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A. A. Bergen, J. C. Booij, J. Kulumbetova, M. J. van Schooneveld, J. B. ten Brink, A. Bakker, R. Florijn; A Novel Strategy for Cost-Effective Mutation Detection in 87 Retinal Disease Genes Using Resequencing Chips. Invest. Ophthalmol. Vis. Sci. 2009;50(13):4125.
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© ARVO (1962-2015); The Authors (2016-present)
Genetic disorders of the retina are extremely heterogeneous, and can be caused by multiple genes (for overview, see:(http://www.sph.uth.tmc.edu/Retnet/home.htm). Screening of all those genes in patients by traditional genetic screening methods (dHPLC, SSCP etc.) or sequencing is neither cost-effective nor efficient. In this study, we present a novel strategy for cost-effective, large scale mutation analysis.
Up to 1600 amplicons from 87 disease genes (per chip) were amplified, and hybridized against custom designed 300 kb affymetrix resequencing chips, using a new strategy. Mutation analysis was carried out with Affymetrix standard software, and the novel, superior, computerprogram SEQC.
At least eight chips were hybridized with (subsets of) amplicons from 87 disease genes, amplified from DNA of patients with a variety of retinal disorders. These genes included, for example, the ABCC6, OPA1, OCA1, OCA2, ABCR, CEP290, and CFH402 genes. Mutation and SNP detection call rates were between 90-100% of hybridized fragments, the average of which will improve further since the SEQC program contains a "learning module". Amongst others, we confirmed and found the following mutations: ABBC6 p.Arg1141X, ABCC6 p.Arg1221Cys, OPA1 p.Trp89X, OCA1 p.Val183Met, OCA1 p.Thr373Lys, OCA2 p.Trp61X, OCA2 p.Cys793Phe, and many more.
We implemented a new, cost-effective, mutation detection strategy for mutation analysis in 87 retinal disease genes for different patients and diseases, which include autosomal recessive retinitis pigmentosa (ARRP), autosomal dominant retinitis pigmentosa (ADRP), cone-rod dystrophies, usher syndrome, congenital stationary nightblindness, Bardet-Biedle syndrome, and others.
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