Chromosomal recombination fragments multigene haplotypes as the distance to that ancestor increases in number of generations.

Among these were coeliac disease, autoimmune active chronic hepatitis, myasthenia gravis, Adrenocortical hyperfunction-Cushing's syndrome, primary biliary cirrhosis.

[14] A recent study of DR3-DQ2/DR4-DQ8 phenotype found that A1-cw7-B8 was actually lower than expected relative to other A-B types, indicating that risk associated genes are located between B8 and DR3.

[15] The type 1 diabetes example shows the inherent difficulty in the use of linkage analysis alone to cipher risk.

[22][23][24] Further asthmatic patients with negative skin tests tended toward higher A1,B8 serotypes.

This locus in part of the HLA A1-B8-DR3-DQ2 haplotype (markers are A1, CW7, B8, BfS, C4AQ0, C4B1, DR3, DQ2) therefore one study concluded that C4AQ0 could explain the increased infectivity to HIV.

[32] The association with viral hepatitis was subsequently demonstrated and patients with antinuclear antibodies were more likely to have A1-B8-DR3.