Table 3.
List of differentially methylated CpG sites in longitudinal analyses.
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Depression phenotype |
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Suicide symtomps |
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| Probe | Chr | Positiona | Distance to closest TSS [bp] |
Closest gene | Raw p-value | Estimate | Methylation Difference % | Raw p-value | FDR-adjusted p-values | Estimate | |
| cg23415434 | 2 | 131,515,339 | 1768 | ARHGEF4 | 7.61e-06 | −0.27 | 3.5 | 0.048 | 0.1 | −0.0077 | |
| cg23897356 | 6 | 30,795,992 | −143 | TUBB | 9.72e-06 | 0.17 | <1 | 0.00051 | 0.0034 | 0.0065 | |
| cg13518442 | 15 | 56,146,171 | −758 | ALDH1A2 | 1.93e-05 | −0.14 | 2 | 0.061 | 0.1 | - | |
| cg18081313 | 12 | 130,944,145 | −1086 | ULK1 | 6.55e-05 | 0.18 | <1 | 0.094 | 0.12 | - | |
| cg09312254 | 12 | 110,935,362 | 10 | AX747754 | 7.03e-05 | 0.11 | <1 | 0.083 | 0.12 | - | |
| cg24627299 | 7 | 116,098,732 | −962 | MET | 8.40e-05 | 0.27 | 5 | 0.00077 | 0.0034 | 0.012 | |
| cg03920003 | 1 | 152,848,631 | −1283 | ADAR | 8.75e-05 | 0.50 | 3 | 0.11 | 0.13 | - | |
| cg02935298 | 22 | 41,366,678 | −127 | ATP5L2 | 8.93e-05 | −0.16 | <1 | 0.13 | 0.13 | - | |
| cg02249030 | 6 | 100,068,675 | 1298 | USP45 | 9.75e-05 | 0.13 | <1 | 0.0038 | 0.011 | 0.0049 | |
Position was according to Human Reference Genome build 37 (hg19).
P-values < 0.05 are written in bold.
The depression phenotype was calculated based on depression DAWBA band risk scores and MADRS-S scores. Participants with depression DAWBA band values ≥3 and MADRS-S scores ≥9 were categorized as ‘cases’, while participants with depression band values <3 and MADRS scores <9 were categorized as ‘controls’. Susceptibility for suicidal symptoms was measured with the SUAS questionnaire.
Chr:, chromosome; TSS: transcription start site; bp: base pair; DAWBA: standardized Development and Well-Being Assessment; MADRS-S: Montgomery-Åsberg Depression Rating Scale-Self; SUAS: Suicide Assessment Scale.