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Cell Res. 2015 Nov;25(11):1250-64. doi: 10.1038/cr.2015.126. Epub 2015 Oct 30.

Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients.

Wen L1, Li J1, Guo H2,3,4, Liu X1, Zheng S5, Zhang D5, Zhu W5, Qu J6, Guo L7, Du D2,3,4, Jin X1,8, Zhang Y1,8, Gao Y1, Shen J1,9, Ge H1,8, Tang F1,10,9, Huang Y1,9,11, Peng J2,3,4.

Author information

1
Biodynamic Optical Imaging Center (BIOPIC), College of Life Sciences, Peking University, Beijing 100871, China.
2
Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.
3
Ninth School of Clinical Medicine, Peking University, Beijing 100044, China.
4
School of Oncology, Capital Medical University, Beijing 100069, China.
5
Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing 100044, China.
6
Center of Therapeutic Research for Liver Cancer, Beijing 302 Hospital, Beijing 100039, China.
7
Department of Hepatobiliary Surgery, Beijing DiTan Hospital, Capital Medical University, Beijing 100015, China.
8
BIMCR, Peking University, Beijing 100871, China.
9
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
10
Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing 100871, China.
11
College of Engineering, Peking University, Beijing 100871, China.

Abstract

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 tandems 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 small 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 cirrhosis 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.

PMID:
26516143
PMCID:
PMC4650428
DOI:
10.1038/cr.2015.126
[Indexed for MEDLINE]
Free PMC Article

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