Single Nucleotide Polymorphisms in Cancer Related Genes

单核苷酸多态性（SNPs）是了解复杂疾病的一个丰富而有用的遗传标记来源。生物学上重要基因编码区的SNPs （cSNPs）可能在功能上改变蛋白质产物。我们使用混合DNA测序来评估白种人、非裔美国人和亚洲人群中癌症相关基因的100多种多态性的频率。这允许在患者队列分型中识别有用的snp。为了对癌症基因snp进行高通量基因分型，我们建立了针对药物代谢酶、激素受体基因、免疫反应基因和趋化因子及其受体的已知变异的5′核酸酶（TaqMan）检测方法。这些变异已在非裔美国人乳腺癌、高加索人肺癌和中国肺癌患者中进行了基因分型。我们开发了一种聚合酶和参考染料的混合物，用于使用5'核酸酶（TaqMan） SNP基因分型系统进行基因分型。这种混合物提供了更好的等位基因识别，而且比商业产品便宜。我们正在将这种方法应用于384孔板，这将进一步降低成本，增加通量并减少DNA的消耗。对于无法通过TaqMan进行的分析，我们已经建立了一种基于熔体曲线的方法，只需要低成本的引物。在非裔美国人乳腺癌队列中分析了几种趋化因子和趋化因子受体基因的多态性。一些重要的关联被发现，正在更大的队列中进行分析，试图复制这些发现。利用克雷超级计算机上的高性能计算，对人类基因组中的短串联重复序列进行了详尽的搜索。这些数据在浏览器中，可以通过基因或位置进行搜索。在编码区含有三核苷酸重复序列的30个新基因被鉴定为候选疾病基因。

Single nucleotide polymorphisms (SNPs) represent an abundant and useful source of genetic markers to understand complex diseases. SNPs in coding regions (cSNPs) of biologically important genes are likely to functionally alter the protein product. We have used pooled DNA sequencing to evaluate the frequency of over 100 polymorphisms in cancer-related genes in Caucasian, African American and Asian populations. This allows the identification of SNPs useful in typing patient cohorts. To perform high throughput genotyping of cancer gene SNPs we have established 5' nuclease (TaqMan) assays for known variants in drug metabolizing enzymes, hormone receptor genes, immune response genes and chemokines and their receptors. These variants have been genotyped on cohorts of African American breast cancer, Caucasian lung cancer and Chinese lung cancer patients. We have developed a cocktail of polymerase and reference dyes for use in genotyping using the 5' nuclease (TaqMan) SNP genoptyping system. This cocktail provides better allele discrimination and is less expensive than the commercial product. We are adapting this method to 384-well plates that will allow a further reduction in cost, increase in throughput and reduced consumption of DNA. For assays that cannot be typed by TaqMan we have established a melt curve-based method that requires only low cost primers. Polymorphisms in several chemokine and chemokine receptor genes have been analyzed in an African American breast cancer cohort. Several significant associations were found that are being analyzed in larger cohorts to attempt to replicate the findings. Using high performance computing on the Cray supercomputer, an exhaustive search for short tandem repeats has been performed in the human genome. This data is in a browser and is searchable by gene or location. Thirty new genes that contain trinucleotide repeats in the coding region were identified that are candidate disease genes.