Journal
OPHTHALMOLOGY
Volume 126, Issue 6, Pages 888-907Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.ophtha.2018.12.050
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Funding
- Rosetrees Trust
- Moorfields Eye Hospital Special Trustees, Microphthalmia, Anophthalmia and Coloboma Support (MACS)
- Action Medical Research
- National Institute for Health Research Great Ormond Street Hospital Biomedical Research Centre
- National Institute for Health Research Moorfields Biomedical Research Centre
- Great Ormond Street Hospital Children's Charity
- National Institute for Health Research
- UCL Graduate Research Scholarship
- UCL Overseas Research Scholarship
- Action Medical Research charity
- Fondo Nacional de Desarrollo Cientifico y Tecnologico, Santiago, Chile [11160951]
- Moorfields Eye Charity
- FFS
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Purpose: To develop a comprehensive next-generation sequencing panel assay that screens genes known to cause developmental eye disorders and inherited eye disease and to evaluate its diagnostic yield in a pediatric cohort with malformations of the globe, anterior segment anomalies, childhood glaucoma, or a combination thereof. Design: Evaluation of diagnostic test. Participants: Two hundred seventy-seven children, 0 to 16 years of age, diagnosed with nonsyndromic or syndromic developmental eye defects without a genetic diagnosis. Methods: We developed a new oculome panel using a custom-designed Agilent SureSelect QXT target capture method (Agilent Technologies, Santa Clara, CA) to capture and perform parallel high-throughput sequencing analysis of 429 genes associated with eye disorders. Bidirectional Sanger sequencing confirmed suspected pathogenic variants. Main Outcome Measures: Collated clinical details and oculome molecular genetic results. Results: The oculome design covers 429 known eye disease genes; these are subdivided into 5 overlapping virtual subpanels for anterior segment developmental anomalies including glaucoma (ASDA; 59 genes), microphthalmia-anophthalmia-coloboma (MAC; 86 genes), congenital cataracts and lens-associated conditions (70 genes), retinal dystrophies (RET; 235 genes), and albinism (15 genes), as well as additional genes implicated in optic atrophy and complex strabismus (10 genes). Panel development and testing included analyzing 277 clinical samples and 3 positive control samples using Illumine sequencing platforms; more than 30 x read depth was achieved for 99.5% of the targeted 1.77-Mb region. Bioinformatics analysis performed using a pipeline based on Freebayes and ExomeDepth to identify coding sequence and copy number variants, respectively, resulted in a definitive diagnosis in 68 of 277 samples, with variability in diagnostic yield between phenotypic subgroups: MAC, 8.2% (8 of 98 cases solved); ASDA, 24.8% (28 of 113 cases solved); other or syndromic, 37.5% (3 of 8 cases solved); RET, 42.8% (21 of 49 cases solved); and congenital cataracts and lens-associated conditions, 88.9% (8 of 9 cases solved). Conclusions: The oculome test diagnoses a comprehensive range of genetic conditions affecting the development of the eye, potentially replacing protracted and costly multidisciplinary assessments and allowing for faster targeted management. The oculome enabled molecular diagnosis of a significant number of cases in our sample cohort of varied ocular birth defects. (C) 2019 by the American Academy of Ophthalmology
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