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Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips

ABSTRACT: We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis. Bisulfite modification of 1µg DNA was conducted using an EZ DNA Methylation Kit (Zymo Research, Irvine, CA) according to the manufacturer’s procedure. The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol. Six HCC tumor/adjacent non-tumor tissue pairs were processed on the same chip to avoid chip-to-chip variation.

ORGANISM(S): Homo sapiens

SUBMITTER: Jing Shen 

PROVIDER: E-GEOD-54503 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips.

Shen Jing J   Wang Shuang S   Zhang Yu-Jing YJ   Wu Hui-Chen HC   Kibriya Muhammad G MG   Jasmine Farzana F   Ahsan Habibul H   Wu David P H DP   Siegel Abby B AB   Remotti Helen H   Santella Regina M RM  

Epigenetics 20121203 1

Hepatocellular carcinoma (HCC) incidence has increased in the US and also has one of the fastest growing death rates of any cancer. The purpose of the current study was to discover novel genome-wide aberrant DNA methylation patterns in HCC tumors that are predominantly HCV-related. Infinium HumanMethylation 450K BeadChip arrays were used to examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sit  ...[more]

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