Table 2 Comprehensive DNAm signature testing can help diagnosing previously unsolved individuals.
Case number | Phenotype | Prior genetic diagnostics | Result EpiSign | Episignature corresponding with phenotype | Relevant diagnostics afterwards to clarfiy EpiSign result | Episignature explaining DNA variant identified | Post-EpiSign ACMG classification/criteria |
|---|---|---|---|---|---|---|---|
Case 2 | ID | ES complete duo | Silver Russel methylation signature, hypomethylation H19 locus | yes | Hypomethylation 11p15, confirmed with MLPA | n/a (imprinting disorder) | n/a (imprinting disorder) |
Case 6 | ID + MCA | ES complete trio | Koolen de Vries syndrome methylation signature | yes | NM_001193466.1(KANSL1):c.2725-6T>C, p.?, inherited from mother (which turned out to be also affected) | yes | Likely pathogenic (PS3, PM2, PP1strong) |
Case 11 | MCA | Targeted analysis CHD7 gene | CHARGE syndrome methylation signature | yes | NM_017780.4(CHD7):c.5210+1091T>G, p.?, clinical phenotype matching CHARGE syndrome | yes | Likely pathogenic (PS3, PM2, PM6) |
Case 20 | ID + short stature | ES complete trio | Kabuki syndrome methylation signature | no | No variants detected in KMT2D and KDM6A. | no | n/a |
Case 21 | ID | ES MCA/ID panel trio | Coffin-Siris syndrome methylation signature | yes | Mosaic variant (19%): NM_006015.6(ARID1A):c.666C>A, p.Tyr222*, clinical phenotyping matching | yes | Pathogenic (PVS1, PM2, PM6) |
Case 29 | ID + MCA | ES complete trio | Hunter-McAlpine syndrome methylation signature, weak pattern | yes | 5q35 duplication, inherited from the affected mother, identified upon re-analysis, phenotype matching | yes | Pathogenic (1 A, 2 A, 3 C, 4 L, 5D) |
Case 31 | ID + MCA | ES complete single | UBE2A methylation signature | no | No variants detected in UBE2A. | no | n/a |
Case 49 | ID + epilepsy | ES complete trio | Beckwith-Wiedemann syndrome methylation signature | no | Hypomethylation of the imprinted locus KCNQ1OT1 (11p15) detected but the diagnosis does not match the clinical phenotype | n/a (imprinting disorder) | n/a (imprinting disorder) |
Case 52 | ID + hypotonia | ES MCA/ID panel trio, ES ciliopathy panel | Wiedemann-Steiner syndrome, CHARGE syndrome, and Cornelia de Lange syndrome methylation signatures (with Wiedemann-Steiner syndrome methylation signatures showing the strongest profile, and Cornelia de Lange methylation signature with low confidence) | yes | Targeted ES re-analysis showed a pathogenic de novo variant in KMT2A (NM_001197104.2(KMT2A):c.3790C>T, p.(Arg1264*)), confirming the molecular diagnosis of Wiedemann-Steiner syndrome | yes | Pathogenic (PVS1, PS2, PS4, PM2, PM1) |
Case 59 | ID + MCA | ES complete trio | Cornelia de Lange syndrome | yes | Clinical phenotype matching for Cornelia de Lange syndrome but re-analysis provided no molecular diagnosis so far | no | n/a |
Case 65 | ID + MCA | ES complete single | X-linked Claes-Jensen syndrome carrier | no | Positive DNA methylation signature for female carrier of Claes-Jensen syndrome, but no variant found in KDM5C, both in ES and in RNA-seq | no | n/a |
Case 80 | ID + obesity | ES complete trio | Kleefstra syndrome methylation signature | partially | No variants found in EHMT1 via ES and RNA-seq | no | n/a |
Case 87 | ID + epilepsy | ES epilepsy panel single | Abnormal methylation GNAS; Pseudohypoparathyereoidy type 1 | partially | Pseudyohypoparathyroidism type 1 (PHP1) based on abberant methylation of GNAS, validated by MLPA | n/a (imprinting disorder) | n/a (imprinting disorder) |
Case 113 | ID + obesity | ES complete trio | Borjeson-Forssman-Lehmann syndrome or Chung-Jansen syndrome methylation signature | yes | NM_017934.6(PHIP):c.1095+5G>C, p.?. Further RNA studies showed an abnormal transcript caused by aberrant splicing. Variant was reclassified to likely pathogenic (class 4) based on the RNA and EpiSign findings. Clinical phenotype matched Chung-Jansen syndrome (CHUJANS) | yes | Likely pathogenic (PS3, PM2, PP3) |
Case 126 | ID + MCA | ES MCA/ID panel trio | Abnormal methylation SNRPN promoter | no | Following the EpiSign, an MLPA was performed, showing a duplication in this region. There was also hypomethylation detected indicating that the duplication was of paternal origin. Paternal 15q duplications do not usually show phenotypic expression | yes | n/a (imprinting disorder) |
Case 135 | MCA | ES complete trio | MRD53 syndrome (SETD5) and KBG syndrome (ANKRD11) methylation signatures | no | No pathogenic variants were detected in both SETD5 and ANKRD11 | no | n/a |
Case 171 | MCA | ES MCA panel trio | Temple syndrome methylation signature | yes | Hypomethylation MEG3 promotor, validated with MLPA | n/a (imprinting disorder) | n/a (imprinting disorder) |
Case 179 | Short stature + MCA | ES complete trio | Inconclusive for BAFopathy methylation signature | no | No matching phenotype for BAFopathy spectrum, and no mutation identified in BAFopathy genes | no | n/a |
Case 212 | Others | ES complete trio | Wieacker-Wolff syndrome methylation signature, low confidence | no | ES and RNA-seq detected no variants in ZC4H2. EpiSign mentioned a low confidence profile. No matching clinical phenotype | no | n/a |
Case 217 | ID + macrocephaly | ES ID panel trio | Rubinstein-Taybi syndrome methylation signature, low confidence | no | EpiSign with a low confidence profile (with a profile of patient localized between positive cases and controls). Clinical phenotype does not fit well | no | n/a |
