[HTML][HTML] Epigenome-wide association studies: current knowledge, strategies and recommendations

MP Campagna, A Xavier, J Lechner-Scott, V Maltby… - Clinical …, 2021 - Springer
The aetiology and pathophysiology of complex diseases are driven by the interaction
between genetic and environmental factors. The variability in risk and outcomes in these …

MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment

M Pelizzola, Y Koga, AE Urban… - Genome …, 2008 - genome.cshlp.org
DNA methylation is an important component of epigenetic modifications that influences the
transcriptional machinery and is aberrant in many human diseases. Several methods have …

DNA methylation data analysis and its application to cancer research

X Ma, YW Wang, MQ Zhang, AF Gazdar - Epigenomics, 2013 - Taylor & Francis
With the rapid development of genome-wide high-throughput technologies, including
expression arrays, SNP arrays and next-generation sequencing platforms, enormous …

[HTML][HTML] Introduction to single-cell DNA methylation profiling methods

J Ahn, S Heo, J Lee, D Bang - Biomolecules, 2021 - mdpi.com
DNA methylation is an epigenetic mechanism that is related to mammalian cellular
differentiation, gene expression regulation, and disease. In several studies, DNA …

Reference-free cell mixture adjustments in analysis of DNA methylation data

EA Houseman, J Molitor, CJ Marsit - Bioinformatics, 2014 - academic.oup.com
Motivation: Recently there has been increasing interest in the effects of cell mixture on the
measurement of DNA methylation, specifically the extent to which small perturbations in cell …

[HTML][HTML] An evaluation of statistical methods for DNA methylation microarray data analysis

D Li, Z Xie, M Le Pape, T Dye - BMC bioinformatics, 2015 - Springer
Background DNA methylation offers an excellent example for elucidating how epigenetic
information affects gene expression. β values and M values are commonly used to quantify …

[HTML][HTML] Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

EA Houseman, KT Kelsey, JK Wiencke, CJ Marsit - BMC bioinformatics, 2015 - Springer
Background The impact of cell-composition effects in analysis of DNA methylation data is
now widely appreciated. With the availability of a reference data set consisting of DNA …

[HTML][HTML] Accounting for cellular heterogeneity is critical in epigenome-wide association studies

AE Jaffe, RA Irizarry - Genome biology, 2014 - Springer
Background Epigenome-wide association studies of human disease and other quantitative
traits are becoming increasingly common. A series of papers reporting age-related changes …

Identification of differentially methylated cell types in epigenome-wide association studies

SC Zheng, CE Breeze, S Beck, AE Teschendorff - Nature methods, 2018 - nature.com
An outstanding challenge of epigenome-wide association studies (EWASs) performed in
complex tissues is the identification of the specific cell type (s) responsible for the observed …

[HTML][HTML] GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease

Y Liu, X Li, MJ Aryee, TJ Ekström, L Padyukov… - The American Journal of …, 2014 - cell.com
Epigenetic marks such as DNA methylation have generated great interest in the study of
human disease. However, studies of DNA methylation have not established population …