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


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Thomson, R, Quinn, SJ, McKay, JD, Silver, J, Bahlo, M, FitzGerald, L, Foote, SJ, Dickinson, JL and Stankovich, J 2007 , 'The advantages of dense marker sets for linkage analysis with very large families' , Human Genetics, vol. 121, no. 3-4 , pp. 459-468 , doi: 10.1007/s00439-007-0323-5.

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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.

Item Type: Article
Authors/Creators:Thomson, R and Quinn, SJ and McKay, JD and Silver, J and Bahlo, M and FitzGerald, L and Foote, SJ and Dickinson, JL and Stankovich, J
Journal or Publication Title: Human Genetics
Publisher: Springer
ISSN: 0340-6717
DOI / ID Number: 10.1007/s00439-007-0323-5
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