Nucleotide sequences of novel HLA-B35 subtypes

In recent reports we described novel hybridization patterns (HP) corresponding to 22 potentially new HLA-B locus alleles in a panel of 547 subjects studied by PCR-SSOP. Three of them correspond to new subtypes of B35. To confirm the hybridization results we have isolated DNA from PBL and performed PCR, DNA cloning and nucleotide sequencing. One of the alleles, locally called B-3505v was found in three individuals: two Hispanic, one Caucasoid. It differs from B^*3505 by 3 nucleotide substitutions that lead to changes in residues 94 (Ile > Thr), 95 (Ile > Leu) and 103 (Val > Leu). B-3505v differs from B^*3501 in residues 97 and 103. Another allele called B-3508v, was found in 7 individuals, (6 of 122 Toba Indians, 1 of 18 Pilaga Indians). It differs from B^*3509 in two silent nucleotide substitutions (codons 135 and 138) and in one substitution in residue 156 (Arg > Leu). The new allele has a hybrid sequence between B^* 3508 and B^*4801. A third subtype, locally called B-3504v, observed in two Hispanic individuals, is identical to B^*3512. B^*3512 differs from B^*3504 by 3 nucleotides and one amino acid. Substitutions in residue 95 contribute to the structure of specificity pocket F, 97 to C and E, and 156 to pockets D and E. Therefore it is possible that some of the new alleles may have different peptide binding profiles. Since differences in residue 156 have been shown to affect allorecognition and mediate GvHD, identification of such variants may have important implications in transplantation and perhaps in studies of immune responses to peptides and pathogens.