Simultaneous genotyping of single nucleotide polymorphisms in the IL-1 gene complex by multiplex polymerase chain reaction-restriction fragment length polymorphism.

The interleukin-1 (IL-1) gene complex consists of the IL-1alpha, IL-1beta and IL-1 receptor antagonist genes. Single-nucleotide polymorphisms (SNP) in all three genes have been associated with human diseases. In this study, primers containing mismatches at 1-3 nucleotide positions were designed to incorporate a restriction site for endonuclease AlwNI or XcmI in the presence of allele-specific nucleotides at the polymorphic positions. Based on this technique, a simple and robust multiplex polymerase chain reaction/restriction fragment length polymorphism (multiplex PCR/RFLP) assay was developed to determine simultaneously three to four informative SNPs (IL-1beta/+3954, IL-1beta/-511 and IL-1Ra/9261 or IL-1alpha/-889, IL-1beta/-31, IL-1beta/5810 and IL-1Ra/11100 SNPs) in the IL-1 gene complex.