The clustering of functionally related genes contributes to CNV-mediated disease

Andrews, Tallulah, Honti, Frantisek, Pfundt, Rolph, De Leeuw, Nicole, Hehir-Kwa, Jayne, Silfhout, Anneke Vulto-cvan, De Vries, Bert and Webber, Caleb ORCID: https://orcid.org/0000-0001-8063-7674 2015. The clustering of functionally related genes contributes to CNV-mediated disease. Genome Research 25 (6) , pp. 802-813. 10.1101/gr.184325.114

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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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	Cold Spring Harbor Laboratory Press
ISSN:	1088-9051
Date of First Compliant Deposit:	22 October 2020
Date of Acceptance:	13 April 2015
Last Modified:	06 May 2023 10:18
URI:	https://orca.cardiff.ac.uk/id/eprint/135765

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