Application of Kinetic Polymerase Chain Reaction and Molecular Beacon Assays to Pooled Analyses and High- Throughput Genotyping for Candidate Genes

BACKGROUND: The addition of DNA analysis to epidemiologic studies that have traditionally incorporated demographic and interview data can provide additional power and open new avenues for investigation. DNA can be obtained from a variety of tissues, but each has attendant variation in sample quantity, quality, and cost of acquisition. Analytic approaches for DNA genotyping are under constant development, but current appli-cations allow small amounts (less than 2 ng per assay) of DNA to be used for genotyping. METHODS: In this report, we designed effective assays for a spectrum of genes using either kinetic polymerase chain reaction (PCR) or molecular beacon applications. We also investigated the extent to which DNA use and reagent cost could be minimized. Kinetic PCR assays were also applied to investigate the potential of pooled sample analysis. RESULTS: Our results show that small amounts of DNA can be successfully amplified in a high-throughput fashion using both kinetic PCR and molecular beacon methods. Greater than 97 % of the genotype results from these two methods are consistent. In addition, error rates in allele frequency measurements using DNA pools of 100 or more samples were often less than 1 % and usually less than 3%, which provides another option for substantially minimizing the costs of genotyping in studies involving large numbers of individuals. CONCLUSIONS: Effective assays have been designed for a spectrum of genes widely studied in birth defects, including: MTHFR, NAT1, TGFA, RFC1, PAX9, EPHX1, and SKI. An efficient assay has been designed for the detection of the presence of X and Y chromosomes, which can be applied to the studies of sex chromosome abnormalities or sample quality control. Birth Defects Research (Part A) 70:65–74, 2004. © 2004 Wiley-Liss, Inc