High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.
OBJECTIVE
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.
Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10 Center Drive, Bethesda,MD 20892, USA.
Jin
J
Song
Nizar
N
Smaoui
Radha
R
Ayyagari
David
D
Stiles
Sonia
S
Benhamed
Ian M
IM
MacDonald
Stephen P
SP
Daiger
Santa J
SJ
Tumminia
Fielding
F
Hejtmancik
Xinjing
X
Wang
D005091:Exons / Q000235:genetics; D005136:Eye Proteins / Q000235:genetics*; D020869:Gene Expression Profiling; D005820:Genetic Testing; D006801:Humans; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D012160:Retina / Q000378:metabolism*; D058499:Retinal Dystrophies / Q000235:genetics*
D005136:Eye Proteins