Summary of MHC relatedness analyses in HapMap Europeans.

Excess MHC dissimilarity reported in Phase 2 (Hap2) European mate pairs [13] was not corroborated in an independent Phase 3 (Hap3) sample from the same population. Hap3 included individuals also present in Hap2 (“Hap2∩3”) as well as an independent cohort (“Hap3-only”). Results are ordered as follows: previous findings in Hap2 [13], their replication, and effects of minor modifications (Hap2, phased); for all Hap2 and for Hap2∩3 samples, analyses based on modified methods (Hap2, unphased); analyses of Hap3 genotypes for Hap2∩3 and Hap3-only samples as well as their union. Mean relatedness (±1 standard deviation) is shown for mate pairs and for opposite-sex non-mate pairs, along with effect size (Z) and nominal significance (P).
1Ph., phased genotypes; un., unphased genotypes.
2Het-het score (see Methods).
3Number of random trials.
4Couples remaining after exclusions due to the presence of close relatives.
5Analysis excluding the single most MHC-dissimilar couple.
6These and subsequent results were based on all possible exclusions due to relatives (see Methods).
7The P value for Hap3-only couples reflects a one-tailed test for the specific hypothesis reported in Hap2 couples.