Article
Author: Gorman, Kathleen ; Gallant, Emily ; McCann, Cathleen ; Sidlow, Richard ; McConkey, Haley ; Ghoumid, Jamal ; O'Shea, Jessica ; Sallevelt, Suzanne ; Hauser, Natalie ; Marin, Victor ; Prasad, Chitra ; Bouman, Arjan ; Wentzensen, Ingrid M ; Hannibal, Mark ; Menke, Leonie A ; Lichtenstein, Yael ; Smol, Thomas ; Weiss, Karin ; Relator, Raissa ; Patel, Chirag ; Balci, Tugce B ; Karimi, Karim ; Motta, Jamie ; Lancaster, Emily ; Reilly, Jack ; Miranda, Valancy ; Tedder, Matthew L ; Louie, Raymond J ; Clarkson, Katie ; Valenzuela Palafoll, Irene ; Barkan, Tali ; Keren, Boris ; Maria-Noelia, Seco Moro ; Diaz de Bustamante, Aranzazú ; Raskin, Salmo ; Poirsier, Celine ; Drazba, Katy ; Marom, Daphna ; Turnpenny, Peter D ; Levy, Michael A ; Kerkhof, Jennifer ; Morrison, Jennifer ; Campeau, Philippe M ; Cohen, Lior ; Symonds, Joseph D ; Sadikovic, Bekim ; Colin, Estelle ; Rankin, Julia
Pathogenic heterozygous variants in CHD4 cause Sifrim-Hitz-Weiss syndrome, a neurodevelopmental disorder associated with brain anomalies, heart defects, macrocephaly, hypogonadism, and additional features with variable expressivity. Most individuals have non-recurrent missense variants, complicating variant interpretation. A few were reported with truncating variants, and their role in disease is unclear. DNA methylation episignatures have emerged as highly accurate diagnostic biomarkers in a growing number of rare diseases. We aimed to study evidence for the existence of a CHD4-related DNA methylation episignature. We collected blood DNA samples and/or clinical information from 39 individuals with CHD4 variants, including missense and truncating variants. Genomic DNA methylation analysis was performed on 28 samples. We identified a sensitive and specific DNA methylation episignature in samples with pathogenic missense variants within the ATPase/helicase domain. The same episignature was observed in a family with variable expressivity, a de novo variant near the PHD domain, variants of uncertain significance within the ATPase/helicase domain, and a sample with compound heterozygous variants. DNA methylation data revealed higher percentages of shared probes with BAFopathies, CHD8, and the terminal ADNP variants encoding a protein known to form the ChAHP complex with CHD4. Truncating variants, as well as a sample with a recurrent pathogenic missense variant, exhibited DNA methylation profiles distinct from the ATPase/helicase domain episignature. These DNA methylation differences, together with the distinct clinical features observed in those individuals, provide preliminary evidence for clinical and molecular sub-types in the CHD4-related disorder.