title: The clustering of functionally related genes contributes to CNV-mediated disease.
abstract: Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three different functional networks, we identified unexpectedly large numbers of functionally related genes within de novo CNVs from two large independent cohorts of individuals with developmental disorders. The presence of multiple functionally related genes was a significant predictor of a CNV's pathogenicity when compared to CNVs from apparently healthy individuals and a better predictor than the presence of known disease or haploinsufficient genes for larger CNVs. The functionally related genes found in the de novo CNVs belonged to 70% of all clusters of functionally related genes found across the genome. De novo CNVs were more likely to affect functional clusters and affect them to a greater extent than benign CNVs (P = 6 × 10(-4)). Furthermore, such clusters of functionally related genes are phenotypically informative: Different patients possessing CNVs that affect the same cluster of functionally related genes exhibit more similar phenotypes than expected (P < 0.05). The spanning of multiple functionally similar genes by single CNVs contributes substantially to how these variants exert their pathogenic effects.
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
authors.forename: Tallulah
authors.initials: T
authors.lastname: Andrews
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
authors.forename: Frantisek
authors.initials: F
authors.lastname: Honti
authors.affiliation: Department of Human Genetics and the Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
authors.forename: Rolph
authors.initials: R
authors.lastname: Pfundt
authors.affiliation: Department of Human Genetics and the Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
authors.forename: Nicole
authors.initials: N
authors.lastname: de Leeuw
authors.affiliation: Department of Human Genetics and the Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
authors.forename: Jayne
authors.initials: J
authors.lastname: Hehir-Kwa
authors.affiliation: Department of Human Genetics and the Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
authors.forename: Anneke
authors.initials: A
authors.lastname: Vulto-van Silfhout
authors.affiliation: Department of Human Genetics and the Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.
authors.forename: Bert
authors.initials: B
authors.lastname: de Vries
authors.affiliation: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
authors.forename: Caleb
authors.initials: C
authors.lastname: Webber
mesh_terms: D002877:Chromosomes, Human / Q000235:genetics; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D002658:Developmental Disabilities / Q000175:diagnosis / Q000235:genetics*; D053263:Gene Regulatory Networks; D015894:Genome, Human; D064368:Healthy Volunteers; D006801:Humans; D016015:Logistic Models; D005810:Multigene Family; D010641:Phenotype