Allelic imbalance analysis of oral tongue squamous cell carcinoma by high-density single nucleotide polymorphism arrays using whole-genome amplified DNA.
Allelic imbalance analysis of oral tongue squamous cell carcinoma by high-density single nucleotide polymorphism arrays using whole-genome amplified DNA.
复制标题
使用全基因组扩增 DNA 通过高密度单核苷酸多态性阵列对口腔舌鳞状细胞癌进行等位基因不平衡分析。
DOI：
10.1007/s00439-005-0069-x
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发表时间：
2005
期刊：
影响因子：
5.3
通讯作者：
Wong,DavidTW
中科院分区：
文献类型：
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作者：
Zhou,Xiaofeng;Temam,Stephane;Chen,Zugen;Ye,Hui;Mao,Li;Wong,DavidTW
基于多重置换的全基因组DNA扩增是一种很有前途的工具，可以从小组织样本中获得足够的DNA，用于各种遗传分析，如基于SNP阵列的分析。使用Affymetrix 10K和100K SNP定位阵列，我们评估了基于Phi29 DNA聚合酶的基因组扩增的性能。两个阵列的扩增DNA和非扩增DNA在基因分型呼叫中获得了大于99%的一致性。利用Affymetrix基因芯片染色体拷贝数工具，根据10K和100K SNP定位阵列结果生成晚期口腔舌鳞状细胞癌(OTSCC)的等位基因失衡图谱。这两个阵列平台的结果非常吻合，但从100kSNP定位阵列数据中可以揭示更精确的等位基因失衡模式。此外，我们的数据显示，晚期OTSCC的3p11-p12经常丢失。
Multiple displacement-based whole-genome DNA amplification is a promising tool to obtain sufficient DNA from small tissue specimens for various genetic analyses, such as SNP array-based analysis. Using Affymetrix 10 K and 100 K SNP mapping array, we evaluated the performance of the Phi29 DNA polymerase-based genome amplification. Greater than 99% concordance in genotyping calls were achieved between amplified and non-amplified DNAs for both arrays. By utilizing the Affymetrix GeneChip Chromosome Copy Number Tool, the allelic imbalance profiles for the advanced stage oral tongue squamous cell carcinoma (OTSCC) were generated based on 10 K and 100 K SNP mapping array results. The results from these two array platforms agree closely, but more precise allelic imbalance patterns can be revealed from the 100 K SNP mapping array data. Furthermore, our data suggested a frequent loss at 3p11–p12 for advanced stage OTSCC.