Mapping allele-specific DNA methylation: a new tool for maximizing information from GWAS.
In this issue of The Journal, an article by Schalkwyk et al.(1) shows the landscape of allele-specific DNA methylation (ASM) in the human genome. ASM has long been studied as a hallmark of imprinted genes, and a chromosome-wide version of this phenomenon occurs, in a random fashion, during X chromosome inactivation in female cells. But the type of ASM motivating the study by Schalkwyk et al. is different. They used a high-resolution, methylation-sensitive SNP array (MSNP) method for genome-wide profiling of ASM in total peripheral-blood leukocytes (PBL) and buccal cells from a series of monozygotic twin pairs. Their data bring a new level of detail to our knowledge of a newly recognized phenomenon-nonimprinted, sequence-dependent ASM. They document the widespread occurrence of this phenomenon among human genes and discuss its basic implications for gene regulation and genetic-epigenetic interactions. But this paper and recent work from other laboratories(2,3) raises the possibility of a more immediate and practical application for ASM mapping, namely to help extract maximum information from genome-wide association studies.
Institute for Cancer Genetics and Taub Institute, Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA. bt12@columbia.edu
Benjamin
B
Tycko
D000483:Alleles; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D051379:Mice; D020641:Polymorphism, Single Nucleotide / Q000235:genetics