A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data

Julian Heckera Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USACorrespondence[email protected]

https://orcid.org/0000-0001-7918-089X View further author information

Sanghun Leea Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA;b Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;c Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, South KoreaView further author information

Priyadarshini Kachrooa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information

Dmitry Prokopenkod Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USAView further author information

Anna Maaser-Heckerd Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USAView further author information

Sharon M. Lutzb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;e Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care and Harvard Medical School, Boston, MA, USAView further author information

Georg Hahnb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USAView further author information

Rafael Irizarryb Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA;f Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USAView further author information

Scott T. Weissa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information

Dawn L. DeMeoa Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USAView further author information

Christoph Langea Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA;b Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USAView further author information

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Figures & data

Figure 1. Proportions of variance explained by slide effects in VDAART, CAMP (offspring, mothers, fathers), GACRS (offspring, mothers, fathers), and URECA (PBMC and CBMC), partitioned by $S_{0 - 20}, S_{20 - 40}, S_{40 - 60}, S_{60 - 80,}$ and $S_{80 - 100}$ .

Figure 2. PCA plot (first two PCs) of estimated slide effects (mixed model random effects) in $S_{80_100}$ , colored by median methylation beta-values (50% cutoff) in the respective cohort.

Supplemental material

Supplemental Material

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Data availability statement

GACRS and CAMP: All TOPMed data can be requested for access and can be made available through the TOPMed consortium after careful review and approval by the TOPMed Data Access Committee (https://topmed.nhlbi.nih.gov/). Participant consent and Data Use Limitations differ within and across TOPMed studies and should be requested individually. Additional documentation, such as local IRB approval and/or letters of collaboration with the primary study PI(s) may be required. DNA methylation data for the URECA cohort is available in the Gene Expression Omnibus (GEO) repository under the accession number GSE132181 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132181).

EWAS atlas: https://ngdc.cncb.ac.cn/ewas/atlas.

EWAS Toolkit: https://ngdc.cncb.ac.cn/ewas/toolkit.

Illumina EPIC v1.0 support files: https://support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html.

Illumina EPIC v2.0 support files: https://emea.support.illumina.com/downloads/infinium-methylationepic-v2-0-product-files.html.

R statistical software, version 4.1.0: https://www.r-project.org/.

cgageR R package: https://rdrr.io/github/metamaden/cgageR/.