Human Molecular Genetics Advance Access originally published online on November 12, 2003
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Human Molecular Genetics, 2004, Vol. 13, No. 1 25-33
DOI: 10.1093/hmg/ddh001
© 2004 Oxford University Press
Extent of linkage disequilibrium in a Sardinian sub-isolate: sampling and methodological considerations
1Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK, 2MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK and 3Istituto di Genetica delle Popolazioni, CNR, Alghero, Italy
Received July 16, 2003; Revised October 6, 2003; Accepted October 22, 2003
The extent of linkage disequilibrium (LD) is an important factor when designing experiments for mapping disease or trait loci using LD mapping methods. It depends on the population history and hence is a characteristic of each population. Here, we have assessed the extent of LD in a sub-isolate of the general Sardinian population (775 members of one village) using 22 polymorphic markers on chromosome 19. We found high levels of disequilibrium that extended to 8 cM, when based on D', and 11 cM when based on the significance level of the allelic association. The fact that conclusions based on both methods are similar suggests that the estimates are quite robust. We have also shown, through a simple resampling technique, that small sample sizes can overestimate both the mean value of D' and its variance up to a factor of about 2 and 16, respectively, when the number of diplotypes (the pair of haplotypes that compose the genotype) decreased from 186 to 26. We evaluated the effect on D' of the depth of the pedigree available when using phased founders, and compared the estimates with those obtained when using unphased founders, and also the effect of grouping alleles on the value of D' and the significance level. Owing to the high sampling variance of LD, we recommend the use of at least 200 unrelated individuals when characterizing the extent of LD.
* To whom correspondence should be addressed. Tel: +44 1316505440; Fax: +44 1316506564; Email: albert.tenesa{at}ed.ac.uk
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