The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers

• Published in: European Journal of Human Genetics
• Main Authors: Bataillon, Thomas, Mailund, Thomas, Thorlacius, Steinunn, Steingrimsson, Eirikur, Rafnar, Thorunn, Halldorsson, Magnus, Calian, Violeta, Schierup, Mikkel Heide
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2006
• Subjects: Iceland
• Online Access: https://pure.au.dk/portal/da/publications/the-effective-size-of-the-icelandic-population-and-the-prospects-for-ld-mapping-inference-from-unphased-microsatellite-markers(cb18bcc0-a495-11db-bee9-02004c4f4f50).html; https://doi.org/10.1038/sj.ejhg.5201669; http://www.nature.com/ejhg/journal/v14/n9/abs/5201669a.html

Characterizing the extent of linkage disequilibrium (LD) in the genome is a pre-requisite for association mapping studies. Patterns of LD also contain information about the past demography of populations. On this study we focus on the Icelandic population where LD was investigated in 12 regions of ~15 cM using regularly spaced microsatellite loci. In total 1753 individuals were genotyped for 179 markers. LD was estimated using a composite disequilibrium measure based on unphased data. LD decreases with distance in all 12 regions and can be detected over approximately 4 cM for the given sample size. Differences in the patterns of decrease of LD with distance among genomic regions were mostly due to two regions exhibiting respectively higher and lower proportions of pairs in LD than average within the first 4 cM. We pooled data from all regions except these two and summarized patterns of LD by computing the proportion of pairs of loci exhibiting significant LD (at the 5% level) as a function of distance. We compared observed patterns of LD with simulated datasets obtained under scenarios with varying demography and intensity of recombination. We show that unphased data allow to make inferences on scaled recombination rates from patterns of LD. Patterns of LD in Iceland suggest a genome-wide scaled recombination rate of ρ* = 200 [130–330] per cM which is equivalent to a long term effective population size of ~5000 in the range of estimates recently reported in three populations using extensive SNPs data from the HapMap project. We discuss the implication of our findings for association mapping studies using the Icelandic population and expected pattern of LD between SNPs markers.