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Article
Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes
American Journal of Human Genetics
  • Erfan Aref-Eshghi, Western University
  • David I Rodenhiser, Western University
  • Laila C Schenkel, Western University
  • Hanxin Lin, Western University
  • Cindy Skinner, Greenwood Genetics Center
  • Peter Ainsworth, Western University
  • Guillaume Paré, McMaster University
  • Rebecca L Hood, University of Ottawa
  • Dennis E Bulman, University of Ottawa
  • Kristin D Kernohan, University of Ottawa
  • Care4Rare Canada Consortium, Care4Rare Canada Consortium
  • Kym M Boycott, University of Ottawa
  • Philippe M Campeau, University of Montreal
  • Charles Schwartz, Greenwood Genetics Center
  • Bekim Sadikovic, Western University
Document Type
Article
Publication Date
1-4-2018
URL with Digital Object Identifier
https://doi.org/10.1016/j.ajhg.2017.12.008
Disciplines
Abstract

Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.

Citation Information
Erfan Aref-Eshghi, David I Rodenhiser, Laila C Schenkel, Hanxin Lin, et al.. "Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes" American Journal of Human Genetics Vol. 102 Iss. 1 (2018) p. 156 - 174
Available at: http://works.bepress.com/bekim-sadikovic/17/