Tuziak Tomasz, Jeong Joon, Majewski Tadeusz, Kim Mi-Sook, Steinberg Jordan, Wang Zhi, Yoon Dong-Sup, Kuang Tang C, Baggerly Keith, Johnston Dennis, Czerniak Bogdan
Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Lab Invest. 2005 May;85(5):689-701. doi: 10.1038/labinvest.3700270.
We attempted to identify deleted segments in two model tumor suppressor gene loci on chromosomes 13q14 and 17p13 that were associated with clonal expansion of in situ bladder preneoplasia using single nucleotide polymorphisms (SNPs)-based whole-organ histologic and genetic mapping. For mapping with SNPs, the sequence-based maps spanning approximately 27 and 5 Mb centered around RB1 and p53, respectively, were assembled. The integrated gene and SNP maps of the regions were used to select 661 and 960 SNPs, which were genotyped by pyrosequencing. Genotyping of SNPs was performed on DNA samples corresponding to histologic maps of the entire bladder mucosa in human cystectomy specimens with invasive urothelial carcinoma. By using this approach, we have identified deleted regions associated with clonal expansion of intraurothelial neoplasia; which ranged from 0.001 to 4.3 Mb (average 0.67 Mb) and formed clusters of discontinuous deleted segments. The high resolution of such maps is a prerequisite for future positional targeting of genes involved in early phases of bladder neoplasia. This approach also permits analysis of the overall genomic landscape of the involved region and discloses that a unique composition of noncoding DNA characterized by a high concentration of repetitive sequences may predispose to deletions.
我们试图利用基于单核苷酸多态性（SNP）的全器官组织学和基因图谱，确定13q14和17p13染色体上两个模型肿瘤抑制基因位点中的缺失片段，这些片段与原位膀胱肿瘤前病变的克隆性扩增相关。为了用SNP进行图谱绘制，分别构建了以RB1和p53为中心、跨度约27 Mb和5 Mb的基于序列的图谱。利用这些区域的整合基因和SNP图谱选择了661个和960个SNP，通过焦磷酸测序进行基因分型。对浸润性尿路上皮癌患者膀胱切除标本中整个膀胱黏膜组织学图谱对应的DNA样本进行SNP基因分型。通过这种方法，我们确定了与尿路上皮内瘤变克隆性扩增相关的缺失区域；其范围为0.001至4.3 Mb（平均0.67 Mb），并形成了不连续缺失片段的簇。这种图谱的高分辨率是未来对参与膀胱肿瘤形成早期阶段的基因进行定位靶向的先决条件。这种方法还允许分析相关区域的整体基因组格局，并揭示以高浓度重复序列为特征的非编码DNA的独特组成可能易导致缺失。
