We have developed a single DNA typing method which uses 144 sequence-specific primer (SSP) reactions to simultaneously detect all known HLA-A, B, C, DRB1, DRB3, DRB4, DRB5 and DQB1 specificities in an allele specific or group specific manner using the same method, reagents, PCR parameters and protocols for all loci. The results from this integrated class I & II method can be visualized on a single photographic or electronic image and hence is described as "Phototyping". Phototyping has an overall resolution greater than or equivalent to good serology and results can be obtained in under 3 hours making the method suitable for genotyping potential cadaver donor peripheral blood without serological backup. This in turn produces the potential for reducing cold ischaemia times in renal transplantation as well as the application of prospective matching to cardiac and liver transplantation. The method has capacity to detect new alleles, for example, novel amplification patterns suggestive of 4 new HLA-B alleles have been detected. The Phototyping set has been used as the sole method of HLA typing for over 1010 individuals. Phototyping is not problem-free; deviations from the standard protocol, poor quality DNA and unsuitable PCR machines can result in individual PCR failures or in incorrect assignment of antigens. Approximately 5% of genotypes were repeated (either partially or fully) because of incomplete or equivocal results.

The risk of disease associated with persistent virus infections such as HIV-I, hepatitis B and C, and human T-lymphotropic virus-I (HTLV-I) is strongly determined by the virus load. However, it is not known whether a persistent class I HLA-restricted antiviral cytotoxic T lymphocyte (CTL) response reduces viral load and is therefore beneficial or causes tissue damage and contributes to disease pathogenesis. HTLV-I-associated myelopathy (HAM͞TSP) patients have a high virus load compared with asymptomatic HTLV-I carriers. We hypothesized that HLA alleles control HTLV-I provirus load and thus inf luence susceptibility to HAM͞TSP. Here we show that, after infection with HTLV-I, the class I allele HLA-A*02 halves the odds of HAM͞TSP (P < 0.0001), preventing 28% of potential cases of HAM͞TSP. Furthermore, HLA-A*02 ؉ healthy HTLV-I carriers have a proviral load one-third that (P ‫؍‬ 0.014) of HLA-A*02 ؊ HTLV-I carriers. An association of HLA-DRB1*0101 with disease susceptibility also was identified, which doubled the odds of HAM͞TSP in the absence of the protective effect of HLA-A*02. These data have implications for other persistent virus infections in which virus load is associated with prognosis and imply that an efficient antiviral CTL response can reduce virus load and so prevent disease in persistent virus infections.

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Susceptibility to rheumatoid arthritis (RA) may be due to the presence of shared functional epitopes common to the HLA-DR (3 chains of several RA-associated haplotypes. We have obtained direct evidence for this hypothesis by using the polymerase chain reaction and sequencing the DRBI and DQBI genes from RA patients. A highly conserved epitope present on DR .8 chains of DR4 and DR1 haplotypes was found in 83% of 149 patients with classical or definite RA but was found in only 46% of 100 control individuals (P < 0.0001). Two Dw subtypes of DR4 (Dw4 and Dw14) were associated with disease susceptibility but two other subtypes (DwlO and Dw13) were not. Sequence differences between these subtypes implicate those residues around the putative antigen binding site of the DR (B molecule in the pathogenesis of RA. These data provide a basis for understanding host susceptibility to RA at a molecular level.The polymorphism in class II gene products from the major histocompatibility complex (MHC) is known to be localized in the N-terminal domain of these molecules (1), particularly in discrete regions termed allelic hypervariable regions (AHVRs) (2, 3). These influence peptide binding and T-cell recognition by their position on the a-helices and P-strands that form the sides and floor of the putative antigen binding site (4). AHVRs are often shared between several different class II alleles, suggesting that the polymorphism in these molecules has been in part generated by recombination events that have shuffled these AHVRs between haplotypes (3, 5).Identification of the exact locus within the MHC responsible for particular disease susceptibilities has become more feasible now that sequences are available for most ofthe class II alleles (3, 6). Attribution of susceptibility to a particular locus relies heavily on comparison of sequences between haplotypes that confer susceptibility or protection (7,8). Haplotypes associated with rheumatoid arthritis (RA) share a common third AHVR located between residues 67 and 74 of the ,3 chain of the HLA-DR protein (DRB); this finding has given rise to the shared-epitope hypothesis for susceptibility to this disease (9)(10)(11). This hypothesis holds that the third AHVR of certain DR4 subtypes (Dw4 and. Dw14) MATERIALS AND METHODSPatients and Controls. We recruited 149 Caucasian patients with classical or definite RA (12). All had an erosive arthropathy and had received disease-modifying drugs, but extraarticular features were not a prerequisite for inclusion. IgM rheumatoid factor was assayed (rheumatoid arthritis particle agglutination test; Fujirebio Inc., Tokyo) and considered positive in a titer of >1:40 but negative only if absent on three occasions during active disease. One hundred healthy unrelated Caucasian individuals served as controls for the DR genotyping studies. The frequencies of DR4 subtypes in 178 DR4-positive patients were compared with those in 185 healthy DR4-positive blood donors.Amplification of HLA Class H Alleles. DRB and DQBI alleles were amplified from...