Irregular polymerase chain reaction—sequence-specific oligonucleotide hybridization patterns reveal seven new HLA-DRB1 alleles related to DR2, DR3, DR6, DR8, and DR11: Implications for sequence-specific priming

• Published in: Human immunology 1995, Vol.42 (1), p.15-22
• Main Authors: Anholts, Jacqueline D.H., Verduyn, Willem, Parlevliet, Annie, Doxiadis, Ilias I.N., D'Amaro, Joe, Giphart, Marius J., Persijn, Guido G., Schreuder, Geziena M.Th
• Format: Article
• Language: English
• Subjects: Alleles; Amino Acid Sequence; Base Sequence; Biotin; European Continental Ancestry Group - genetics; Gene Conversion; Genetic Variation; Histocompatibility Testing; HLA-DQ Antigens - genetics; HLA-DQ beta-Chains; HLA-DR Antigens - genetics; HLA-DR Serological Subtypes; HLA-DR2 Antigen - genetics; HLA-DR3 Antigen - genetics; HLA-DR6 Antigen - genetics; HLA-DRB1 Chains; Humans; Molecular Sequence Data; Nucleic Acid Hybridization; Oligonucleotide Probes; Point Mutation; Polymerase Chain Reaction; Sequence Alignment; Sequence Homology
• ISSN: 0198-8859; 1879-1166
• DOI: 10.1016/0198-8859(94)00072-X

In the past 3 years we have typed over 7000 individuals for HLA-DRB using a nonradioactive PCR-SSO method. The use of locally developed computer programs simplified data input and the interpretation of the DRB PCR-SSO readings. In this way we detected a number of samples with unexpected hybridization patterns. DRB1 exon 2 segments of these samples were amplified, cloned, and sequenced and appeared to identify seven new DRB alleles: DRB1 ∗0304, a DRB1 ∗0301 variant, was observed in three unrelated Caucasoid individuals; DRB1 ∗1606, which is very similar to ∗1603; DRB1 ∗1113 is a ∗1101 variant with some ∗1401 sequences; DRB1 ∗1310 is ∗1301-like; DRB1 ∗1311 is similar to ∗1305 and ∗1307; DRBl ∗1416 is a ∗1401 sequence with a HV3 derived from ∗1301; DRB1 ∗0808 was found in an Ethiopian individual. Next, we studied the effectiveness of PCR-SSP typing of the newly defined DRB1 alleles. Only two variants were distinguished as odd by PCR-SSP and two were typed as regular specificities. Three alleles were not amplified by the primer sets used. As compared to PCR-SSO, the PCR-SSP typing method using currently available typing kits clearly has limitations as far as the recognition of new and variant alleles is concerned. The products of some of these new alleles may be distinguished using conventional serology.