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Matthew Carrigan, Emma Duignan, Conor Patrick Malone, Kirk Stephenson, David J Keegan, Peter Humphries, Paul Kenna, G Jane Farrar; Target 5000: Next-Generation Sequencing of the Irish Inherited Retinal Degeneration Population. Invest. Ophthalmol. Vis. Sci. 2016;57(12):No Pagination Specified.
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© ARVO (1962-2015); The Authors (2016-present)
Next-generation sequencing has emerged as the diagnostic tool of choice for inherited retinal degenerations, but most inherited retinal degeneration (IRD) patients have not yet been sequenced and still do not know the causative mutation(s) underlying their disease. Target 5000 is the first large-scale study applying NGS to the Irish IRD patient population, with the goal of providing clear and actionable genetic diagnoses to this patient cohort.
Exons of known retinopathy genes at time of panel design were captured for sequencing using target-capture panels. All samples were sequenced on Illumina MiSeq and HiSeq instruments. Results were computationally filtered by an internally-developed pipeline to remove common population polymorphisms and highlight known-pathogenic mutations previously reported in the literature. Novel variants of unknown pathological significance were assessed using ensemble machine-learned models to maximize classification accuracy.
Target-capture NGS was undertaken on 501 individuals from 279 IRD pedigrees and causative mutations identified in 54% (152/279) of pedigrees. Rates of mutation detection differed between conditions, with monogenic conditions like Stargardt disease and choroideremia having the highest detection rates. Retinitis pigmentosa (RP), the most common condition in the patient cohort, was more challenging due to the large number of candidate genes, however a diagnosis could still be made in over half of cases (56/108). Many novel mutations were identified in this IRD cohort, including homozygous nonsense mutations in GNAT1 and SLC24A1 causing a very late-onset mild pigmentary retinopathy; both of these genes have hitherto only been implicated in congenital stationary night-blindness (CSNB).
Target-capture NGS is a cost-effective and sensitive tool for identifying causative mutations in IRD patients – both known and novel mutation in retinopathy genes were identified in this IRD cohort, as was a new disease phenotype associated with two CSNB genes. Future studies using expanded panels or whole-genome sequencing may be required to identify the causative gene in the patients whose mutations could not be detected by the targeted NGS approach.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.
Breakdown of genes found to be implicated in common inherited retinal conditions. When cases are rediagnosed based on NGS findings, the original diagnosis is used for this figure.
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