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Table 2 DNA methylation analysis—results

From: Novel candidate genes for ECT response prediction—a pilot study analyzing the DNA methylome of depressed patients receiving electroconvulsive therapy

Gene Gene location CpG Analysis of variance SNP MAF [1.0 = 100%]
AQP10 chr1:154321116…154325325 chr1:154322027 Time F(3, 30) = 17.22 p < 0.001 FDR = 0.04 rs1158005561 C > T < 0.01 T
Response F(1, 10) = 0.47 p > 0.1 FDR = 1
Response × time F(3, 30) = 1.61 p > 0.1 FDR = 0.98
RNF175 chr4:153710125…153760235 chr4:153750274 Time F(3, 40) = 3.11 p < 0.05 FDR = 0.92 rs562725996 G > A 0.0002 A
Response F(1, 40) = 46.08 p < 0.001 FDR < 0.001
Response × time F(3, 40) = 1.92 p > 0.1 FDR = 0.98
RNF213 chr17:80260866…80395312 chr17:80353909 Time F(3, 40) = 2.32 p = 0.09 FDR = 0.93 rs34269699 G > A 0.04014 A
Response F(1, 40) = 729.15 p < 0.001 FDR < 0.001
Response × time F(3, 40) = 2.21 p > 0.1 FDR = 0.98
chr17:80353946 Time F(3, 40) = 2.28 p = 0.09 FDR = 0.93 rs11656211 C > T 0.03934 T
Response F(1, 40) = 538.15 p < 0.001 FDR < 0.001
Response x time F(3, 40) = 2.71 p = 0.06 FDR = 0.98
chr17:80388468 Time F(3, 40) = 2.71 p = 0.06 FDR = 0.93 rs1452340062 C > T < 0.01 T
Response F(1, 40) = 415.46 p < 0.001 FDR < 0.001
Response × time F(3, 40) = 2.87 p < 0.05 FDR = 0.98
chr17:80388469 Time F(3, 40) = 1.22 p > 0.1 FDR = 0.97 rs6565682 G > A 0.1476 A
Response F(1, 40) = 340.88 p < 0.001 FDR < 0.001
Response × time F(3, 40) = 1.61 p > 0.1 FDR = 0.98
TBC1D14 chr4:6909242…6923771 chr4:6917947 Time F(3, 40) = 2.56 p = 0.07 FDR = 0.93 rs7668673 C > T 0.2264 T
Response F(1, 40) = 88.62 p < 0.001 FDR < 0.001
Response × time F(3, 40) = 1.17 p > 0.1 FDR = 0.99
TMC5 chr16:19410539…19498140 chr16:19488803 Time F(3, 30) = 0.16 p > 0.1 FDR = 0.97 rs16972066 C > T 0.07807 T
Response F(1, 10) = 9.99 p < 0.01 FDR = 0.02
Response × time F(3, 30) = 3.31 p < 0.05 FDR = 0.98
TRERF1 chr6:42225225…42452045 chr6:42344977 Time F(3, 30) = 19.40 p < 0.001 FDR = 0.02 None   None  
Response F(1, 10) = 1.32 p > 0.1 FDR = 1
Response × time F(3, 30) = 1.70 p > 0.1 FDR = 0.98
WSCD1 chr17:6069106…6124427 chr17:6102035 Time F(3, 40) = 0.32 p > 0.1 FDR = 0.98 rs59151763 G > A 0.1661 A
Response F(1, 40) = 51.20 p < 0.001 FDR = 0.001
Response × time F(3, 40) = 0.56 p > 0.1 FDR = 0.99
Long non-coding RNA
AC018685.2 chr2:2638178…2696285 chr2:2650193 Time F(3, 30) = 2.52 p = 0.08 FDR = 0.93 rs6719244 C/G/T 0.07688 C
Response F(1, 10) = 330.13 p < 0.001 FDR < 0.001
Response × time F(3, 30) = 2.52 p = 0.08 FDR = 0.98
AC098617.1 chr2:191846539…192044525 chr2:191882169 Time F(3, 30) = 11.75 p < 0.001 FDR = 0.27 rs1455524094 G > A < 0.01 A
Response F(1, 10) = 22.10 p < 0.001 FDR = 1
Response × time F(3, 30) = 20.03 p < 0.001 FDR = 0.019
CLCN3P1 chr9:14921013…15146401 chr9:15079849 Time F(3, 30) = 0.26 p > 0.1 FDR = 0.99 rs10961870 G > A 0.2228 A
Response F(1, 10) = 229.65 p < 0.001 FDR < 0.001
Response × time F(3, 30) = 0.03 p > 0.1 FDR = 1
  1. DNA methylation analysis of 1476812 single CpG sites (repeated ANOVA) revealed five novel protein-coding candidate genes (RNF175, RNF213, TBC1D14, TMC5, WSCD1) and three non-protein coding genes (AC018685.2, AC098617.1, CLCN3P1) to be implicated in ECT response. DNA methylation of two CpGs was found to change significantly during the treatment course (AQP10, TRERF1). All significant CpG sites (but one) do overlap with the loci of a listed single-nucleotide polymorphism (SNP)