Identification of Single Nucleotide Polymorphisms in Cancer-Related Genes

单核苷酸多态性（SNPs）代表了理解复杂疾病的遗传标记的丰富和有用的来源。 生物学上重要基因编码区的SNPs（cSNPs）可能会在功能上改变蛋白质产物。 我们研究了80个与癌症相关的基因的DNA序列变异性，包括癌基因、肿瘤抑制基因和参与细胞周期控制的基因。 设计扩增每个外显子和内含子边界的引物对，并用于扩增来自四个欧洲裔美国人（CEPH家族父母）、四个非洲裔美国人和四个亚裔美国人样品的DNA。共鉴定了72种变体。 为了进行癌症基因SNP的高通量基因分型，我们已经建立了用于药物代谢酶、激素受体基因、免疫应答基因和趋化因子及其受体中的已知变体的5'核酸酶（TaqMan）测定。已经设计了超过75种检测方法，并对55种进行了测试，发现可以提供准确的基因型。 这些变体已在非裔美国人乳腺癌、高加索人肺癌和中国肺癌患者的队列中进行了基因分型。 使用同一基因中的多个变体来估计单倍型频率的方法也已被测试，并显示出准确的估计。 这将允许对单个基因进行详细分析。

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 investigated the variability in DNA sequence in 80 genes related to cancer including oncogenes, tumor suppressor genes, and genes involved in cell cycle control. Primer pairs amplifying each exon and intron boundary were designed and used to amplify DNA from four European Americans (CEPH family parents), four African Americans, and four Asian American samples. A total of 72 variants have been characterized. In order 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. Over 75 assays have been designed and 55 have been tested and found to give accurate genotypes. These variants have been genotyped on cohorts of African American breast cancer, Caucasian lung cancer and Chinese lung cancer patients. Methods to use multiple variants in the same gene to estimate haplotype frequencies have also been tested and shown to give accurate estimations. This will allow detailed analysis of individual genes to be pursued.