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Genome-wide DNA methylation profiling and exome sequencing resolved a long-time misdiagnosed case


The search for aetiology of Mendelian disorders is traditionally based on the observation of clinical phenotypes and molecular screening of associated genes. However, a disease-specific diagnosis can be challenging. In this study we detail how the combinatorial genomic and epigenomic assessment allowed to find the underlying molecular event of a clinical case that remained misdiagnosed for years. The individual was referred as affected by an atypical form of Kabuki syndrome with a variant of uncertain significance in the KMT2D gene. However, significant inconsistencies with this diagnosis emerged upon familial segregation of the variant and after the clinical re-evaluation. Therefore, we applied an epigenomic strategy by studying the DNA methylation profile which resulted not consistent with the Kabuki syndrome episignature or with any other disorder-specific episignature described so far, providing strong evidence that the Kabuki syndrome diagnosis does not apply. This result led us to further investigate for epigenetic machinery diseases by using a multigene panel for chromatinopathies. Since this analysis yielded negative results, we applied a whole exome sequencing and identified a de novo pathogenic variant in the CTNNB1 gene associated to NEDSDV syndrome, a neurodevelopmental disorder characterized by intellectual disability and craniofacial anomalies. Based on molecular results and the updated clinical features, we confirmed the NEDSDV diagnosis. Our findings show that the combination of genomic and epigenomics strategies, along with a deeper analysis of clinical phenotype, may provide a significant improvement in the diagnostic protocols for rare genetic disorders and help resolve long-time misdiagnosed and unsolved case.

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We are grateful to the patient and parents for their cooperation in this study and for giving consent to publish data and photographs. Funding for this study was provided by Telethon - Italy (Grant no. GGP13231), Italian Ministry of Health, Jerome Lejeune Foundation, Daunia Plast to GM; by the London Health Sciences Molecular Diagnostics Development Fund and Genome Canada Genomic Applications Partnership Program Grant (Beyond Genomics: Assessing the Improvement in Diagnosis of Rare Diseases using Clinical Epigenomics in Canada, EpiSign-CAN) awarded to BS. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the paper.

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Authors and Affiliations



Conceptualization: AP, GM, GMS. Investigation and Methodology: AP, ED, EC, JK; Data curation and formal analysis: JK, HMC, BS, TM, SC; Patients and clinical follow-up: LS, MCD; Writing—original draft: AP, MCD, GM; Writing-review & editing: AP, MCD, BS, JK, GMS, HMC, TM, GM. Funding acquisition: GM, BS. All authors have read and agreed to the published version of the paper. The corresponding author has had full access to the data in the study and final responsibility for the decision to submit for publication.

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Correspondence to Giuseppe Merla.

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Paparella, A., Squeo, G.M., Di Venere, E. et al. Genome-wide DNA methylation profiling and exome sequencing resolved a long-time misdiagnosed case. J Hum Genet 67, 547–551 (2022).

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