Linkage disequilibrium and haplotype analysis of two single nucleotide polymorphisms in STK15 in Chinese

STK15 (Serine/Threonine protein kinase 15) is a serine/threonine kinase encoding gene, whose overexpression in mammalian cells leads to centrosome amplification, chromosomal instability, and oncogenic transformation. 91A-->T, a single nucleotide polymorphism (SNP) in exon 3 of STK15, has recently been shown to be associated with human cancer susceptibility. Within exon 3 of STK15, there are three nonsynonymous SNPs: 91 A-->T, 169G-->A and 311C-->T. We have determined STK15 genotypes and haplotypes composed of 91A-->T and 169G-->A by PCR-RFLP in a randomly sampled cohort of 193 normal individuals from Northeast China. DNA samples from all individuals were subjected to first round of PCR using a pair of specific primers. For the subsequent nested PCR,a mismatch forward primer, which could introduce an EcoR I restriction site to the 91A allele, was included. The nested PCR products were digested with the restriction endonucleases EcoRI and AccII. The double restriction digests were separated by polyacrylamide gel electrophoresis. Three haplotypes,91A-169G, 91T-169A and 91T-169G, were detected and their frequencies were 68.65%, 10.88% and 20.47%, respectively. Six genotypes composed of the above three haplotypes were found,and their frequencies were 91A-169G/91 A-169G (46.11%), 91A-169G/91 T-169A (14.51%), 91A-169G/91T-169G (30.57%), 91T-169G/91T-169G (3.11%), 91T-169G/91T-169A (4.15%), 91T-169A/91T-169A (1.55%). Whereas no 91A-169A haplotype was detected in all individuals examined in the current study, linkage disequilibrium (LD) between the two SNPs was found.