HSC transplantation, printed

HLA typing by sequence-specific primers (PCR-SSP)

Amplification with sequence-specific primers yields only a product if the target sequences are present in the DNA sample (compare lane 7 and 8 with the figure) In total 16 primers are used for the analysis of HLA-DR4 allele.

The techniques

The procedure relies on the specificity of primer extension that is matched or mismatched with the template at its 3’end. A combination of 2 primers designed for each of 2 polymorphic sequence motifs in cis allows the identification of an allele or a group of alleles that are chracterized by these 2 motifs. The presence or absence of the 2 motifs in cis is usually detected by gel electrophoresis, but other detection methods have been developped. The method is rapid and ideally suited for small numbers of samples. Because very few sequences are absolutely allele specific, SSP combine several primer to discriminate a particular allele unambigously.


The method can be applied for low resolution typing, using primer combinations that detect all alleles within a given serotype, as well as for high resolution typing. Low resolution HLA-A/B/DR typing can be achieved by a combination of 72 primer mixes. Depending on the HLA phenotype, a combination of 300-400 different primer mixes are necessary to determine the HLA-A/B/C/DRB1/DRB3/DRB4/DRB5/DQB1 alleles in a given individual.