DNA methylation episignature, extension of the clinical features and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7

Liselot van der Laan, Karim Karimi, Kathleen Rooney, Peter Lauffer, Haley McConkey, Pilar Caro, Raissa Relator, Michael A Levy, Pratibha Bhai, Cyril Mignot, Boris Keren, Silvana Briuglia, Andrew K Sobering, Dong Li, Lisenka E L M Vissers, Alexander J M Dingemans, Irene Valenzuela, Eline A Verberne, Mala Misra-Isrie, Petra J G ZwijnenburgQuinten Waisfisz, Mariëlle Alders, Sebastian Sailer, Christian P Schaaf, Marcel M A M Mannens, Bekim Sadikovic, Mieke M van Haelst, Peter Henneman

Research output: Contribution to journalArticleAcademicpeer-review


PURPOSE: Hao-Fountain syndrome (HAFOUS) is a neurodevelopmental disorder caused by pathogenic variants in USP7. HAFOUS is characterized by developmental delay, intellectual disability, speech delay, behavioral abnormalities, autism spectrum disorder, seizures, hypogonadism and mild dysmorphic features. We investigated the phenotype of eighteen participants with HAFOUS and performed DNA methylation (DNAm) analysis, aiming to generate a diagnostic biomarker. Furthermore, we performed comparative analysis with known episignatures to gain more insight into the molecular pathophysiology of Hao-Fountain syndrome.

METHODS: We assessed genomic DNAm profiles of eighteen individuals with pathogenic variants and variants of uncertain significance (VUS) in USP7 to map and validate a specific episignature. The comparison between the USP7 cohort and 56 rare genetic disorders with earlier reported DNAm episignatures was performed with statistical and functional correlation.

RESULTS: We mapped a sensitive and specific DNAm episignature for pathogenic variants in USP7 and utilized this to reclassify the VUS. Comparative epigenomic analysis showed evidence of HAFOUS similarity to a number of other rare genetic episignature disorders.

CONCLUSIONS: We discovered a sensitive and specific DNAm episignature as a robust diagnostic biomarker for HAFOUS that enables VUS reclassification in USP7. We also expand the phenotypic spectrum of nine new and five previously reported individuals with HAFOUS.

Original languageEnglish
Pages (from-to)101050
JournalGenetics in medicine
Publication statusE-pub ahead of print - 18 Dec 2023

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