Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders

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.