Abstract
Disease-causing variants in chromatin regulator genes cause many developmental disorders. DNA methylation (DNAm) signatures are emerging as a diagnostic tool to identify disease causes and classify variants of uncertain significance (VUS). This study evaluates their diagnostic utility in a routine clinical setting. We retrospectively analyzed 298 patients from the Erasmus MC who underwent DNAm signature testing using the commercial EpisignTM platform between February 2019 and June 2023. The cohort included 75 targeted analyses for follow-up on prior genetic findings and 223 complete analyses for cases unsolved after prior diagnostic testing. In the 75 targeted analyses, DNAm signatures were positive in 18% (10/55) for (VUS), 91% (10/11) for likely pathogenic variants, and 89% (8/9) for pathogenic variants. In 223 complete analyses, a disease-linked DNAm signature was observed in 9.0% (20/223), with a (partial) phenotypic match in 55% of those (11/20) but no match in 45% (9/20). In 81.8% (9/11) of those DNAm signature positive cases with a phenotypic match, retrospective analysis identified a causative DNA variant or confirmed independently an imprinting disorder that was unidentified previously, providing valuable diagnostic insights with an overall diagnostic yield of 4.0% (9/223) for these molecular confirmed cases. In conclusion, this study supports the clinical utility of DNAm signatures to assist in interpreting and classifying VUS, but also as a complementary tool when prior genetic testing, including exome sequencing, failed to provide a diagnosis.
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Data availability
All relevant data are included in this paper. Underlying raw genetic and methylation data cannot be shared due to the given consent under which the individuals were recruited.
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All relevant data are within the paper or its Supporting Information files.
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Acknowledgements
We thank all patients and families for their participation in this study. We thank Marielle Alders (Amsterdam UMC) for helpful discussions and Burcu Akman (IBG Izmir) for critical reading of the manuscript.
Funding
The Barakat lab acknowledges general support from the Netherlands Organization for Scientific Research and other ongoing support for rare disease research from Stichting 12q, EpilepsieNL, CURE Epilepsy and the Spastic Paraplegia Foundation, Inc. CD’s PhD project is supported by the Sophia Kinderziekenhuis Fonds (CAM19-09D) and acknowledges support from the Erasmus MC Centrum voor Zeldzame Aandoeningen. Funding bodies did not have any influence on study design, results, and data interpretation or final manuscript.
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Conceptualization DJS, TSB; data curation DJS, CD; formal analysis DJS, CD, TSB, RS, FF; funding acquisition TSB; methodology DJS, CD, TSB; supervision TSB, ASB; writing original draft, writing—review and editing CD, DJS, DR, AB, VJMV, LDK, SGK, YB, SD, SZ, MFD, SHD, LHH, MAS, MW, FS, MD, HTB, RM, AG, JAH, IMBHL, YI, AK, VS, KES, GMSM, MWW, TJH, TK, TSB.
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The authors declare no competing interests.
Ethics approval
Using genome-wide technologies for diagnostic purposes was previously approved by the Erasmus MC institutional review board (MEC-2012-387). All individuals or legal guardians provided written consent to use pseudoanonymized clinical and analysis data.
Web resources
OMIM, http://omim.org/. gnomAD, http://gnomad.broadinstitute.org. SIFT, https://sift.bii.a-star.edu.sg/. PolyPhen2, http://genetics.bwh.harvard.edu/pph2/.
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Smits, D.J., Debuy, C., Brooks, A.S. et al. Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders. Eur J Hum Genet 33, 1281–1289 (2025). https://doi.org/10.1038/s41431-025-01919-5
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DOI: https://doi.org/10.1038/s41431-025-01919-5
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