SEQUENCING-BASED TYPING REVEALS NEW INSIGHT IN HLA-DPA1 POLYMORPHISM

An HLA-DPA1 sequencing-based typing (SET) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined . Six can be discriminated based upon exon 2 polymorphism. The three s ubtypes of DPA101: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences wer e known for only the three DPA101 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown seg ments at the 3' end of exon 2. Additionally with the use of this seque ncing technique it is also possible to identify previously unidentifie d polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA101 new, was identified which differs by one nucleotide in exon 2 from DPA10103, resulting in an aspartic acid at codon 28. The DPA1*0 1 subtypes DPA10101 and DPA1*0102 could not be confirmed in samples w hich previously were used to define these subtypes, and consequently t hey do not exist. The exon 4 sequence of DPA10201 is corrected based on sequence data of DAUDI, the cell line in which DPA10202 was origin ally defined. The exon 4 regions of the remaining four alleles were re solved: the exon 4 regions; of the alleles DPA102021 and DPA1*02022 w ere found to be identical to the - corrected - DPA10201 whereas the e xon 4 region of DPA10301 differs by one nucleotide compared to DPA1*0 103. The DPA10401 exon 4 region differs by one nucleotide compared to the corrected DPA10201. As is found in other class II genes, all exo ns of DPA1 show some polymorphism but the polymorphism in exon 2 is su fficient to identify the different alleles.