DNA methylation profiling in the clinic: applications and challenges

H Heyn, M Esteller - Nature Reviews Genetics, 2012 - nature.com
Abstract Knowledge of epigenetic alterations in disease is rapidly increasing owing to the
development of genome-wide techniques for their identification. The ever-growing number …

Analysing and interpreting DNA methylation data

C Bock - Nature Reviews Genetics, 2012 - nature.com
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range
of biological processes and diseases. The technology is now available for studying DNA …

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

A Akalin, M Kormaksson, S Li, FE Garrett-Bakelman… - Genome biology, 2012 - Springer
DNA methylation is a chemical modification of cytosine bases that is pivotal for gene
regulation, cellular specification and cancer development. Here, we describe an R package …

Distinct DNA methylomes of newborns and centenarians

H Heyn, N Li, HJ Ferreira, S Moran… - Proceedings of the …, 2012 - National Acad Sciences
Human aging cannot be fully understood in terms of the constrained genetic setting.
Epigenetic drift is an alternative means of explaining age-associated alterations. To address …

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

AE Jaffe, P Murakami, H Lee, JT Leek… - International journal …, 2012 - academic.oup.com
Background During the past 5 years, high-throughput technologies have been successfully
used by epidemiology studies, but almost all have focused on sequence variation through …

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

M Kulis, S Heath, M Bibikova, AC Queirós, A Navarro… - Nature …, 2012 - nature.com
We have extensively characterized the DNA methylomes of 139 patients with chronic
lymphocytic leukemia (CLL) with mutated or unmutated IGHV and of several mature B-cell …

The transcriptional landscape and mutational profile of lung adenocarcinoma

JS Seo, YS Ju, WC Lee, JY Shin, JK Lee… - Genome …, 2012 - genome.cshlp.org
All cancers harbor molecular alterations in their genomes. The transcriptional consequences
of these somatic mutations have not yet been comprehensively explored in lung cancer …

Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease

CL Relton, G Davey Smith - International journal of …, 2012 - academic.oup.com
The burgeoning interest in the field of epigenetics has precipitated the need to develop
approaches to strengthen causal inference when considering the role of epigenetic …

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

GC Hon, RD Hawkins, OL Caballero, C Lo… - Genome …, 2012 - genome.cshlp.org
While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic
alterations during tumorigenesis including aberrant DNA hypermethylation of tumor …

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

TK Kelly, Y Liu, FD Lay, G Liang, BP Berman… - Genome …, 2012 - genome.cshlp.org
DNA methylation and nucleosome positioning work together to generate chromatin
structures that regulate gene expression. Nucleosomes are typically mapped using …