Linkage analysis of affected sib pairs allowing for parent-of-origin effects

Chih Chieh Wu, Sanjay Shete, Christopher I. Amos

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)

Abstract

Parent-of-origin effects, also known as genomic imprinting, exist for many mammalian genes. For imprinted genes the expression of an allele depends upon the sex of the transmitting parent. Here we have developed a method based on alleles that are shared identical by descent by affected sib pairs, that allows for parent-of-origin effects. Our method allows for sex-specific recombination rates, an important consideration in studying imprinted genes. We have also derived a tetrahedron for the true identical-by-descent frequencies accounting for parent-of-origin effects. Using this tetrahedron, we propose a robust generalized minmax test for linkage and discuss its properties in the presence of genomic imprinting. We have also performed power comparisons of various allele sharing tests and provide regions of the tetrahedron in which the different tests are optimal. We also provide useful strategies to determine the optimal tests to use while performing a genome scan.

Original languageEnglish
Pages (from-to)113-126
Number of pages14
JournalAnnals of Human Genetics
Volume69
Issue number1
DOIs
Publication statusPublished - 2005 Jan

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

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