Chunk #35 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Using detected recombinations for association scans of hotspot usage
To demonstrate the utility of our recombination detection method we conducted association testing between genetic variants in the PRDM9 region (chr5:23007723–24028706) and the “hotspot usage” phenotype described in Coop et al. (2008) [39]. Substantial association in this region was also found in Kong et al. (2010) [12] and Hinch (2011) [41]. We calculated the same phenotype as Coop et al. (2008), the proportion of crossover events, , that occur in a recombination hotspot for individual (the parent). This value was corrected for the probability that events occur in one of these hotspot regions by chance via simulation.
