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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
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Clinical Epigenetics

ISSN: 1868-7083

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