The GPS tests performed best in immune/immune pairs but identified as associated a high proportion of ostensibly unrelated disease pairs.

The percentage of pairs for which a nominally significant (p ≤ 0.05) test statistic was computed given by number of cases and MHC inclusion status, and the median genetic correlation estimate in each group. ‘No. of cases’ gives the smaller number of disease cases in each pair of case-control UKBB GWAS. ‘Median ’ denotes the median genetic correlation estimate obtained from the exemplary data sets for each group of pairs.