'Fingerprinting' of HLA-DQA by polymerase chain reaction and heteroduplex analysis

We have developed a rapid, non-radioisotopic PCR fingerprinting technique for analysis of the HLA-Class II DQA gene second exon polymorphism, and have applied it to DNA samples from 210 healthy individuals. The technique is based on the formation of specific patterns (fingerprints) of homoduplexes or heteroduplexes between in vitro amplified DNA sequences. After electrophoresis on non-denaturing polyacrylamide gels and ethidium bromide fluorescence or silver staining, different HLA-DQA types give allele-specific banding patterns. HLA DQA typing is done by visual comparison between the sample's fingerprint patterns and appropriate controls. Similar fingerprints can be resolved by mixing the sample with a standard DNA in an amplified 'DNA crossmatch'. This application of PCR fingerprinting is useful to confirm the HLA-DQA serological typing and to improve the molecular characterization of this polymorphic region.