Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling

LA Salas, Z Zhang, DC Koestler, RA Butler… - Nature …, 2022 - nature.com
DNA methylation microarrays can be employed to interrogate cell-type composition in
complex tissues. Here, we expand reference-based deconvolution of blood DNA …

A systematic assessment of cell type deconvolution algorithms for DNA methylation data

J Song, PF Kuan - Briefings in bioinformatics, 2022 - academic.oup.com
We performed systematic assessment of computational deconvolution methods that play an
important role in the estimation of cell type proportions from bulk methylation data. The …

Cell types in environmental epigenetic studies: biological and epidemiological frameworks

KA Campbell, JA Colacino, SK Park… - Current environmental …, 2020 - Springer
Abstract Purpose of Review This article introduces the roles of perinatal DNA methylation in
human health and disease, highlights the challenges of tissue and cellular heterogeneity to …

Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data

K Gervin, LA Salas, KM Bakulski, MC Van Zelm… - Clinical …, 2019 - Springer
Background Umbilical cord blood (UCB) is commonly used in epigenome-wide association
studies of prenatal exposures. Accounting for cell type composition is critical in such studies …

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation

Z Zhang, JK Wiencke, KT Kelsey, DC Koestler… - Frontiers in …, 2023 - frontiersin.org
Introduction The human brain comprises heterogeneous cell types whose composition can
be altered with physiological and pathological conditions. New approaches to discern the …

Uncertainty quantification of reference-based cellular deconvolution algorithms

DS Vellame, G Shireby, A MacCalman, EL Dempster… - Epigenetics, 2023 - Taylor & Francis
The majority of epigenetic epidemiology studies to date have generated genome-wide
profiles from bulk tissues (eg, whole blood) however these are vulnerable to confounding …

SOX14 hypermethylation as a tumour biomarker in cervical cancer

J Zhao, H Cao, W Zhang, Y Fan, S Shi, R Wang - Bmc Cancer, 2021 - Springer
Background The association between SOX14 and cancer has been reported. The aim of this
study was to identify and validate the potential value of SOX14 methylation in the early …

Prenatal exposures to per-and polyfluoroalkyl substances and epigenetic aging in umbilical cord blood: The Healthy Start study

SS Niemiec, K Kechris, J Pattee, IV Yang… - Environmental …, 2023 - Elsevier
Background Per-and polyfluoroalkyl substances (PFAS) are ubiquitous, environmentally
persistent chemicals, and prenatal exposures have been associated with adverse child …

Prenatal exposure to endocrine disrupting chemicals is associated with altered DNA methylation in cord blood

K Mattonet, N Nowack-Weyers, V Vogel, D Moser… - Epigenetics, 2022 - Taylor & Francis
Prenatal exposure to endocrine disrupting chemicals can interfere with development, and
has been associated with social-cognitive functioning and adverse health outcomes later in …

Human non-CpG methylation patterns display both tissue-specific and inter-individual differences suggestive of underlying function

P Titcombe, R Murray, M Hewitt, E Antoun, C Cooper… - Epigenetics, 2022 - Taylor & Francis
ABSTRACT DNA methylation (DNAm) in mammals is mostly examined within the context of
CpG dinucleotides. Non-CpG DNAm is also widespread across the human genome, but the …