Identification of two new HLA-A alleles, A*2419 and A*3011, by sequence-based typing

Polymorphism of intron 4 in HLA-A, -B and -C genes

The sequence database of HLA class I genes focuses on the coding sequences, the exons. Limited information is available on the non-coding sequences of the different class I alleles. In this study we have determined the intron 4 nucleotide sequence of at least one representative of each major allelic group of HLA-A, -B and -C. The intron 4 sequences were determined for 27 HLA-A, 81 HLA-B and 30 HLA-C alleles by allele-specific sequencing, using primers located in adjacent exons and introns. The sequences revealed that the length of intron 4 varies with a minimum of 93 and a maximum of 124 nucleotides as a result of insertions and deletions. There were remarkable similarities and differences within HLA-A, -B and -C, as well as between them. Within HLA-A, a deletion of three nucleotides was detected in several HLA-A alleles. The HLA-B alleles could be divided into two groups with one group having a deletion of 11 nucleotides compared with the second group. Within HLA-C, all Cw*07 alleles showed remarkable differences with the other Cw alleles. Cw*07 had an insertion of three nucleotides, shared only by the Cw*17 group. Moreover, Cw*07 was found to have an aberrant nucleotide sequence. Differences between HLA-A, -B and -C alleles were also observed. Remarkable was the deletion of 20 nucleotides in all HLA-A and -B alleles compared with HLA-C, whereas the HLA-A alleles showed an insertion of one nucleotide and a deletion of three nucleotides compared with HLA-B and -C. Furthermore, 32 different polymorphic positions were detected between HLA-A, -B and -C.

Identification of HLA-A*0249 and confirmation of A*2615

A new HLA-A*02 allele, A*0249, and the confirmatory sequence of A*2615 are here reported. Both alleles were detected by irregular patterns during routine molecular typing. A*0249 showed two mismatches with A*02011 in exon 3 at positions 538 and 539, changing amino acid 156 from leucine to arginine. Remarkable was a mismatch in exon 4, at position 779, where the C of A*0201 was changed to A in A*0249. As A*0209 has the same substitution, A*0249 may have arisen from A*0209. The A*2615 allele was identical to A*2601 in exons 2 and 3 except for a single nucleotide difference at nucleotide position 180, changing codon 36 from phenylalanine to leucine. This is a unique amino acid change, as in all the class I alleles a phenylalanine was identified at this position.

Molecular and serological identification of the HLA-A*3404 allele

In this report we describe a novel HLA-A*34 allele, A*3404, which was initially detected by an unusual serological pattern in two unrelated individuals. Sequencing revealed that the new allele was identical to A*3402 in exons 2 and 3, except for a single nucleotide difference at position 238, changing codon 56 from glycine to arginine. The codon change resulted in positive serological reactions with several sera recognizing A30 and/or A31, implicating an important role for this position in epitope recognition. The allele was identified twice on the haplotype A*3404, B*1402, Cw*0802, DRB1*14, DQB1*05.