title: Mining cancer methylomes: prospects and challenges.
abstract: There are over 28 million CpG sites in the human genome. Assessing the methylation status of each of these sites will be required to understand fully the role of DNA methylation in health and disease. Genome-wide analysis, using arrays and high-throughput sequencing, has enabled assessment of large fractions of the methylome, but each protocol comes with unique advantages and disadvantages. Notably, except for whole-genome bisulfite sequencing, most commonly used genome-wide methods detect <5% of all CpG sites. Here, we discuss approaches for methylome studies and compare genome coverage of promoters, genes, and intergenic regions, and capacity to quantitate individual CpG methylation states. Finally, we examine the extent of published cancer methylomes that have been generated using genome-wide approaches.
authors.affiliation: Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia.
authors.forename: Clare
authors.initials: C
authors.lastname: Stirzaker
authors.affiliation: Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia.
authors.forename: Phillippa C
authors.initials: PC
authors.lastname: Taberlay
authors.affiliation: Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia.
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Statham
authors.affiliation: Epigenetics Program, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Sydney 2010, NSW, Australia; St Vincent's Clinical School, University of NSW, Sydney 2010, NSW, Australia. Electronic address: s.clark@garvan.org.au.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Clark
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D055106:Genome-Wide Association Study / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D009369:Neoplasms / Q000235:genetics*; D059467:Transcriptome
keywords: DNA methylation; cancer methylome; epigenetics