Functional correlation of genome‐wide DNA methylation profiles in genetic neurodevelopmental disorders
Open accessAbstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive, and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes, which can share significant overlap among different conditions. In this study, we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders.
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As genomic DEE episignatures are identified, testing may clarify the pathogenicity of variants of unknown significance and identify other pathogenic variants with imprinting and repeat expansion disorders.
“As genomic DEE episignatures are identified, testing may clarify the pathogenicity of variants of unknown significance and identify other pathogenic variants with imprinting and repeat expansion disorders 142, 179 .”
From Developmental and epileptic encephalopathies (2024) · cites this paper as [179]
Section 4.1 says episignature analysis can be used as a reflex test for a variant of unknown significance, supporting its potential to help clarify a variant’s significance. The cited paper does not establish the claim about identifying pathogenic variants in imprinting or repeat-expansion disorders, or address DEE episignatures specifically. (LLM, conf=0.82)
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Developmental and epileptic encephalopathies
Scheffer, I. E., Zuberi, S., Mefford, H. C., Guerrini, R., & McTague, A. (2024) · Nature Reviews Disease Primers · doi:10.1038/s41572-024-00546-6 · Cited by 128 · see citing works
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- Authors
- Levy, M. A., Relator, R., McConkey, H., Pranckeviciene, E., Kerkhof, J., Barat‐Houari, M., Bargiacchi, S., Biamino, E., Palomares Bralo, M., Cappuccio, G., Ciolfi, A., Clarke, A., DuPont, B. R., Elting, M. W., Faivre, L., Fee, T., Ferilli, M., Fletcher, R. S., Cherick, F., Foroutan, A., Friez, M. J., Gervasini, C., Haghshenas, S., Hilton, B. A., Jenkins, Z., Kaur, S., Lewis, S., Louie, R. J., Maitz, S., Milani, D., Morgan, A. T., Oegema, R., Østergaard, E., Pallares, N. R., Piccione, M., Plomp, A. S., Poulton, C., Reilly, J., Rius, R., Robertson, S., Rooney, K., Rousseau, J., Santen, G. W. E., Santos‐Simarro, F., Schijns, J., Squeo, G. M., John, M. S., Thauvin‐Robinet, C., Traficante, G., van der Sluijs, P. J., Vergano, S. A., Vos, N., Walden, K. K., Azmanov, D., Balci, T. B., Banka, S., Gecz, J., Henneman, P., Lee, J. A., Mannens, M. M. A. M., Roscioli, T., Siu, V., Amor, D. J., Baynam, G., Bend, E. G., Boycott, K., Brunetti‐Pierri, N., Campeau, P. M., Campion, D., Christodoulou, J., Dyment, D., Esber, N., Fahrner, J. A., Fleming, M. D., Genevieve, D., Heron, D., Husson, T., Kernohan, K. D., McNeill, A., Menke, L. A., Merla, G., Prontera, P., Rockman‐Greenberg, C., Schwartz, C., Skinner, S. A., Stevenson, R. E., Vincent, M., Vitobello, A., Tartaglia, M., Alders, M., Tedder, M. L., & Sadikovic, B.
- Affiliations
- London Health Sciences Centre (CA)
- Verspeeten Clinical Genome Centre London Health Sciences Centre London Ontario Canada
- Centre Hospitalier Universitaire de Montpellier (FR)
- Meyer Children's Hospital (IT)
- University of Turin (IT)
- Institute of Medical and Molecular Genetics (INGEMM) Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII Madrid Spain
- Telethon Institute Of Genetics And Medicine (IT)
- Bambino Gesù Children's Hospital (IT)
- Cardiff University (GB)
- Greenwood Genetic Center (US)
- Amsterdam University Medical Centers (NL)
- Inserm (FR)
- Genetic Medical Center, CHU Clermont Ferrand France
- Western University (CA)
- University of Milan (IT)
- University of Otago (NZ)
- The University of Melbourne (AU)
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine University of British Columbia
- Azienda Ospedaliera San Gerardo (IT)
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico (IT)
- Utrecht University (NL)
- University of Copenhagen (DK)
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine CHU Montpellier Montpellier France
- University of Palermo (IT)
- King Edward Memorial Hospital (AU)
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute Melbourne Australia
- CHU Sainte-Justine Research Center (CA)
- Leiden University Medical Center (NL)
- Hospital Universitario La Paz (ES)
- Amsterdam UMC Location University of Amsterdam (NL)
- University of Naples Federico II (IT)
- Department of Clinical Genetics LUMC Leiden The Netherlands
- Eastern Virginia Medical School (US)
- Queen Elizabeth II Medical Centre (AU)
- Department of Pediatrics, Division of Medical Genetics Western University London Ontario Canada
- University of Manchester (GB)
- School of Medicine, Robinson Research Institute University of Adelaide Adelaide Australia
- UNSW Sydney (AU)
- The Kids Research Institute Australia (AU)
- PreventionGenetics Marshfield Wisconsin USA
- University of Ottawa (CA)
- KAT6A Foundation New York New York USA
- Johns Hopkins University (US)
- Boston Children's Hospital (US)
- Montpellier University, Reference Center for Rare Disease Medical Genetic Department for Rare Disease and Personalize Medicine CHU Montpellier Montpellier France
- AP‐HP, Département de Génétique Médicale Groupe Hospitalier Pitié Salpétrière Paris France
- Sheffield Children's NHS Foundation Trust (GB)
- Casa Sollievo della Sofferenza (IT)
- University of Perugia (IT)
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences University of Manitoba and Program in Genetics and Metabolism, Shared Health MB Winnipeg Manitoba Canada
- Centre National de la Recherche Scientifique (FR)
- ORCID
- Levy, Michael A.
