To address the new generation of problems in molecular genetic epidemiology will require the introduction of new genetic analysis technologies. This will include both the """"""""hardening"""""""" of laboratory instrumentation and the development of new informatics infrastructure and analytic tools. The LPG has explored several new technology platforms and their suitability for high-throughput genetic analysis. These include capillary electrophoresis instruments, the use of photolithographic DNA chips, enzymatic cleavage genotyping assays, and MALDI TOF mass spectrometry for genotyping. Most recently we have added a single base primer extension assay that will allow multiplexing of approximately 10 different probes in a single reaction. At optimal throughput this SNaPshot assay will allow the evaluation of roughly 5,500 single nucleotide polymorphisms (SNPs) in a 24-hour period. The LPG has designed assays for the detection of genetic polymorphisms in genes of interest to molecular epidemiology for each of these technology platforms. The utility and efficiency of protocols critical to large-scale molecular epidemiology have also been evaluated. More specifically, applications of whole genome amplification from various starting materials (paraffin tissue blocks, and buccal washes) are being explored to assess whether sufficient quantity and quality of DNA can be obtained to perform whole genome scans. The amplification of small amounts of total RNA (100ng-1ug) is also being explored for application with Affymetrix GeneChip Arrays for expression and genotyping analysis. In the area of informatics, new tools to facilitate the bridging of the laboratory to the analytic environment have been prototyped. These include testing of tools that generate WWW-based applications, which interface directly with industrial scale relational databases. In the area of analytic tools, significant effort has been invested in the generation of approaches to address the inherent heterogeneity present in human populations. Analytic approaches that utilize DNA fingerprints to measure this heterogeneity have been explored.
