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Rare, potentially pathogenic variants in ZNF469 are not enriched in keratoconus in a large Australian cohort of European descent

Citation

Lucas, SE and Zhou, T and Blackburn, NB and Mills, RA and Ellis, J and Leo, P and Souzeau, E and Ridge, B and Charlesworth, JC and Brown, MA and Lindsay, RC and Craig, JE and Burdon, KP, Rare, potentially pathogenic variants in ZNF469 are not enriched in keratoconus in a large Australian cohort of European descent, Investigative Ophthalmology and Visual Science (Iovs), 58, (14) pp. 6248-6256. ISSN 0146-0404 (2017) [Refereed Article]


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Copyright 2017 The Authors. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. https://creativecommons.org/licenses/by-nc-nd/4.0/

DOI: doi:10.1167/iovs.17-22417

Abstract

Purpose: The Zinc Finger Protein 469 (ZNF469) gene has been proposed as a candidate gene for keratoconus due to the association of an upstream polymorphism (rs9938149) with the disease in two independent studies, and the role of the gene in the autosomal recessive disease Brittle Cornea Syndrome. Coding variants in ZNF469 have been assessed for association with keratoconus in several small studies, with conflicting results. We assessed rare, potentially pathogenic variants in ZNF469 for enrichment in keratoconus patients in a cohort larger than all previous studies combined.

Methods: ZNF469 was sequenced in 385 Australian keratoconus patients of European descent, 346 population controls, and 230 ethnically matched screened controls by either whole exome sequencing or targeted gene sequencing. The frequency of rare and very rare potentially pathogenic variants was compared between cases and controls using χ2 or Fisher's exact tests and further explored using a gene based test (Sequence Kernel Association Test [SKAT]), weighting on the rarity of variants.

Results: A total of 49 rare, including 33 very rare, potentially pathogenic variants were identified across all groups. No enrichment of rare or very rare potentially pathogenic variants in ZNF469 was observed in our cases compared to the control groups following analysis using χ2 or Fisher's exact tests. This finding was further supported by the SKAT results, which found no significant difference in the frequency of variants predicted to be damaging between cases and either control group (P = 0.06).

Conclusions: Rare variants in ZNF469 do not contribute to keratoconus susceptibility and do not account for the association at rs9938149.

Item Details

Item Type:Refereed Article
Keywords:DNA sequencing, genomics, cornea, keratoconus, candidate genes
Research Division:Biomedical and Clinical Sciences
Research Group:Ophthalmology and optometry
Research Field:Ophthalmology
Objective Division:Health
Objective Group:Clinical health
Objective Field:Clinical health not elsewhere classified
UTAS Author:Lucas, SE (Ms Sionne Lucas)
UTAS Author:Blackburn, NB (Mr Nicholas Blackburn)
UTAS Author:Charlesworth, JC (Dr Jac Charlesworth)
UTAS Author:Burdon, KP (Professor Kathryn Burdon)
ID Code:123220
Year Published:2017
Web of Science® Times Cited:9
Deposited By:Menzies Institute for Medical Research
Deposited On:2017-12-20
Last Modified:2018-07-23
Downloads:99 View Download Statistics

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