- Relator, Raissa
- Kerkhof, Jennifer
- Barat‐Houari, Mouna
- Bargiacchi, Sara
- Biamino, Elisa
- Cappuccio, Gerarda
- Ciolfi, Andrea
- Clarke, Angus
- Elting, Mariet W.
- Faivre, Laurence
- Ferilli, Marco
- Foroutan, Aidin
- Gervasini, Cristina
- Haghshenas, Sadegheh
- Hilton, Benjamin A.
- Jenkins, Zandra
- Kaur, Simranpreet
- Louie, Raymond J.
- Maitz, Silvia
- Milani, Donatella
- Morgan, Angela T.
- Oegema, Renske
- Østergaard, Elsebet
- Piccione, Maria
- Plomp, Astrid S.
- Reilly, Jack
- Robertson, Stephen
- Rooney, Kathleen
- Rousseau, Justine
- Santen, Gijs W. E.
- Santos‐Simarro, Fernando
- Squeo, Gabriella M.
- John, Miya St
- Thauvin‐Robinet, Christel
- Traficante, Giovanna
- Vergano, Samantha A.
- Vos, Niels
- Azmanov, Dimitar
- Banka, Siddharth
- Gecz, Jozef
- Henneman, Peter
- Lee, Jennifer A.
- Mannens, Marcel M. A. M.
- Roscioli, Tony
- Siu, Victoria
- Amor, David J.
- Baynam, Gareth
- Bend, Eric G.
- Boycott, Kym
- Brunetti‐Pierri, Nicola
- Campeau, Philippe M.
- Campion, Dominique
- Christodoulou, John
- Dyment, David
- Esber, Natacha
- Fahrner, Jill A.
- Fleming, Mark D.
- Husson, Thomas
- Kernohan, Kristin D.
- McNeill, Alisdair
- Menke, Leonie A.
- Merla, Giuseppe
- Prontera, Paolo
- Schwartz, Charles
- Skinner, Steven A.
- Stevenson, Roger E.
- Vincent, Marie
- Vitobello, Antonio
- Tartaglia, Marco
- Alders, Marielle
- Tedder, Matthew L.
- Sadikovic, Bekim
- Venue
- Human Mutation
- Publisher
- Wiley
- Published
- 2022-08-21
- Volume
- 43
- Issue
- 11
- Pages
- 1609-1628
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- OpenAlex
- W4288535921
- Cited by
- 76
- References
- 46
- Citations by year
- 2026: 9 · 2025: 19 · 2024: 31 · 2023: 15 · 2022: 2
- FWCI
- 5.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- HAL (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Nova Science Publishers (Nova Science Publishers, Inc.) (submittedVersion, other-oa)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Pure Amsterdam UMC (submittedVersion, other-oa)
- Research Explorer (The University of Manchester) (submittedVersion, other-oa)
- Funders
- Genome Canada (OGI-188)
- London Health Sciences Centre
- Children’s Hospital of Wisconsin Research Institute
- Children's Hospital Foundation
- Ontario Genomics
- Murdoch Children's Research Institute
- Royal Children's Hospital Foundation
- Government of Canada (OGI-188)
- Ontario Genomics Institute (OGI-188)
- Ministero della Salute ("5 x 1000"., RCR‐2020‐23670068_001, FOE 2019, “5×1000”, CCR-2017-23669081)
- State Government of Victoria
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- DNA methylation, genetic neurodevelopmental disorders, differentially methylated regions, differentially methylated probes, epigenetic biomarkers, promoter, CpG islands, neurogenesis, synaptic signaling, synaptic transmission, molecular etiology
- MeSH terms
- Humans, Syndrome, CpG Islands, DNA Methylation, DNA, Intergenic, Epigenesis, Genetic, Neurodevelopmental Disorders
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