REFERENCES
3. Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet 2013;14:204-20.
4. Morgan HD, Santos F, Green K, Dean W, Reik W. Epigenetic reprogramming in mammals. Hum Mol Genet 2005;14:R47-58.
5. Numata S, Ye T, Hyde TM, Guitart-Navarro X, Tao R, et al. DNA methylation signatures in development and aging of the human prefrontal cortex. Am j hum genet 2012;90:260-72.
6. Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao R, et al. Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature 2011;478:519-23.
7. Tatton-Brown K, Loveday C, Yost S, Clarke M, Ramsay E, et al. Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability. Am J Hum Genet 2017;100:725-36.
8. Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: postnatal malleability and therapeutic prospects. Hum Mol Genet 2019;28:R254-64.
9. Cytrynbaum C, Choufani S, Weksberg R. Epigenetic signatures in overgrowth syndromes: Translational opportunities. Am J Med Genet A 2019;181:491-501.
10. Butcher DT, Cytrynbaum C, Turinsky AL, Siu MT, Inbar-Feigenberg M, et al. CHARGE and kabuki syndromes: gene-specific DNA methylation signatures identify epigenetic mechanisms linking these clinically overlapping conditions. Am J Hum Genet 2017;100:773-88.
11. Chater-Diehl E, Ejaz R, Cytrynbaum C, Siu MT, Turinsky A, et al. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. BMC Med Genomics 2019;12:105.
13. Torres IO, Fujimori DG. Functional coupling between writers, erasers and readers of histone and DNA methylation. Curr opin struct biol 2015;35:68-75.
14. Fuks F. DNA methylation and histone modifications: teaming up to silence genes. Curr Opin Genet Dev 2005;15:490-5.
15. Choufani S, Cytrynbaum C, Chung BH, Turinsky AL, Grafodatskaya D, et al. NSD1 mutations generate a genome-wide DNA methylation signature. Nat Commun 2015;6:10207.
16. Aref-Eshghi E, Bend EG, Hood RL, Schenkel LC, Carere DA, et al. BAFopathies’ DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin-Siris and Nicolaides-Baraitser syndromes. Nat Commun 2018;9:4885.
17. Aref-Eshghi E, Bend EG, Colaiacovo S, Caudle M, Chakrabarti R, et al. Diagnostic utility of genome-wide DNA methylation testing in genetically unsolved individuals with suspected hereditary conditions. Am J Hum Genet 2019;104:685-700.
18. Kleefstra T. Disruption of the gene euchromatin histone methyl transferase1 (Eu-HMTase1) is associated with the 9q34 subtelomeric deletion syndrome. J Med Genet 2005;42:299-306.
19. Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, et al. Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype. J Med Genet 2009;46:598-606.
20. Pontén F, Jirström K, Uhlen M. The Human Protein Atlas - a tool for pathology. J Pathol 2008;216:387-93.
21. Yatsenko SA, Brundage EK, Roney EK, Cheung SW, Chinault AC, et al. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet 2009;18:1924-36.
22. Kleefstra T, de Leeuw N. Kleefstra Syndrome. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens K, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; .
23. Cormier-Daire V, Molinari F, Rio M, Raoul O, de Blois MC, et al. Cryptic terminal deletion of chromosome 9q34: a novel cause of syndromic obesity in childhood? J Med Genet 2003;40:300-3.
24. Stewart DR, Huang A, Faravelli F, Anderlid BM, Medne L, et al. Subtelomeric deletions of chromosome 9q: A novel microdeletion syndrome. Am J Med Genet A 2004;128A:340-51.
25. Yatsenko SA. Deletion 9q34.3 syndrome: genotype-phenotype correlations and an extended deletion in a patient with features of Opitz C trigonocephaly. J Med Genet 2005;42:328-35.
26. Willemsen MH, Vulto-van Silfhout AT, Nillesen WM, Wissink-Lindhout WM, van Bokhoven H, et al. Update on Kleefstra Syndrome. Mol Syndromol 2012;2:202-12.
27. Team RC. R: A language and environment for statistical computing. Vienna, Austria; 2013. Available from: https://www.R-project.org. [Last accessed on 25 May 2020].
28. Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, et al. Discovery of cross-reactive probes and polymorphic CpGs in the illumina infinium HumanMethylation450 microarray. Epigenetics 2013;8:203-9.
29. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 2014;30:1363-9.
30. Houseman EA, Houseman E, Accomando WP, Koestler DC, Christensen BC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC bioinformatics 2012;13:86.
31. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43:e47.
33. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000;25:25-9.
34. Lee H, Graham JM, Rimoin DL, Lachman RS, Krejci P, et al. Exome sequencing identifies PDE4D mutations in acrodysostosis. Am J Hum Genet 2012;90:746-51.
35. Campbell CL, Collins RT II, Zarate YA. Severe neonatal presentation of Kleefstra syndrome in a patient with hypoplastic left heart syndrome and 9q34.3 microdeletion. Birth Defects Res A Clin Mol Teratol 2014;100:985-90.
36. Yatsenko SA, Hixson P, Roney EK, Scott DA, Schaaf CP, et al. Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization. Hum Genet 2012;131:1895-910.
37. Schwaibold EMC, Smogavec M, Hobbiebrunken E, Winter L, Zoll B, et al. Intragenic duplication of EHMT1 gene results in Kleefstra syndrome. Mol Cytogenet 2014;7:74.
38. Ferry L, Fournier A, Tsusaka T, Adelmant G, Shimazu T, et al. Methylation of DNA ligase 1 by G9a/GLP recruits UHRF1 to replicating DNA and regulates DNA methylation. Mol Cell 2017;67:550-65.e5.
39. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007;317:1760-4.
40. von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol Cell 2016;62:848-61.
41. Krzyzewska IM, Maas SM, Henneman P, Lip KVD, Venema A, et al. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin epigenet 2019;11:156-15.
42. Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, et al. Evaluation of DNA methylation episignatures for diagnosis and phenotype correlations in 42 mendelian neurodevelopmental disorders. Am J Hum Genet 2020;106:356-70.
43. Hayashi S, Takeichi M. Emerging roles of protocadherins: from self-avoidance to enhancement of motility. J Cell Sci 2015;128:1455-64.
44. El Hajj N, Dittrich M, Haaf T. Epigenetic dysregulation of protocadherins in human disease. Semin Cell Dev Biol 2017;69:172-82.
45. Strong E, Butcher DT, Singhania R, Mervis CB, Morris CA, et al. Symmetrical dose-dependent DNA-methylation profiles in children with deletion or duplication of 7q11.23. Am J Hum Genet 2015;97:216-27.
46. Iacono G, Dubos A, Meziane H, Benevento M, Habibi E, et al. Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome. Nucleic Acids Res 2018;46:4950-65.
47. Tachibana M, Matsumura Y, Fukuda M, Kimura H, Shinkai Y. G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. EMBO J 2008;27:2681-90.
48. Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, et al. Age-associated DNA methylation in pediatric populations. Gen Res 2012;22:623-32.
