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Table 2 Overview of epigenetic analyses and results

From: Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation

Methylation data Research question Statistical modela Results Significance threshold
EPIC array Are CpG-sites on the EPIC array differentially methylated with regard to BET exposure? summary (lm (beta ~ child’s sex + gestational age + PC1 + PC2 + PC3 + PC4 + pregnant person’s age + smoking during pregnancy + cell type PC1 + cell type PC2 + BET)) cg22363520 (chr6, bp 35,558,488) is differentially methylated with BET epigenome-wide, p < 9 × 10–08, based on Mansell et al. [31]
TBS FKBP5 Are CpG-sites within FKBP5 differentially methylated with regard to BET exposure? summary (lm (beta ~ child’s sex + gestational age + PC1 + PC2 + PC3 + PC4 + pregnant person’s age + smoking during pregnancy + cell type PC1 + cell type PC2 + plate + BET)) PCR_2_29 (intron7, bp 35,558,488) is differentially methylated with BET FDR 5% over all investigated CpG-sites in FKBP5
TBS FKBP5 Are CpG-sites within FKBP5 differentially methylated with regard to the functional variant rs1360780? summary (lm (beta ~ child’s sex + gestational age + PC1 + PC2 + PC3 + PC4 + pregnant person’s age + smoking during pregnancy + cell type PC1 + cell type PC2 + plate + rs1360780)) PCR_2_262
(intron 7, bp 35,558,721)
PCR_12_47
(intron 1, bp 35,630,996)
PCR_12_62
(intron 1, bp 35,631,011)
PCR_12_211
(intron 1, bp 35,631,160)
PCR_17_63
(proximal enhancer,
bp 35,695,192)
PCR_20_191
(proximal enhancer,
bp 35,696,886)
are differentially methylated with rs1360780
FDR 5% over all investigated CpG-sites in FKBP5
TBS FKBP5 Are additive effects of the functional variant rs1360780 and BET on DNAm in FKBP5 present? summary (lm (beta ~ child’s sex + gestational age + PC1 + PC2 + PC3 + PC4 + pregnant person’s age + smoking during pregnancy + cell type PC1 + cell type PC2 + plate + rs1360780 + BET)) additive effects of rs1360780 and BET on DNAm of PCR_2_29 (intron7, bp 35,558,488) FDR 5% over all investigated CpG-sites in FKBP5
TBS FKBP5 Are interactive effects of the functional variant rs1360780 and BET on DNAm in FKBP5 present? summary (lm (beta ~ child’s sex + gestational age + PC1 + PC2 + PC3 + PC4 + pregnant person’s age + smoking during pregnancy + cell type PC1 + cell type PC2 + plate + rs1360780 + BET + rs1360780 x BET)) no interactive effects after correction for multiple testing FDR 5% over all investigated CpG-sites in FKBP5
  1. PC1–PC4 refer to the first four MDS components, correcting for ethnicity. Cell type PC1, cell type PC2 refer to the first two components from a PCA on the cell types (see Methods). Plate refers to TBS plate (see Methods). bp is the base-pair position (hg19).
  2. aStatistical model refers to linear model as set up in R