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Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation

John Dou, Rebecca J. Schmidt, Kelly S. Benke, Craig Newschaffer, Irva Hertz-Picciotto, Lisa A. Croen, Ana-Maria Iosif, Janine M. LaSalle, M. Daniele Fallin, Kelly M. Bakulski
doi: https://doi.org/10.1101/181057
John Dou
1University of Michigan, School of Public Health, Department of Epidemiology
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Rebecca J. Schmidt
2University of California Davis, Department of Public Health Sciences
3University of California Davis, MIND Institute
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Kelly S. Benke
4Johns Hopkins University, Bloomberg School of Public Health, Department of Mental Health
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Craig Newschaffer
5Drexel University, Dornsife School of Public Health, Department of Epidemiology and Biostatistics
6Drexel University, A.J. Drexel Autism Institute
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Irva Hertz-Picciotto
2University of California Davis, Department of Public Health Sciences
3University of California Davis, MIND Institute
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Lisa A. Croen
7Kaiser Permanente, Division of Research
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Ana-Maria Iosif
2University of California Davis, Department of Public Health Sciences
3University of California Davis, MIND Institute
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Janine M. LaSalle
3University of California Davis, MIND Institute
8University of California Davis, Department of Medical Microbiology and Immunology, Genome Center
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M. Daniele Fallin
4Johns Hopkins University, Bloomberg School of Public Health, Department of Mental Health
9Johns Hopkins University, Wendy Klag Center for Autism and Developmental Disabilities
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Kelly M. Bakulski
1University of Michigan, School of Public Health, Department of Epidemiology
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Abstract

Background 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 by 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.

Objectives To evaluate differences in cell composition and DNA methylation between buffy coat and whole cord blood samples.

Methods Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in 8 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.

Results DNA methylation PCs were associated with individual (PPC1=1.4x10-9; PPC2=2.9x10-5; PPC3=3.8x10-5; PPC4=4.2x10-6; PPC5=9.9x10-13), and not with sample type (PPC1-5>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired individual 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 (5 sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P=0.86), and estimated cell counts were highly correlated between paired samples (r=0.99).

Conclusions 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.

Footnotes

  • Funding: Funding for the EARLI study was provided by the National Institutes of Health (R01ES016443, PI: Newschaffer) and Autism Speaks. The DNA methylation measures in this study were supported by the National Institutes of Health (R01 ES025574, PI: Schmidt).

  • Disclosures of interest: The authors report no conflict of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 31, 2017.
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Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
John Dou, Rebecca J. Schmidt, Kelly S. Benke, Craig Newschaffer, Irva Hertz-Picciotto, Lisa A. Croen, Ana-Maria Iosif, Janine M. LaSalle, M. Daniele Fallin, Kelly M. Bakulski
bioRxiv 181057; doi: https://doi.org/10.1101/181057
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Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
John Dou, Rebecca J. Schmidt, Kelly S. Benke, Craig Newschaffer, Irva Hertz-Picciotto, Lisa A. Croen, Ana-Maria Iosif, Janine M. LaSalle, M. Daniele Fallin, Kelly M. Bakulski
bioRxiv 181057; doi: https://doi.org/10.1101/181057

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