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Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability

Lee, Chaeyoung, Bengani, Hemant, Grozeva, Detelina, Moyon, Lambert, Bhatia, Shipra, Louros, Susana R., Hope, Jilly, Jackson, Adam, Prendergast, James G., Owen, Liusaidh J., Naville, Magali, Rainger, Jacqueline, Grimes, Graeme, Halachev, Mihail, Murphy, Laura C., Spasic-Boskovic, Olivera, van Heyningen, Veronica, Kind, Peter, Abbott, Catherine M., Osterweil, Emily, Raymond, F. Lucy, Roest Crollius, Hugues and FitzPatrick, David R. 2021. Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability. PLoS ONE 16 (8) , e0256181. 10.1371/journal.pone.0256181

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Abstract

Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Medicine
Additional Information: This is an open access article distributed under the terms of the Creative Commons Attribution License
Publisher: Public Library of Science
ISSN: 1932-6203
Date of First Compliant Deposit: 8 October 2021
Date of Acceptance: 1 August 2021
Last Modified: 08 Oct 2021 09:45
URI: http://orca.cardiff.ac.uk/id/eprint/144680

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