Detecting linkage disequilibrium in the presence of locus heterogeneity

Deli Wang, J. Huang

Research output: Journal article publicationJournal articleAcademic researchpeer-review

2 Citations (Scopus)


Locus heterogeneity is a common phenomenon in complex diseases and is one of the most important factors that affect the power of either linkage or linkage disequilibrium (LD) analysis. In linkage analysis, the heterogeneity LOD score (HLOD) rather than LOD itself is often used. However, the existing methods for detecting linkage disequilibrium, such as the TDT and many of its variants, do not take into account locus heterogeneity. We propose two novel likelihood-based methods, an LD-Het likelihood and an LD-multinomial likelihood, to test linkage disequilibrium (LD) that explicitly incorporate locus heterogeneity in the analysis. The LD-Het is applicable to general nuclear family data but requires a working penetrance model. The LD-multinomial is only applicable to affected sib-pair data but does not require specification of a trait model. For affected sib-pair data, both methods have similar power to detect LD under the recessive model, but the LD-multinomial model has greater power when the underlying model is dominant or additive.

Original languageEnglish
Pages (from-to)397-409
Number of pages13
JournalAnnals of Human Genetics
Issue number3
Publication statusPublished - 1 May 2006
Externally publishedYes


  • Likelihood
  • Linkage disequilibrium
  • Locus heterogeneity
  • SNP
  • Tight linkage

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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