Table 3 Differentially methylated regions (DMRs) associated with maternal adverse childhood experiences (ACEs)
From: Maternal adverse childhood experiences (ACEs) and DNA methylation of newborns in cord blood
Chr | Start a | End | Width | # CpGs | Šidák p value | Mean OR (2.5, 97.5 percentile) | Baseline maximum likelihood (95% Range) % methylated b | Maximum likelihood (95% Range) % methylation change c | Gene annotation | Feature category | |
|---|---|---|---|---|---|---|---|---|---|---|---|
Total number of ACEs | Â | ||||||||||
6 | 31,734,265 | 31,734,450 | 186 | 5 | \(7.14\times {10}^{-3}\) | 0.98 (0.97, 0.98) | 39.42 (23.59, 51.51) | − 0.56 (− 0.72, − 0.40) | VWA7 | Body | |
7 | 39,170,545 | 39,171,071 | 527 | 5 | \(4.82\times {10}^{-8}\) | 0.94 (0.93, 0.96) | 84.94 (72.31, 94.29) | − 0.81 (− 1.53, − 0.22) | POU6F2 | Body | |
11 | 316,088 | 316,505 | 418 | 4 | \(5.72\times {10}^{-10}\) | 0.95 (0.93, 0.97) | 39.69 (17.51, 61.91) | − 1.05 (− 1.41, − 0.66) | – | – | |
16 | 84,346,770 | 84,346,979 | 210 | 4 | \(3.98\times {10}^{-6}\) | 1.02 (1.02, 1.03) | 63.93 (61.88, 67.33) | 0.50 (0.44, 0.54) | WFDC1 | Body | |
Total number of ACEs categorized | Â | ||||||||||
4–10 versus 0 total ACEs |  | ||||||||||
7 | 73,894,932 | 73,895,279 | 348 | 5 | \(6.85\times {10}^{-13}\) | 1.20 (1.11, 1.29) | 33.81 (25.07, 42.00) | 4.12 (2.02, 6.36) | GTF2IRD1 | 5’UTR | |
Mutually adjusted ACEs | Â | ||||||||||
Emotional abuse | Â | ||||||||||
3 | 126,007,325 | 126,007,564 | 240 | 4 | \(3.26\times {10}^{-7}\) | 0.69 (0.61, 0.83) | 28.89 (22.20, 37.96) | − 7.04 (− 8.49, − 4.36) | – |  | |
8 | 95,962,132 | 95,962,512 | 381 | 6 | \(1.36\times {10}^{-6}\) | 1.41 (1.33, 1.50) | 44.33 (31.06, 59.17) | 9.48 (7.36, 11.45) | TP53INP1 | TSS1500 | |
15 | 74,218,577 | 74,218,970 | 394 | 9 | \(6.76\times {10}^{-10}\) | 1.23 (1.16, 1.36) | 46.63 (34.23, 61.96) | 5.12 (3.75, 6.87) | LOXL1, LOXL1-AS1 | TSS200, 5'UTR, 1st Exon | |
Sexual abuse | Â | ||||||||||
2 | 128,453,260 | 128,453,533 | 274 | 4 | \(1.17\times {10}^{-5}\) | 0.44 (0.30, 0.54) | 26.07 (14.01, 31.99) | − 12.02 (− 14.43, − 9.04) | – | – | |
4 | 4,543,812 | 4,544,026 | 215 | 8 | \(6.96\times {10}^{-4}\) | 1.17 (1.10, 1.25) | 2.45 (1.18, 5.48) | 0.38 (0.25, 0.61) | STX18-AS1 | TSS200, TSS1500 | |
7 | 27,155,036 | 27,155,283 | 248 | 5 | \(3.01\times {10}^{-4}\) | 0.86 (0.83, 0.90) | 95.28 (92.40, 98.32) | − 0.65 (− 1.04, − 0.35) | HOXA3 | 5’UTR, TSS1500 | |
7 | 38,350,921 | 38,351,155 | 235 | 4 | \(1.17\times {10}^{-4}\) | 0.61 (0.58, 0.65) | 13.52 (9.83, 17.25) | − 4.83 (− 5.94, − 3.69) | – | – | |
