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 …

Epigenome-based cancer risk prediction: rationale, opportunities and challenges

M Widschwendter, A Jones, I Evans, D Reisel… - Nature reviews Clinical …, 2018 - nature.com
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary
prevention strategies are urgently required. The ideal risk-predictive test should: integrate …

DNA methylation arrays as surrogate measures of cell mixture distribution

EA Houseman, WP Accomando, DC Koestler… - BMC …, 2012 - Springer
Background There has been a long-standing need in biomedical research for a method that
quantifies the normally mixed composition of leukocytes beyond what is possible by simple …

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

T Hinoue, DJ Weisenberger, CPE Lange… - Genome …, 2012 - genome.cshlp.org
Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are
characterized by distinct genetic and epigenetic alterations. Here we performed …

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 …

A DNA methylation fingerprint of 1628 human samples

AF Fernandez, Y Assenov, JI Martin-Subero… - Genome …, 2012 - genome.cshlp.org
Most of the studies characterizing DNA methylation patterns have been restricted to
particular genomic loci in a limited number of human samples and pathological conditions …

Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional …

JC Madan, DC Koestler, BA Stanton, L Davidson… - MBio, 2012 - Am Soc Microbiol
Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung by
microbial communities is the proximal cause of respiratory failure. While there has been an …

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

D Wang, L Yan, Q Hu, LE Sucheston, MJ Higgins… - …, 2012 - academic.oup.com
The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density
microarray for quantifying the methylation level of over 450 000 CpG sites within human …

Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis

DC Koestler, BC Christensen, MR Karagas, CJ Marsit… - Epigenetics, 2013 - Taylor & Francis
The potential influence of underlying differences in relative leukocyte distributions in studies
involving blood-based profiling of DNA methylation is well recognized and has prompted …

[HTML][HTML] Ionizing radiation biomarkers for potential use in epidemiological studies

E Pernot, J Hall, S Baatout, MA Benotmane… - … Research/Reviews in …, 2012 - Elsevier
Ionizing radiation is a known human carcinogen that can induce a variety of biological
effects depending on the physical nature, duration, doses and dose-rates of exposure …