Molecular Genetic Epidemiology of Leading U.S. Cancers

对35个候选位点进行了基因分型。从全血样品中分离DNA。使用具有引物延伸的均质MassEXTENDTM测定法（Sequenom，San Diego，CA; www.sequenom.com）确定单个核苷酸多态性（SNP）基因型。Sequenom是一种高通量、多重SNP基因分型化学，它采用基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF）区分等位基因特异性延伸产物。 每个SNP位点可以用2-4 ng DNA进行测定。使用定制引物（Applied Biosystems，Foster City，CA）进行短串联重复多态性片段（STRP）的PCR扩增。用ABI 3730 DNA分析仪（Applied Biosystems，Foster City，CA）检测和分离PCR产物，并使用GeneMapper 3.0软件（Applied Biosystems，Foster City，CA）进行等位基因大小测定和识别。 我们同时评估了多个基因的变体之间的相关性，将它们视为一个复合系统，并基于先前存在的生物学文献最终确定了一条途径。我们已经证明，通过将整个系统作为药物反应的标志物，可以克服评估个体遗传变异所固有的局限性，每个遗传变异对临床结果的影响很小。这一过程的关键是潜在的候选基因方法，从现有的生物学文献中已知的变异提供了一个定性的框架，在此基础上对实际数据进行定量建模。我们的应用程序的途径分析，他莫昔芬代谢的遗传网络的能力，辨别两种药物暴露之间的差异。

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.