Journal article
Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
Epigenetics, v 13(1)
01 Jan 2018
PMID: 29451060
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (P-PC1 = 1.4x 10(-9); P-PC2 = 2.9x 10(-5); P-PC3 = 3.8x 10(-5); P-PC4 = 4.2x 10(-6); P-PC5 = 9.9x 10(-13), P-PC6 = 1.3x 10(-11)) and not with sample type (PPC1-6>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted P<10(-5)). Estimated cell type proportions did not differ by sample type (P = 0.46), and estimated proportions were highly correlated between paired samples (r = 0.99). Differences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.
Metrics
Details
- Title
- Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
- Creators
- John Dou - University of Michigan–Ann ArborRebecca J. Schmidt - University of California, DavisKelly S. Benke - Johns Hopkins UniversityCraig Newschaffer - Drexel UniversityIrva Hertz-Picciotto - University of California, DavisLisa A. Croen - Kaiser PermanenteAna-Maria Iosif - University of California, DavisJanine M. LaSalle - University of California, DavisM. Daniele Fallin - Johns Hopkins UniversityKelly M. Bakulski - University of Michigan–Ann Arbor
- Publication Details
- Epigenetics, v 13(1)
- Publisher
- Taylor & Francis
- Number of pages
- 9
- Grant note
- P30CA093373 / NATIONAL CANCER INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI) 003953 / Autism Speaks R01AG055406 / NATIONAL INSTITUTE ON AGING; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Aging (NIA) R01ES016443 / NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Environmental Health Sciences (NIEHS) R01 ES016443; R01 ES025574; P30 ES017885 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA S10OD018223 / OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- A.J. Drexel Autism Institute
- Web of Science ID
- WOS:000426913700011
- Scopus ID
- 2-s2.0-85042219081
- Other Identifier
- 991019168145804721
UN Sustainable Development Goals (SDGs)
This publication has contributed to the advancement of the following goals:
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Genetics & Heredity