BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin–Siris and Nicolaides–Baraitser syndromes. Issue 1 (December 2018)

• Record Type: Journal Article
• Authors: Aref-Eshghi, Erfan; Bend, Eric; Hood, Rebecca; Schenkel, Laila; Carere, Deanna; Chakrabarti, Rana; Nagamani, Sandesh; Cheung, Sau; Campeau, Philippe; Prasad, Chitra; Siu, Victoria; Brady, Lauren; Tarnopolsky, Mark; Callen, David; Innes, A.; White, Susan; Meschino, Wendy; Shuen, Andrew; Paré, Guillaume; Bulman, Dennis; Ainsworth, Peter; Lin, Hanxin; Rodenhiser, David; Hennekam, Raoul; Boycott, Kym; Schwartz, Charles; Sadikovic, Bekim
• Is Part Of: Nature communications. Volume 9:Issue 1(2018)
• Page Start: 1
• Page End: 15
• Publication Date: 2018-12
• Subjects: Biology -- Periodicals; Physical sciences -- Periodicals; 505
• DOI: 10.1038/s41467-018-07193-y
• Languages: English
• ISSNs: 2041-1723

Abstract

Abstract Coffin–Siris and Nicolaides–Baraitser syndromes (CSS and NCBRS) are Mendelian disorders caused by mutations in subunits of the BAF chromatin remodeling complex. We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, andSMARCA4 ) and NCBRS (SMARCA2 ). We demonstrate that the degree of similarity in the epi-signatures of some CSS subtypes and NCBRS can be greater than that within CSS, indicating a link in the functional basis of the two syndromes. We show that chromosome 6q25 microdeletion syndrome, harboringARID1B deletions, exhibits a similar CSS/NCBRS methylation profile. Specificity of this epi-signature was confirmed across a wide range of neurodevelopmental conditions including other chromatin remodeling and epigenetic machinery disorders. We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening. Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations.