Rapid Detection of SNP

• Published in: PloS one 2013-04, Vol.8 (4), p.e60151
• Main Authors: Enokida, Yasuaki, Shimizu, Kimihiro, Atsumi, Jun, Lezhava, Alexander, Tanaka, Yuki, Kimura, Yasumasa, Soma, Takahiro, Hanami, Takeshi, Kawai, Yuki, Usui, Kengo, Okano, Yasuko, Kakegawa, Seiichi, Ogawa, Hiroomi, Miyamae, Yohei, Miyagi, Yohei, Nakayama, Haruhiko, Ishikawa, Toshihisa, Hayashizaki, Yoshihide, Takeyoshi, Izumi
• Format: Article
• Language: English
• Subjects: Genetic aspects; Physiological aspects; Single nucleotide polymorphisms; Tumor proteins
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0060151

Genetic polymorphisms in the human MDM2 gene are suggested to be a tumor susceptibility marker and a prognostic factor for cancer. It has been reported that a single nucleotide polymorphism (SNP) c.309T>G in the MDM2 gene attenuates the tumor suppressor activity of p53 and accelerates tumor formation in humans. In this study, to detect the SNP c.309T>G in the MDM2 gene, we have developed a new SNP detection method, named "Duplex SmartAmp," which enabled us to simultaneously detect both 309T and 309G alleles in one tube. To develop this new method, we introduced new primers i.e., nBP and oBPs, as well as two different fluorescent dyes that separately detect those genetic polymorphisms. By the Duplex SmartAmp method, the genetic polymorphisms of the MDM2 gene were detected directly from a small amount of genomic DNA or blood samples. We used 96 genomic DNA and 24 blood samples to validate the Duplex SmartAmp by comparison with results of the conventional PCR-RFLP method; consequently, the Duplex SmartAmp results agreed totally with those of the PCR-RFLP method. Thus, the new SNP detection method is considered useful for detecting the SNP c.309T>G in the MDM2 gene so as to judge cancer susceptibility against some cellular stress in the clinical setting, and also to handle a large number of samples and enable rapid clinical diagnosis.