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Open Access Research article

DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach

Marie Loh1234, Natalia Liem15, Aparna Vaithilingam1, Pei Li Lim15, Nur Sabrina Sapari1, Eiram Elahi1, Zuan Yu Mok1, Chee Leong Cheng6, Benedict Yan6, Brendan Pang6, Manuel Salto-Tellez167, Wei Peng Yong5, Barry Iacopetta2 and Richie Soong16*

Author Affiliations

1 Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore

2 School of Surgery, The University of Western Australia, Perth, Australia

3 Department of Epidemiology and Biostatistics, Imperial College London, London, UK

4 Institute of Health Sciences, University of Oulu, Oulu, Finland

5 National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore

6 Department of Pathology, National University Health System, Singapore, Singapore

7 Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, UK

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BMC Gastroenterology 2014, 14:55  doi:10.1186/1471-230X-14-55

Published: 28 March 2014



Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.


The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.


A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.


High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.

Methylation; Gastric cancer; Microarray; CIMP; GoldenGate