Allelic polymorphism in introns 1 and 2 of the HLA‐DQA1 gene

Abstract

Human leukocyte antigen (HLA) class II antigens are highly polymorphic membrane glycoproteins, encoded by the A and B genes of DR, DQ, and DP. The polymorphism is mainly located in exon 2, with the exception of DQA1. Of the 27 DQA1 alleles presently known, 18 cannot be identified on the basis of exon 2 alone, but need additional information from the other exons. DQA1 has been reported to be the most ancient class II gene. For evolutionary comparison and to assess the degree of polymorphism outside the exons, the sequences of introns 1 and 2 were determined from 30 different cell lines, encompassing 15 different DQA1 alleles. The sequences revealed major nucleotide differences between the different lineages, whereas within each lineage few differences were present. Phylogenetic analysis of intron and exon sequences confirmed this lineage specificity. Altogether, the present data indicate that the HLA-DQA1 lineages represent ancient entities. The observed variation of the introns in alleles with identical exon sequences implicates conservative selection of the exons within a given lineage. Intron sequences may provide the means to set up an accurate typing system.

HLA-DQA1 Introns 2 and 3 Sequencing: DQA1 Sequencing-Based Typing and Characterization of a Highly Polymorphic Microsatellite at Intron 3 of DQA1*0505

“…Although intron 2 sequences have been recently reported [16], we found in our population a new, single nucleotide polymorphism to those previously reported by Voorter et al Intron 2 obtained from different DQA1*050101 samples showed a single nucleotide polymorphism (T/G) at position 53. Intron 2 region from 14 additional individuals showing the haplotype DR17-DQA1*050101-DQB1* 0201 were analyzed to characterize the frequency and HLA haplotypic distribution of the T53G polymorphism.…”

“…Genbank accession numbers for DQA1 allele-associated introns are indicated in Table 3. DQA1 intron 2 sequences for 15 DQA1 alleles have been previously reported [16]. Intron 3 polymorphism analysis for the most frequent DQA1 alleles was an essential previous objective for the subsequent group-specific amplification primers design.…”

“…For DQA1 gene, besides to the described in this report for DQA1*050101, intra-allelic single-nucleotide polymorphisms have been also defined in intron 1 of DQA1*0103 and intron 2 of DQA1*010202 and DQA1*060101 alleles [16]. The presence of a high number of intronic differences for genes showing the same coding information in a reduced number of samples would suggest that intra-allelic polymorphism could be higher than described for other class II genes [23].…”

Sequence-Based Typing of the Complete Coding Sequence of DQA1 and Phenotype Frequencies in the Dutch Caucasian Population

“…Primers were initially designed based on the in- 3= sequencing primer CY5 RTCTCAAWCTTACCTTC 3= UT (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33) tron sequences of the DQA1‫1050ء‬ and ‫1030ء‬ alleles and used to sequence homozygous cell lines [21]. After elucidation of the 5= UT region and the 5= end of intron 1 the primers for exon 1 were shown to have a mismatch with several alleles.…”

“…The amplification primers for exon 2 were designed on the basis of known intron sequences [21]. They were located in conserved regions of intron 1 and 2, with only one nucleotide difference between the different allele groups.…”