This article is part of the supplement: Beyond the Genome 2012

Open Access Open Badges Oral presentation

Exploring the cancer methylome

Benjamin P Berman1, Daniel J Weisenberger1, Toshinori Hinoue1, Houtan Noushmehr1, Yaping Liu1, Joseph F Aman1, Toshinori Hinoue1, Hui Shen1, Simeen Malik1, Swapna Mahurkar1, Timothy Triche1, Zachary Ramjan1, Charles M Nicolet1, David Van Den Berg1, Leslie Cope2, James G Herman2, Stephen B Baylin2 and Peter W Laird1*

  • * Corresponding author: Peter W Laird

Author Affiliations

1 USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA

2 Johns Hopkins School of Medicine, Baltimore, MD, USA

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BMC Proceedings 2012, 6(Suppl 6):O24  doi:10.1186/1753-6561-6-S6-O24

The electronic version of this article is the complete one and can be found online at:

Published:1 October 2012

© 2012 Berman et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Oral presentation

Cancer develops not only as a result of genetic mutations and genomic rearrangements, but also as a consequence of numerous epigenetic alterations, including extensive changes in the distribution of DNA methylation throughout the genome. DNA methylation changes contribute directly to cancer by transcriptional silencing of tumor-suppressor genes through promoter CpG island hypermethylation. Broad epigenomic analysis of human tumors can reveal relationships between large numbers of epigenetic events and can provide insight into the mechanisms underlying concerted epigenetic change. Genomic loci targeted by Polycomb Group Repressors in embryonic stem cells, and involved in cellular differentiation, are predisposed to aberrant DNA methylation in cancer cells, suggesting that an epigenetic block to cellular differentiation may sometimes be an initiating event in carcinogenesis. The very strong associations between distinct epigenetic subtypes, such as CpG Island Methylator Phenotypes (CIMP) and specific somatic genetic events, such as BRAF mutation in colorectal cancer and IDH1 mutation in glioblastoma multiforme are consistent with an early role for DNA methylation alterations, providing a favorable cellular context for the subsequent somatic mutation. The analysis of whole methylomes at single-basepair resolution reveals that cancer-associated changes occur differentially across defined regions of the genome associated with the nuclear lamina. It is apparent that epigenomic analysis is essential for a full understanding of the relationship between alterations in the cancer genome and the origin and clinical diversity of individual tumors.