The advantages of dense marker sets for linkage analysis with very large families.

Abstract:

:Dense sets of hundreds of thousands of markers have been developed for genome-wide association studies. These marker sets are also beneficial for linkage analysis of large, deep pedigrees containing distantly related cases. It is impossible to analyse jointly all genotypes in large pedigrees using the Lander-Green Algorithm, however, as marker density increases it becomes less crucial to analyse all individuals' genotypes simultaneously. In this report, an approximate multipoint non-parametric technique is described, where large pedigrees are split into many small pedigrees, each containing just two cases. This technique is demonstrated, using phased data from the International Hapmap Project to simulate sets of 10,000, 50,000 and 250,000 markers, showing that it becomes increasingly accurate as more markers are genotyped. This method allows routine linkage analysis of large families with dense marker sets and represents a more easily applied alternative to Monte Carlo Markov Chain methods.

journal_name

Hum Genet

journal_title

Human genetics

authors

Thomson R,Quinn S,McKay J,Silver J,Bahlo M,FitzGerald L,Foote S,Dickinson J,Stankovich J

doi

10.1007/s00439-007-0323-5

subject

Has Abstract

pub_date

2007-05-01 00:00:00

pages

459-68

issue

3-4

eissn

0340-6717

issn

1432-1203

journal_volume

121

pub_type

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