12 | 2,339,439 | 2,339,663 | 225 | 3 | \(2.17\times {10}^{-4}\) | 0.83 (0.77, 0.87) | 44.98 (40.00, 51.01) | − 4.70 (− 6.19, − 3.43) | CACNA1C | Body | |
20 | 36,148,505 | 36,149,456 | 952 | 34 | \(<1.0\times {10}^{-13}\) | 0.87 (0.79, 0.94) | 58.73 (41.48, 75.15) | − 3.41 (− 5.80, − 1.48) | BLCAP | 5’UTR, TSS1500, TSS200 | |
Emotional neglect | Â | ||||||||||
6 | 31,733,847 | 31,734,148 | 302 | 8 | \(4.07\times {10}^{-5}\) | 0.82 (0.77, 0.85) | 80.46 (56.65, 92.09) | − 2.95 (− 4.92, − 1.53) | VWA7 | Body | |
17 | 40,274,703 | 40,274,741 | 39 | 5 | \(7.38\times {10}^{-4}\) | 0.86 (0.81, 0.92) | 95.38 (93.90, 96.93) | − 0.86 (− 1.33, − 0.39) | HSPB9, KAT2A | TSS200, TSS1500 | |
Physical neglect | Â | ||||||||||
1 | 234,367,322 | 234,367,587 | 266 | 4 | \(4.84\times {10}^{-5}\) | 1.56 (1.50, 1.64) | 70.24 (59.59, 80.26) | 8.22 (6.97, 9.59) | SLC35F3 | Body | |
6 | 28,829,230 | 28,829,689 | 460 | 19 | \(6.06\times {10}^{-5}\) | 1.27 (0.98, 1.58) | 83.40 (31.61, 96.99) | 1.19 (− 0.45, 2.58) | LINC01623 | Body | |
6 | 32,063,487 | 32,064,307 | 821 | 26 | \(<1.0\times {10}^{-13}\) | 1.51 (1.17, 1.99) | 43.51 (12.35, 78.93) | 8.48 (3.03, 16.83) | TNXB | Body | |
11 | 6,291,625 | 6,292,512 | 888 | 7 | \(8.09\times {10}^{-10}\) | 1.67 (1.42, 2.06) | 82.46 (72.74, 86.98) | 6.27 (4.12, 10.16) | CCKBR | Body | |
11 | 67,383,425 | 67,383,863 | 439 | 7 | \(2.06\times {10}^{-5}\) | 1.43 (1.34, 1.60) | 42.56 (29.66, 63.22) | 7.94 (6.31, 10.23) | – |  | |
11 | 68,782,024 | 68,782,260 | 237 | 5 | \(5.73\times {10}^{-6}\) | 1.72 (1.37, 2.39) | 55.43 (39.63, 75.69) | 11.27 (5.05, 20.37) | MRGPRF | Body | |
13 | 20,751,257 | 20,751,994 | 738 | 5 | \(5.23\times {10}^{-12}\) | 1.46 (1.40, 1.62) | 55.70 (36.31, 88.56) | 8.56 (3.16, 13.07) | – |  | |
15 | 42,371,635 | 42,371,935 | 301 | 5 | \(1.44\times {10}^{-3}\) | 1.35 (1.24, 1.47) | 84.80 (72.88, 92.42) | 3.24 (1.97, 5.06) | PLA2G4D | Body | |
18 | 44,562,067 | 44,562,137 | 71 | 6 | \(4.78\times {10}^{-4}\) | 1.48 (1.32, 1.63) | 97.69 (97.08, 98.31) | 0.68 (0.65, 0.71) | KATNAL2, TCEB3B | 5’UTR, TSS200 | |
Domestic violence in household | Â | ||||||||||
4 | 4,543,474 | 4,544,026 | 553 | 11 | \(2.81\times {10}^{-7}\) | 0.86 (0.83, 0.91) | 2.44 (1.19, 5.20) | − 0.33 (− 0.49, − 0.17) | STX18, STX18-AS1 | TSS200, TSS1500, Body, 1st Exon, 5'UTR, | |
6 | 31,803,880 | 31,804,462 | 583 | 7 | \(4.15\times {10}^{-6}\) | 1.40 (1.30, 1.57) | 26.18 (2.22, 63.76) | 3.79 (1.11, 6.02) | SNHG32, SNORD52 | 5’UTR, TSS1500 | |
11 | 368,351 | 368,761 | 411 | 12 | \(1.42\times {10}^{-6}\) | 1.24 (1.15, 1.34) | 31.02 (10.81, 71.04) | 3.71 (1.67, 6.52) | B4GALNT4 | TSS1500 | |
