sharing 0, 1 or 2 chromosomes identical by descent for each pair of individuals (see Supplementary Text 4). In addition to identifying a few close relationships (as reported in HapMap Phase I3), we estimate that, on average, any two individuals from the same population share approximately 0.5% of their genome through recent IBD (Table 5). Using a hidden Markov model approach27 (see Supplementary Text 5), we searched for such shared segments over 1-megabase (Mb) long and containing at least 50 SNPs, after first pruning the list of SNPs to remove local linkage disequilibrium. We find that 10–30% of pairs in each analysis panel share regions of extended identity resulting from sharing a common ancestor within 10–100 generations. These regions typically span hundreds of SNPs and can extend over tens of megabases (Table 5).
