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Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
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Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
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Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
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Journal Article
Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
2015
Overview
Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA （ccfDNA） remain limited. Here we describe a methylated CpG tan- dems amplification and sequencing （MCTA-Seq） method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples （n = 151） of hepatocellular carcinoma （HCC） patients and control subjects, identifying dozens of high-performance markers in blood for detecting smaU HCC （≤ 3 cm）. Among these markers, 4 （RGS10, ST8SIA6, RUNX2 and VIM） are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients （n = 36） and control subjects including cirrho- sis patients （n = 17） and normal individuals （n = 38）. Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ A基因组
/ Biomedical and Life Sciences
/ Carcinoma, Hepatocellular - blood
/ Carcinoma, Hepatocellular - diagnosis
/ Carcinoma, Hepatocellular - genetics
/ CpG岛
/ DNA
/ DNA技术
/ Humans
/ Islands
/ Nucleic Acid Amplification Techniques - methods
/ Original
/ Sequence Analysis, DNA - methods
/ Tissues
/ 循环
/ 患者
/ 甲基化分析
/ 肝细胞癌
/ 肿瘤检测
