Mapping Allele-specific DNA Methylation: a New Tool for Maximizing Information from GWAS

Overview

Journal Am J Hum Genet

Publisher Cell Press

Specialty Genetics

Date 2010 Feb 18

PMID 20159108

Citations 27

Authors

Benjamin Tycko

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs.

Do C, Dumont E, Salas M, Castano A, Mujahed H, Maldonado L Genome Biol. 2020; 21(1):153.

PMID: 32594908 PMC: 7322865. DOI: 10.1186/s13059-020-02059-3.

Breast cancer family history and allele-specific DNA methylation in the legacy girls study.

Wu H, Do C, Andrulis I, John E, Daly M, Buys S Epigenetics. 2018; 13(3):240-250.

PMID: 29436922 PMC: 5997170. DOI: 10.1080/15592294.2018.1435243.

The Protein Encoded by the CCDC170 Breast Cancer Gene Functions to Organize the Golgi-Microtubule Network.

Jiang P, Li Y, Poleshko A, Medvedeva V, Baulina N, Zhang Y EBioMedicine. 2017; 22:28-43.

PMID: 28687497 PMC: 5552109. DOI: 10.1016/j.ebiom.2017.06.024.

Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era.

Do C, Shearer A, Suzuki M, Terry M, Gelernter J, Greally J Genome Biol. 2017; 18(1):120.

PMID: 28629478 PMC: 5477265. DOI: 10.1186/s13059-017-1250-y.

Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies.

Xiao X, Chang H, Li M Mol Psychiatry. 2017; 22(4):497-511.

PMID: 28044063 PMC: 5378805. DOI: 10.1038/mp.2016.241.

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