Human leukocyte antigen distributions do not share a copula across sub-populations

Abstract The distribution of human leukocyte antigens in the population assists in matching solid organ donors and recipients when the typing methods used do not provide sufficiently precise information. This is made possible by linkage disequilibrium (LD), where alleles co-occur more often than random chance would suggest. There is a trade-off between the high bias and low variance of a broad sample from the population and the low bias but high variance of a focused sample. Some of this trade-off could be alleviated if sub-populations shared LD despite having different allele frequencies. These experiments show that Bayesian estimation can balance bias and variance by tuning the effective sample size of the reference panel, but the LD as represented by an additive or multiplicative copula is not shared.