Treatment of uninformative families in mean allele sharing tests for linkage

Indranil Mukhopadhyay, Eleanor Feingold, Tao Wang, Robert C. Elston, Daniel E. Weeks

Research output: Contribution to journalArticle

Abstract

Using affected sibling pairs, the mean allele sharing statistic tests for linkage by testing if the mean proportion of alleles that are identical-by-descent (IBD) is equal to a half. The behavior of some versions of the mean allele sharing test statistic depends on whether or not families that are uninformative for their IBD status are included; the SIBPAL version provides less significant values when all families (informative and uninformative) are used than when only informative families are used. Here, we investigate this behavior both analytically and by simulation. Our investigation shows that the main issue is the choice of the variance estimator in the denominator of the statistic. The choice of the denominator is very important and is still not totally resolved. Our mathematical explanation supported by our simulation study might aid in the search for an optimum solution.

Original languageEnglish (US)
Article number13
JournalStatistical Applications in Genetics and Molecular Biology
Volume5
Issue number1
DOIs
StatePublished - May 12 2006
Externally publishedYes

Keywords

  • Linkage analysis
  • Mean allele sharing tests
  • SIBPAL

ASJC Scopus subject areas

  • Statistics and Probability
  • Molecular Biology
  • Genetics
  • Computational Mathematics

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