BWS | TND | ||||||||
---|---|---|---|---|---|---|---|---|---|
Candidate | Chr | Gene name | CpG island | Probe region* | No. probes† | Lowest p value‡ | Probe region* | No. probes† | Lowest p value‡ |
Novel candidate DMRs | 1 | LOC728448/PPIEL | No | 40 024 971–40 025 411 | 3 | 1.47E−18 | 40 024 971–40 025 232 | 2 | 3.09E−22 |
4 | JAKMIP1 | Yes | 6 107 021–6 107 339 | 4 | 2.48E−16 | 6 107 021–6 107 339 | 4 | 5.83E−36 | |
7 | SVOPL | Yes | 138 348 774–138 349 443 | 3 | 6.30E−41 | 138 348 774–138 349 443 | 3 | 7.21E−20 | |
9 | FANCC | Yes | 98 075 481–98 075 492 | 2 | 8.29E−58 | 98 075 481–98 075 492 | 2 | 7.28E−55 | |
17 | GLP2R | No | 9 729 250–9 729 424 | 3 | 3.33E−16 | 9 729 250–9 729 422 | 4 | 1.81E−23 | |
21 | WRB | Yes | 40 757 691–40 758 208 | 2 | 2.51E−20 | 40 757 691–40 758 208 | 4 | 6.71E−29 | |
8 | LOC728024/ERLIN2 | No | 37 605 517–37 605 783 | 4 | 3.87E−40 | 37 605 359–37 605 978 | 6 | 2.69E−42 | |
18 | LOC100130522/PARD6G-AS1 | Yes | 77 905 355–77 905 947 | 3 | 1.01E−19 | 77 905 298–77 905 947 | 9 | 4.38E−71 | |
22 | NHP2L1 | Yes | 42 078 217–42 078 723 | 6 | 4.08E−15 | 42 078 217–42 078 723 | 6 | 4.25E−54 | |
Imprinted—not associated with ID | 1 | DIRAS343 | Yes | 68 512 539–68 517 273 | 21 | 6.69E−31 | 68 512 539–68 517 273 | 20 | 5.45E−64 |
6 | FAM50B20 44 | Yes | 3 849 235–3 849 818 | 17 | 1.70E−18 | 3 849 272–3 849 818 | 17 | 1.64E−39 | |
15 | IGF1R45 | No | 99 408 636–99 409 506 | 5 | 2.23E−15 | 99 408 636–99 409 957 | 6 | 1.04E−36 | |
19 | ZNF33146 47 | Yes | 54 040 774–54 058 085 | 11 | 1.39E−40 | 54 040 813–54 058 085 | 10 | 9.13E−53 | |
20 | L3MBTL48 | Yes | 42 142 417–42 143 502 | 13 | 1.32E−17 | 42 142 417–42 143 489 | 18 | 7.60E−25 | |
Imprinted—associated with ID | 6 | PLAGL1 | Yes | 144 328 421–144 329 909 | 14 | 1.06E−55 | 144 328 482–144 329 909 | 15 | 1.22E−129 |
7 | MEST | Yes | 130 130 187–130 133 110 | 42 | 6.12E−42 | 130 130 383–130 133 110 | 42 | 1.73E−45 | |
11 | KCNQ1 | Yes | 2 715 837–2 722 258 | 26 | 1.14E−73 | 2 720 463–2 722 119 | 9 | 4.86E−13 |
Datasets from five patients with BWS-HIL and five with TND-HIL were compared with datasets from 245 and 211 batch-matched normal controls, respectively. Probes with M-values between −1 and +1 in controls and relative hypomethylation in patients with a p value of <1.33E−7 were identified. This subset was further filtered by minimal criteria for a hypomethylated locus, that is, ≥2 hypomethylated probes spaced by <2000 nucleotides. Candidate regions that meet these criteria in both BWS-HIL and TND-HIL are listed in this table.
*Genome position of most proximal and distal probe fulfilling hypomethylation criteria.
†Number of probes within the locus fulfilling hypomethylation criteria.
‡Minimum p value among probes fulfilling hypomethylation criteria.
BWS, Beckwith–Wiedemann syndrome; DMR, differentially methylated region; HIL, hypomethylation of imprinted loci; ID, imprinting disorder; TND, transient neonatal diabetes.