Recombination hotspots

This track shows recombination hotspots, downloaded from the HapMap website.

Recombination hotspots are estimated using the LDhot likelihood ratio test described in McVean et al. (2004) and Winckler et al. (2005). For successive intervals of 200kb, the maximum likelihood of a model with a constant recombination rate is compared to the maximum likelihood of a model in which the central 2kb is a recombination hotspot (likelihoods are approximated by the composite likelihood method of Hudson 2001). The observed difference in log composite likelihood is compared against the null distribution, which is obtained by simulations. Simulations are matched for sample size, SNP density, background recombination rate and an approximation to the ascertainment scheme.

Both recombination rates and hotspots were estimated separately for each HapMap analysis panel (YRI, CEU, CHB+JPT). Recombination rates were averaged across populations and p-values for hotspots were combined such that a hotspot requires that two of the three populations show some evidence of a hotspot (p<0.05) and at least one population showed stronger evidence for a hotspot (p<0.01). Hotspot centres were estimated at those locations where distinct recombination rate estimate peaks (with at least a factor of two separation between peaks) occurred, within the low p-value intervals. The width of the hotspot represents the region where the estimated rate is within a factor of two of the maximum. Last Download from Source: 2011/10/19