Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

E Rahmani, N Zaitlen, Y Baran, C Eng, D Hu… - Nature …, 2016 - nature.com
In epigenome-wide association studies (EWAS), different methylation profiles of distinct cell
types may lead to false discoveries. We introduce ReFACTor, a method based on principal …

Epigenome-wide association studies without the need for cell-type composition

J Zou, C Lippert, D Heckerman, M Aryee, J Listgarten - Nature methods, 2014 - nature.com
In epigenome-wide association studies, cell-type composition often differs between cases
and controls, yielding associations that simply tag cell type rather than reveal fundamental …

EpiDISH web server: epigenetic dissection of intra-sample-heterogeneity with online GUI

SC Zheng, CE Breeze, S Beck, D Dong, T Zhu, L Ma… - 2020 - academic.oup.com
It is well recognized that cell-type heterogeneity hampers the interpretation of Epigenome-
Wide Association Studies (EWAS). Many tools have emerged to address this issue …

Recommendations for the design and analysis of epigenome-wide association studies

KB Michels, AM Binder, S Dedeurwaerder… - Nature …, 2013 - nature.com
Epigenome-wide association studies (EWAS) hold promise for the detection of new
regulatory mechanisms that may be susceptible to modification by environmental and …

[HTML][HTML] MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

P Lutsik, M Slawski, G Gasparoni, N Vedeneev, M Hein… - Genome biology, 2017 - Springer
It is important for large-scale epigenomic studies to determine and explore the nature of
hidden confounding variation, most importantly cell composition. We developed MeDeCom …

Cell-type deconvolution in epigenome-wide association studies: a review and recommendations

AE Teschendorff, SC Zheng - Epigenomics, 2017 - Taylor & Francis
A major challenge faced by epigenome-wide association studies (EWAS) is cell-type
heterogeneity. As many EWAS have already demonstrated, adjusting for changes in cell …

[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 …

Estimation of a significance threshold for epigenome‐wide association studies

A Saffari, MJ Silver, P Zavattari, L Moi… - Genetic …, 2018 - Wiley Online Library
Epigenome‐wide association studies (EWAS) are designed to characterise population‐level
epigenetic differences across the genome and link them to disease. Most commonly, they …

Statistical and integrative system-level analysis of DNA methylation data

AE Teschendorff, CL Relton - Nature Reviews Genetics, 2018 - nature.com
Epigenetics plays a key role in cellular development and function. Alterations to the
epigenome are thought to capture and mediate the effects of genetic and environmental risk …