Objective: To search novel SNPs in exons and regulatory regions of CDKN2A and two novel putative tumor suppressor genes NGX6 and UBAP1, which all reside on chromosome 9p21-22.
Methods: The exons and regulatory regions of those genes were amplified and sequenced in 96 subjects.
Results: Two novel SNPs were found, one resides on the sixth exon of UBAP1 gene and the other on the fourth exon of CDKN2A gene. Two novel SNPs were submitted to the dbSNP database, and their access ID are rs3135929 and rs3088440. The polymorphic information contents of them are 0.102 and 0.213 respectively. There is linkage equilibrium between them, and the polymorphic information content of their haplotype is 0.302, higher than any of them individually.
Conclusion: The polymorphic information content can be improved by using haplotype analysis of several SNPs.