title: HLA-DQA1 introns 2 and 3 sequencing: DQA1 sequencing-based typing and characterization of a highly polymorphic microsatellite at intron 3 of DQA1*0505.
abstract: DQA1 class II gene encodes the alpha-chain of the human leukocyte antigen (HLA)-DQ heterodimer. Sequencing-based typing (SBT) for HLA genes is the most powerful methodology described. However, most of the SBT procedures reported for HLA class II genes are not able to define complete exon 2 region. For that purpose, we have characterized introns 2 and 3 from most DQA1 alleles to design amplification procedures that were able to obtain complete exon 2 and 3 sequences from DQA1 genes. This coding information allowed us to reduce the number of ambiguities for DQA1 typing. DQA1 intron 2 and 3 characterization demonstrated the presence of two polymorphisms for alleles with the same exons 2 and 3 sequence from DQA1*05 group. Different samples including the DQA1*050101 alleles showed a single nucleotide polymorphism at position 53 of intron 2 (G53T). Additional haplotypic analysis showed the possible association of T53 allele with the Ax-Cw5-B18-DR17-DQ2 extended haplotype. On the other hand, DQA1*0505 sequencing from different control samples noticed the existence of a microsatellite (TTTC/AAAG)n located at position 126 of intron 3. Fragment length analysis demonstrated a high polymorphism for this short tandem repeat system (0505STR), defining alleles that ranged from 8 to 20 repetitions in our population.
authors.affiliation: Histocompatibility and Molecular Biology Department. Regional Transfusion Centre of Madrid, Madrid, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Balas
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Aviles
authors.forename: Manuela
authors.initials: M
authors.lastname: Alonso-Nieto
authors.forename: Loreto
authors.initials: L
authors.lastname: Zarapuz
authors.forename: Lydia
authors.initials: L
authors.lastname: Blanco
authors.forename: Felix
authors.initials: F
authors.lastname: García-Sánchez
authors.forename: Jose L
authors.initials: JL
authors.lastname: Vicario
mesh_terms: D001483:Base Sequence; D005091:Exons; D006683:HLA-DQ Antigens / Q000235:genetics*; D059848:HLA-DQ alpha-Chains; D006801:Humans; D007438:Introns / Q000235:genetics*; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D006683:HLA-DQ Antigens; D059848:HLA-DQ alpha-Chains; C069050:HLA-DQA1 antigen