Newborn Umbilical Cord Blood DNA Methylation

Newborn umbilical cord blood DNAm was assessed with the Illumina® HumanMethylation450 (450k) or HumanMethylationEPIC (EPIC) BeadChip assay at Illumina or cohort-specific laboratories. Cohorts performed sample processing, quality control and normalization as described in Supplementary methods.
We used normalized, untransformed beta values, ranging from 0 (completely unmethylated) to 1 (completely methylated), after trimming extreme outliers (3×interquartile range from the quartile limit).
We excluded probes mapped to X/Y chromosomes, polymorphic CpGs (overlapping with known single-nucleotide-polymorphisms [SNPs]),^{29 (link)} control or cross-reactive probes (targeting repetitive sequences/co-hybridizing to alternate sequences).^{30 (link),31 (link)}Function-related information was derived from GeneCards and GWAS Catalog (https://www.genecards.org; https://www.ebi.ac.uk/gwas, accessed August 17^th, 2020).

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Sammallahti S., Hidalgo A.P., Tuominen S., Malmberg A., Mulder R.H., Brunst K.J., Alemany S., McBride N.S., Yousefi P., Heiss J.A., McRae N., Page C.M., Jin J., Pesce G., Caramaschi D., Rifas-Shiman S.L., Koen N., Adams C.D., Magnus M.C., Baïz N., Ratanatharathorn A., Czamara D., Håberg S.E., Colicino E., Baccarelli A.A., Cardenas A., DeMeo D.L., Lawlor D.A., Relton C.L., Felix J.F., van IJzendoorn M.H., Bakermans-Kranenburg M.J., Kajantie E., Räikkönen K., Sunyer J., Sharp G.C., Houtepen L.C., Nohr E.A., Sørensen T.I., Téllez-Rojo M.M., Wright R.O., Annesi-Maesano I., Wright J., Hivert M.F., Wright R.J., Zar H.J., Stein D.J., London S.J., Cecil C.A., Tiemeier H, & Lahti J. (2021). Maternal anxiety during pregnancy and newborn epigenome-wide DNA methylation. Molecular psychiatry, 26(6), 1832-1845.

Publication 2021

HumanMethylation450 (450k)

Assay Cpgs Cross reactive Gwas Newborn Polymorphic Repetitive sequences Single nucleotide polymorphisms Umbilical cord blood Y chromosomes

Corresponding Organization :

Other organizations : Erasmus MC, University of Helsinki, University of Cincinnati Medical Center, Barcelona Institute for Global Health, University of Bristol, Icahn School of Medicine at Mount Sinai, Norwegian Institute of Public Health, Inserm, Harvard University, Harvard Pilgrim Health Care, University of Cape Town, City of Hope, Columbia University, Max Planck Institute of Psychiatry, Brigham and Women's Hospital, Erasmus University Rotterdam, Leiden University, Finnish Institute for Health and Welfare, Pompeu Fabra University, University of Southern Denmark, Instituto Nacional de Salud Pública, Bradford Teaching Hospitals NHS Foundation Trust, National Institutes of Health, National Institute of Environmental Health Sciences

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Variable analysis

independent variables

None explicitly mentioned.

dependent variables

Newborn umbilical cord blood DNAm

control variables

Probes mapped to X/Y chromosomes
Polymorphic CpGs (overlapping with known single-nucleotide-polymorphisms [SNPs])
Control or cross-reactive probes (targeting repetitive sequences/co-hybridizing to alternate sequences)

positive controls

None explicitly mentioned.

negative controls

None explicitly mentioned.

Annotations

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