Margolin Gennady, Petrykowska Hanna M, Jameel Nader, Bell Daphne W, Young Alice C, Elnitski Laura
Translational and Functional Genomics Branch, National Human Genome Research Institute, Rockville, Maryland.
Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland.
J Mol Diagn. 2016 Mar;18(2):283-98. doi: 10.1016/j.jmoldx.2015.11.004. Epub 2016 Feb 5.
Sites that display recurrent, aberrant DNA methylation in cancer represent potential biomarkers for screening and diagnostics. Previously, we identified hypermethylation at the ZNF154 CpG island in 15 solid epithelial tumor types from 13 different organs. In this study, we measure the magnitude and pattern of differential methylation of this region across colon, lung, breast, stomach, and endometrial tumor samples using next-generation bisulfite amplicon sequencing. We found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue. To evaluate this site as a possible pan-cancer marker, we compare the ability of several sequence analysis methods to distinguish the five tumor types (184 tumor samples) from normal tissue samples (n = 34). The classification performance for the strongest method, measured by the area under (the receiver operating characteristic) curve (AUC), is 0.96, close to a perfect value of 1. Furthermore, in a computational simulation of circulating tumor DNA, we were able to detect limited amounts of tumor DNA diluted with normal DNA: 1% tumor DNA in 99% normal DNA yields AUCs of up to 0.79. Our findings suggest that hypermethylation of the ZNF154 CpG island is a relevant biomarker for identifying solid tumor DNA and may have utility as a generalizable biomarker for circulating tumor DNA.
在癌症中显示出反复出现的异常DNA甲基化的位点代表了用于筛查和诊断的潜在生物标志物。此前，我们在来自13个不同器官的15种实体上皮肿瘤类型中鉴定出ZNF154 CpG岛的高甲基化。在本研究中，我们使用下一代亚硫酸氢盐扩增子测序来测量该区域在结肠癌、肺癌、乳腺癌、胃癌和子宫内膜癌肿瘤样本中的甲基化差异程度和模式。我们发现，与正常组织相比，所有肿瘤类型和亚型在该位点均发生高甲基化。为了评估该位点作为一种可能的泛癌标志物的可能性，我们比较了几种序列分析方法区分五种肿瘤类型（184个肿瘤样本）与正常组织样本（n = 34）的能力。通过（受试者操作特征）曲线下面积（AUC）衡量的最强方法的分类性能为0.96，接近完美值1。此外，在循环肿瘤DNA的计算模拟中，我们能够检测到用正常DNA稀释的有限量肿瘤DNA：在99%正常DNA中的1%肿瘤DNA产生的AUC高达0.79。我们的研究结果表明，ZNF154 CpG岛的高甲基化是鉴定实体肿瘤DNA的相关生物标志物，并且可能作为循环肿瘤DNA的通用生物标志物具有实用价值。
