HLA haplotype sharing was studied in 35 sibships in which there were two or more members with rheumatoid arthritis (RA). Haplotype sharing RA siblings was random in 15 sibships which included members with clinical or immunological features of autoimmune thyroid disease. In the remaining 20 'non-thyroid' sibships the frequencies of RA siblings sharing 0, 1, or 2 haplotypes were 0.04, 0.48, and 0.48 respectively (p = 0.006). 67% of RA probands in the 'thyroid' families and 90% in the other families were HLA-DR4 positive. It is suggested that there is genetic heterogeneity in the pathogenesis of RA with at least two independent genes within the major histocompatibility complex (MHC) predisposing to RA. One gene is in linkage disequilibrium with HLA-DR4, while results of comparison of DR antigen frequencies in DR4 negative RA and control groups suggest that the other is in linkage disequilibrium with HLA-DR1 and 3. In the thyroid disease families both genes are frequently present and as either may predispose to arthritis, HLA haplotype sharing is random. The frequencies of HLA haplotype sharing in the 'non-thyroid' families suggest that there is a dominant susceptibility gene in linkage disequilibrium with HLA-DR4, whose frequency is 5% and penetrance about 20%.
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