title: Methylation profiling of serum DNA from hepatocellular carcinoma patients using an Infinium Human Methylation 450 BeadChip.
abstract: BACKGROUND
  Alterations in DNA methylation frequently occur in hepatocellular cancer (HCC). The methylation status of circulating DNA might serve as a potential biomarker for cancers.
  
  
  METHODS
  Six early stage HCC patients with chronic hepatitis B virus (HBV) infection and six age-matched healthy controls were selected for genome-scale DNA methylation screening of serum by Illumina Infinium Human Methylation 450 BeadChip. The chosen methylation sites were reassessed by bisulfite sequencing in four healthy controls and four early stage HCC patients with chronic HBV infection and were used for bead array screening. Another 27 healthy controls and 31 early stage HCC patients with chronic HBV infection were also chosen for further bisulfite sequencing validation.
  
  
  RESULTS
  Whole-genome methylation was significantly lower in serum from HCC patients than in that from healthy controls. After bioinformatics analysis, methylation at DBX2 and Thy-1 membrane glycoprotein (THY1) was reassessed by bisulfite sequencing. The correlation coefficients of DBX2 and THY1 between the Illumina 450 BeadChip and bisulfite sequencing were respectively 0.9145 and 0.8232. Twenty-seven healthy controls and 31 early stage HCC patients with chronic HBV infection were chosen for further validation. The diagnostic sensitivity and specificity of DBX2 for differentiating healthy controls and early stage HCC were 88.89 and 87.10 % and of THY1 were 85.19 and 80.65 %.
  
  
  CONCLUSIONS
  The results demonstrated that the 450K BeadChip is a useful tool for whole-genome serum DNA methylation screening of HCC, and some HCC-related DNA methylation sites were screened.
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Pengjun
authors.initials: P
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Wen
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Gu
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Dong
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Jiao
authors.affiliation: State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China. tianyp61@gmail.com.|Medical College, Nankai University, Tianjin, China. tianyp61@gmail.com.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Tian
keywords: CpG sites; DNA methylation; Hepatocellular carcinoma; Hypermethylation; Serum