Genes 2017, 8(11), 304; https://doi.org/10.3390/genes8110304
Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations
Adrian Dockery 1,*
, Kirk Stephenson 2, David Keegan 2, Niamh Wynne 3, Giuliana Silvestri 4,5, Peter Humphries 1, Paul F. Kenna 1,3, Matthew Carrigan 1,†
and G. Jane Farrar 1,†
and G. Jane Farrar 1,†1
The School of Genetics & Microbiology, Trinity College Dublin, Dublin 2, Ireland
2
The Mater Misericordiae University Hospital, Dublin 7, Ireland
3
The Research Foundation, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
4
Department of Ophthalmology, The Royal Victoria Hospital, Belfast BT12 6BA, Northern Ireland, UK
5
Centre for Experimental Medicine, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UK
†
Authors contributed equally.
*
Author to whom correspondence should be addressed.
Academic Editor: Frans P.M. Cremers
Received: 8 September 2017 / Revised: 23 October 2017 / Accepted: 27 October 2017 / Published: 3 November 2017
(This article belongs to the Special Issue Inherited Retinal Disease: Novel Candidate Genes, Genotype–Phenotype Correlations and Inheritance Models)
Abstract
There are an estimated 5000 people in Ireland who currently have an inherited retinal degeneration (IRD). It is the goal of this study, through genetic diagnosis, to better enable these 5000 individuals to obtain a clearer understanding of their condition and improved access to potentially applicable therapies. Here we show the current findings of a target capture next-generation sequencing study of over 750 patients from over 520 pedigrees currently situated in Ireland. We also demonstrate how processes can be implemented to retrospectively analyse patient datasets for the detection of structural variants in previously obtained sequencing reads. Pathogenic or likely pathogenic mutations were detected in 68% of pedigrees tested. We report nearly 30 novel mutations including three large structural variants. The population statistics related to our findings are presented by condition and credited to their respective candidate gene mutations. Rediagnosis rates of clinical phenotypes after genotyping are discussed. Possible causes of failure to detect a candidate mutation are evaluated. Future elements of this project, with a specific emphasis on structural variants and non-coding pathogenic variants, are expected to increase detection rates further and thereby produce an even more comprehensive representation of the genetic landscape of IRDs in Ireland. View Full-TextKeywords:
retina; genetics; ophthalmology; retinitis pigmentosa; genomics
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Dockery, A.; Stephenson, K.; Keegan, D.; Wynne, N.; Silvestri, G.; Humphries, P.; Kenna, P.F.; Carrigan, M.; Farrar, G.J. Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations. Genes 2017, 8, 304.
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