Genotyping assays were successfully carried out for 35 candidate loci. DNA was isolated from samples of whole blood. Single Necleotide polymorphism (SNP)genotypes were determined using homogeneous MassEXTENDTM assays with primer extension (Sequenom, San Diego, CA; www.sequenom.com). Sequenom is a high-throughput, multiplex SNP genotyping chemistry, which employs matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF)distinguish between the allele-specific extension products. Each SNP locus could be assayed with 2-4 ng of DNA. PCR amplification of short tandem repeat polymorphic fragments (STRPs) was performed using custom primers (Applied Biosystems, Foster City, CA) PCR products were detected and separated with an ABI 3730 DNA Analyzer (Applied Biosystems, Foster City, CA) and allele sizing and calling was carried out using GeneMapper 3.0 software (Applied Biosystems, Foster City, CA). We have evaluated correlations between variants of multiple genes simultaneously, viewing them as a composite system, and culminating in a pathway based on the pre-existing biological literature. We have shown that by treating the entire system as a marker of drug response, the limitations inherent in evaluating individual genetic variants, each conferring a minor effect on clinical outcome, can be overcome. Critical to this process is the underlying candidate gene approach, with variants known from pre-existing biological literature offering a qualitative framework on which to quantitatively model actual data. Our application of pathway analysis to the genetic network underlying tamoxifen metabolism has shown the ability to discern differences between two drug exposures.
| Wang, Zhining; Fan, Hongtao; Yang, Howard H et al. (2004) Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures. Genomics 83:395-401 |
