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 Episign^TM 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.