Pemphigus vulgaris in Israeli Ashkenazi and non-Ashkenazi Jews and in Austrian non-Jewish patients is strongly associated with the DR4 and DRw6 alleles of the HLA-D region class II genes. Restriction fragment length polymorphism analysis was undertaken with DQ.3, DQoa, and DRP cDNA probes. Hybridization with the DQB probe identifies Pvu II, BamHI, and EcoRV fragments that absolutely discriminate pemphigus vulgaris patients from healthy DR-, DQ-, and ethnic-matched controls. In contrast the DQa and DRB probes failed to identify disease-specific restriction fragment length polymorphism fragments. These studies indicate that DQwl and DQw3 polymorphisms carried by pemphigus vulgaris patients may be directly involved in predisposition to the disease or may be tightly linked to the susceptibility gene itself. To our knowledge, this is the first example of an HLA restriction fragment length polymorphism that is highly associated with susceptibility to autoimmune disease.Pemphigus vulgaris (PV) is a dermatological autoimmune disease mediated by autoantibodies directed against an antigen, intracellular cement substance, in the basement membrane of keratinocytes, resulting in blister formation (1, 2). This disease can be reproduced in monkeys or in mice after transfer of antibodies from PV patients (1, 2). Susceptibility to PV is strongly associated with serologically defined gene products of the HLA-D region (3, 4). technique. HLA-DR and -DQ typing was done on T-celldepleted B-cell-enriched lymphocytes by extended incubation cytotoxicity testing (7). The HLA antisera included alloantisera from the third Asia-Oceania Histocompatibility Workshop and sera of local origin.DNA Extraction, Digestion, and Binding to Nylon Membranes. Genomic DNA was extracted from peripheral leukocytes. After lysis of the erythrocytes, the leukocytes were treated with proteinase K at 0.2 mg/ml (Boehringer Mannheim) for 12 hr at 42°C. Two phenol/chloroform-isoamyl alcohol, 3:1 (vol/vol), and two isoamyl alcohol/chloroform, 1:24 (vol/vol), extractions followed. Thereafter, the DNA was precipitated with two volumes of absolute ethanol. After precipitation and several washes with ethanol, the DNA was dissolved in TE (1 mM Tris HCl/0.1 mM EDTA, pH 7.5) to give a final concentration of 1 mg/ml. Ten micrograms of each DNA sample was digested with 10 units of the following restriction enzymes: BamHI, Dra I, EcoRI, EcoRV, HincII, HindIII, Pst I, Pvu II, and Taq I. Digestion was carried out for 15 hr, and the DNA samples were subjected to electrophoresis at 30 V in agarose gel (0.7% agarose in Tris acetate buffer, pH 6.4, containing ethidium bromide at 20 ,ug/ml) for 36 hr. Gels were then transferred to Hybond N membranes (Amersham) as described by Southern (8).cDNA Probes and Hybridization. The DQa cDNA probe was furnished by Charles Auffray (College de France). The DQ,3 and DR8 cDNA probes were furnished by Hugh McDevitt and John Bell (Stanford University). Full descriptions of the probes appear elsewhere (9, 10). The probes were labeled by t...