scores. / Schaid, Daniel J; McDonnell, Shannon K.; Carlson, Erin E.; Thibodeau, Stephen N; Stanford, Janet L.; Ostrander, Elaine A.

In: Genetic Epidemiology, Vol. 32, No. 5, 07.2008, p. 464-475.

Research output: Contribution to journalArticle

Schaid, Daniel J ; McDonnell, Shannon K. ; Carlson, Erin E. ; Thibodeau, Stephen N ; Stanford, Janet L. ; Ostrander, Elaine A. / Searching for epistasis and linkage heterogeneity by correlations of pedigree-specific linkage scores. In: Genetic Epidemiology. 2008 ; Vol. 32, No. 5. pp. 464-475.
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