Fluorescent-based Single-strand Conformation Polymorphism/Heteroduplex Capillary Electrophoretic Mutation Analysis of the P53 Gene

Genotyping of single nucleotide polymorphism in MDM2 genes by universal fluorescence primer PCR and capillary electrophoresis

Single nucleotide polymorphism (SNP) 309 in the promoter region of the murine double minute 2 (MDM2) gene plays an important role in human tumorigenesis. We established a simple and effective CE method for SNP detection in the MDM2 gene. We designed one universal fluorescence-based nonhuman-sequence primer and one fragment-oriented primer, which were combined in one tube, and proceeded with the polymerase chain reaction (PCR). The amplicons were analyzed by capillary electrophoresis using single-strand conformation polymorphism method. PCR fragments generated from this two-in-one PCR displayed either T/T or G/G homozygosity or T/G heterozygosity. A total of 304 samples were blindly genotyped using this developed method, which included the DNA from 138 healthy volunteers, 43 chronic myeloid leukemia (CML) patients, and 123 colorectal cancer (CRC) patients. The results were confirmed by DNA sequencing and showed good agreement. The SSCP-CE method was feasible for SNP screening of MDM2 in large populations.

Capillary electrophoresis of gene mutation

This chapter illustrates the usefulness of capillary electrophoresis (CE) for the detection of gene mutation, i.e., point mutation, methylation, and microsatellite analysis. In order to provide a general description of the main results and challenges in the field, some relevant applications and reviews on CE of gene mutation are tabulated. Furthermore, some detailed experimental procedures are shown. Several CE methods of gene mutation detection were developed including the following: (1) single-strand conformation polymorphism with capillary electrophoresis; (2) SNaPshot analysis; (3) constant denaturant capillary electrophoresis; (4) microsatellite analysis; and (5) methylation analysis.

Simultaneous analysis of microsatellite instability and loss of heterozygosity by capillary electrophoresis with a homemade kit

Microsatellite instability (MSI) and loss of heterozygosity (LOH), the alteration in length and strength of short tandem repeat sequences are an important molecular characteristic of many human tumors. MSI and LOH analysis has become an attractive method for diagnostic and tumor research purposes. A method for the simultaneous analysis of MSI and LOH at the five microsatellite loci (BAT-26, D17S261, D3S1283, D2S123 and D3S1611) was developed employing a cheap homemade kit to replace the expensive commercial kit on ABI 310 capillary genetic analyzer. After studying the effect of temperature and urea denaturant on microsatellite analysis, 8 mol/L urea and 60 degrees C were selected for assessing accurately fragment size of microsatellite alleles. Based on this method, 52 sporadic gastric cancers were screened, and MSI and LOH, at least one locus was observed in 15 of 52 (28.8%) patients. Moreover, it is found that a statistically significant association exists between MSI and LOH and tumor-differentiated level.