12 | 4,918,848 | 4,919,139 | 292 | 4 | \(5.34\times {10}^{-5}\) | 0.63 (0.54, 0.71) | 3.83 (2.60, 6.63) | − 1.32 (− 2.09, − 0.74) | KCNA6 | 5’UTR, 1st Exon | |
Substance abuse in household | Â | ||||||||||
6 | 33,245,619 | 33,245,780 | 162 | 10 | \(4.30\times {10}^{-3}\) | 1.10 (1.04, 1.15) | 54.43 (26.50, 76.76) | 2.31 (1.02, 3.66) | B3GALT4 | 1st Exon | |
17 | 46,018,923 | 46,019,185 | 263 | 6 | \(4.36\times {10}^{-8}\) | 1.32 (1.24, 1.42) | 2.14 (1.55, 3.21) | 0.67 (0.46, 0.83) | PNPO | 1st Exon, Body, 5’UTR | |
19 | 35,615,444 | 35,615,639 | 196 | 3 | \(4.10\times {10}^{-5}\) | 1.41 (1.31, 1.49) | 5.59 (2.33, 10.33) | 1.92 (1.04, 2.86) | LGI4 | 3’UTR | |
Mental illness in household | Â | ||||||||||
11 | 67,383,425 | 67,383,863 | 439 | 7 | \(1.90\times {10}^{-9}\) | 0.65 (0.55, 0.73) | 42.56 (29.66, 63.22) | − 9.21 (− 11.04, − 6.06) | – |  | |
15 | 81,426,525 | 81,426,670 | 146 | 6 | \(8.92\times {10}^{-3}\) | 1.75 (1.65, 1.86) | 36.18 (27.69, 43.25) | 13.57 (11.17, 14.83) | CFAP161 | TSS200, 1st Exon, 5’UTR | |
18 | 77,905,391 | 77,905,800 | 410 | 8 | \(9.10\times {10}^{-11}\) | 0.67 (0.59, 0.78) | 33.49 (22.27, 46.26) | − 7.87 (− 9.87, − 5.23) | LOC100130522 | TSS1500, TSS200 | |
19 | 38,794,635 | 38,794,894 | 260 | 5 | \(7.41\times {10}^{-5}\) | 0.74 (0.63, 0.80) | 26.57 (11.62, 54.30) | − 4.79 (− 6.47, − 2.87) | C19orf33, YIF1B | 1st Exon, 3’UTR, 5’UTR, TSS200 | |
19 | 50,191,390 | 50,191,732 | 343 | 5 | \(3.80\times {10}^{-5}\) | 1.24 (1.15, 1.35) | 68.29 (50.47, 93.68) | 4.39 (0.90, 6.33) | C19orf76, PRMT1 | TSS1500, Body, 3’UTR | |
Household member incarcerated | Â | ||||||||||
6 | 33,048,086 | 33,048,968 | 883 | 23 | \(3.77\times {10}^{-13}\) | 1.56 (1.18, 2.11) | 86.34 (68.71, 97.78) | 3.85 (0.62, 7.80) | HLA-DPB1 | Body | |
7 | 27,170,600 | 27,171,155 | 556 | 12 | \(2.98\times {10}^{-6}\) | 0.74 (0.67, 0.82) | 29.67 (15.09, 60.04) | − 5.78 (− 7.90, − 4.79) | HOXA4 | TSS1500 | |
17 | 47,092,026 | 47,092,273 | 248 | 5 | \(2.79\times {10}^{-6}\) | 1.42 (1.26, 1.59) | 67.00 (59.08, 75.38) | 8.25 (4.82, 10.90) | IGF2BP1 | Body | |
Parents divorced | Â | Â | |||||||||
5 | 158,531,180 | 158,531,512 | 333 | 4 | \(3.63\times {10}^{-6}\) | 0.83 (0.82, 0.84) | 40.29 (14.60, 73.47) | − 3.19 (− 3.68, − 2.37) | – | – | |
15 | 101,093,778 | 101,093,901 | 124 | 3 | \(9.18\times {10}^{-6}\) | 0.47 (0.44, 0.53) | 72.80 (63.78, 84.96) | − 19.57 (− 23.68, − 12.14) | – | – | |
20 | 61,590,799 | 61,591,067 | 269 | 3 | \(9.70\times {10}^{-6}\) | 2.90 (2.77, 3.02) | 44.52 (41.39, 47.66) | 26.98 (26.05, 27.91) | SLC17A9 | Body | |