DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency

Jet Coenen-van der Spek, Raissa Relator, Jennifer Kerkhof, Haley McConkey, Michael A. Levy, Matthew L. Tedder, Raymond J. Louie, Robin S. Fletcher, Hannah W. Moore, Anna Childers, Ellyn R. Farrelly, Neena L. Champaigne, Michael J. Lyons, David B. Everman, R. Curtis Rogers, Steven A. Skinner, Alicia Renck, Dena R. Matalon, Shelley K. Dills, Berrin MonteleoneSerwet Demirdas, Alexander J.M. Dingemans, Laura Donker Kaat, Sharon M. Kolk, Rolph Pfundt, Patrick Rump, Bekim Sadikovic*, Tjitske Kleefstra, Kameryn M. Butler

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)


Purpose: Witteveen-Kolk syndrome (WITKOS) is a rare, autosomal dominant neurodevelopmental disorder caused by heterozygous loss-of-function alterations in the SIN3A gene. WITKOS has variable expressivity that commonly overlaps with other neurodevelopmental disorders. In this study, we characterized a distinct DNA methylation epigenetic signature (episignature) distinguishing WITKOS from unaffected individuals as well as individuals with other neurodevelopmental disorders with episignatures and described 9 previously unpublished individuals with SIN3A haploinsufficiency. Methods: We studied the phenotypic characteristics and the genome-wide DNA methylation in the peripheral blood samples of 20 individuals with heterozygous alterations in SIN3A. A total of 14 samples were used for the identification of the episignature and building of a predictive diagnostic biomarker, whereas the diagnostic model was used to investigate the methylation pattern of the remaining 6 samples. Results: A predominantly hypomethylated DNA methylation profile specific to WITKOS was identified, and the classifier model was able to diagnose a previously unresolved test case. The episignature was sensitive enough to detect individuals with varying degrees of phenotypic severity carrying SIN3A haploinsufficient variants. Conclusion: We identified a novel, robust episignature in WITKOS due to SIN3A haploinsufficiency. This episignature has the potential to aid identification and diagnosis of individuals with WITKOS.

Original languageEnglish
Pages (from-to)63-75
Number of pages13
JournalGenetics in Medicine
Issue number1
Early online date17 Nov 2022
Publication statusPublished - Jan 2023

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© 2022 American College of Medical Genetics and Genomics


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