NDLI: High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.

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High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.

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High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Benhamed, Sonia Hejtmancik, Fielding Song, Jin Daiger, Stephen P. Tumminia, Santa J. Smaoui, Nizar Ayyagari, Radha Stiles, David MacDonald, Ian M. Wang, Xinjing
Description	Country affiliation: United States Author Affiliation: Song J ( Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10 Center Drive, Bethesda,MD 20892, USA.)
Abstract	PURPOSE: Retinal dystrophy (RD) is a broad group of hereditary disorders with heterogeneous genotypes and phenotypes. Current available genetic testing for these diseases is complicated, time consuming, and expensive. This study was conducted to develop and apply a microarray-based, high-throughput resequencing system to detect sequence alterations in genes related to inherited RD. METHODS: A customized 300-kb resequencing chip, Retina-Array, was developed to detect sequence alterations of 267,550 bases of both sense and antisense sequence in 1470 exons spanning 93 genes involved in inherited RD. Retina-Array was evaluated in 19 patient samples with inherited RD provided by the eyeGENE repository and four Centre d'Etudes du Polymorphisme Humaine reference samples through a high-throughput experimental approach that included an automated PCR assay setup and quantification, efficient post-quantification data processing, optimized pooling and fragmentation, and standardized chip processing. RESULTS: The performance of the chips demonstrated that the average base pair call rate and accuracy were 93.56% and 99.86%, respectively. In total, 304 candidate variations were identified using a series of customized screening filters. Among 174 selected variations, 123 (70.7%) were further confirmed by dideoxy sequencing. Analysis of patient samples using Retina-Array resulted in the identification of 10 known mutations and 12 novel variations with high probability of deleterious effects. CONCLUSIONS: This study suggests that Retina-Array might be a valuable tool for the detection of disease-causing mutations and disease severity modifiers in a single experiment. Retinal-Array may provide a powerful and feasible approach through which to study genetic heterogeneity in retinal diseases.
ISSN	01460404
e-ISSN	15525783
DOI	10.1167/iovs.11-7978
Journal	Investigative Opthalmology & Visual Science
Issue Number	12
Volume Number	52
Language	English
Publisher	Association for Research in Vision and Ophthalmology
Publisher Date	2011-11-25
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Eye Proteins Genetics Gene Expression Profiling Oligonucleotide Array Sequence Analysis Retina Metabolism Retinal Dystrophies Exons Genetic Testing Mutation Polymerase Chain Reaction Research Support, N.i.h., Extramural Research Support, N.i.h., Intramural Discipline Ophthalmology
Content Type	Text
Resource Type	Article
Subject	Ophthalmology Sensory Systems Cellular and Molecular Neuroscience

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