Illumina450K DNA Methylation Analysis

In both PACE and CHARGE, DNA methylation was measured using the Illumina450K Beadchip (Illumina, Inc, CA, USA). In PACE, newborn DNA was extracted from umbilical cord blood in all cohorts except for NFCS, which used neonatal phlebotomy [3 (link)]. In CHARGE, DNA was extracted from whole blood in 14 cohorts, isolated CD4⁺ T cells in GOLDN, and monocytes (CD14⁺) in MESA [2 (link)]. In all PACE and CHARGE cohorts, DNA was subjected to bisulfite conversion using Zymo EZ DNA methylation (Zymo Research, CA, USA). Each cohort performed its own quality control removing low quality samples and low quality CpGs, and normalized their untransformed methylation β-values as previously described [2 (link),3 (link)].

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Sikdar S., Joehanes R., Joubert B.R., Xu C.J., Vives-Usano M., Rezwan F.I., Felix J.F., Ward J.M., Guan W., Richmond R.C., Brody J.A., Küpers L.K., Baïz N., Håberg S.E., Smith J.A., Reese S.E., Aslibekyan S., Hoyo C., Dhingra R., Markunas C.A., Xu T., Reynolds L.M., Just A.C., Mandaviya P.R., Ghantous A., Bennett B.D., Wang T., Consortium T.B., Bakulski K.M., Melen E., Zhao S., Jin J., Herceg Z., van Meurs J., Taylor J.A., Baccarelli A.A., Murphy S.K., Liu Y., Munthe-Kaas M.C., Deary I.J., Nystad W., Waldenberger M., Annesi-Maesano I., Conneely K., Jaddoe V.W., Arnett D., Snieder H., Kardia S.L., Relton C.L., Ong K.K., Ewart S., Moreno-Macias H., Romieu I., Sotoodehnia N., Fornage M., Motsinger-Reif A., Koppelman G.H., Bustamante M., Levy D, & London S.J. (2019). Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking. Epigenomics, 11(13), 1487-1500.

Publication 2019

Illumina450K Beadchip

Bisulfite Blood Cd4 t cells Cpgs Dna methylation Methylation Monocytes Neonatal Phlebotomy Umbilical cord blood

Corresponding Organization :

Other organizations : National Institute of Environmental Health Sciences, National Institutes of Health, Hebrew SeniorLife, Framingham Heart Study, Harvard University, University Medical Center Groningen, University of Groningen, Pompeu Fabra University, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Barcelona Institute for Global Health, Centre for Genomic Regulation, University of Southampton, Erasmus MC, University of Minnesota, University of Bristol, University of Washington, Wageningen University & Research, Inserm, Sorbonne Université, Institut Pierre Louis d‘Épidémiologie et de Santé Publique, Norwegian Institute of Public Health, University of Michigan–Ann Arbor, University of Kentucky, North Carolina State University, RTI International, Helmholtz Zentrum München, Wake Forest University, Icahn School of Medicine at Mount Sinai, Centre International de Recherche sur le Cancer, Karolinska Institutet, Columbia University, Duke University, Oslo University Hospital, University of Edinburgh, Emory University, MRC Epidemiology Unit, University of Cambridge, Michigan State University, Universidad Autónoma Metropolitana, The University of Texas Health Science Center at Houston, National Heart Lung and Blood Institute

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Variable analysis

independent variables

DNA methylation measurement using Illumina450K Beadchip
DNA extraction from umbilical cord blood (PACE) and whole blood, isolated CD4+ T cells (GOLDN), and monocytes (CD14+) (CHARGE)
Bisulfite conversion of DNA using Zymo EZ DNA methylation

dependent variables

Not explicitly mentioned

control variables

Quality control and normalization of untransformed methylation β-values performed by each cohort

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