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Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease

  • Edwin M. Stone
    Correspondence
    Correspondence: Edwin M. Stone, MD, PhD, The Stephen A. Wynn Institute for Vision Research, 375 Newton Road, 4111 MERF, Iowa City, IA 52242.
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Jeaneen L. Andorf
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • S. Scott Whitmore
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Adam P. DeLuca
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Joseph C. Giacalone
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Luan M. Streb
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Terry A. Braun
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Robert F. Mullins
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Todd E. Scheetz
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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  • Val C. Sheffield
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa

    Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa
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  • Budd A. Tucker
    Affiliations
    Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, Iowa

    Stephen A. Wynn Institute for Vision Research, the University of Iowa, Iowa City, Iowa
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      Purpose

      To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician.

      Design

      Retrospective series.

      Participants

      One thousand consecutive families seen by a single clinician.

      Methods

      The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000.

      Main Outcome Measures

      Sensitivity and false genotype rate.

      Results

      Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001).

      Conclusions

      Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost.

      Abbreviations and Acronyms:

      AD (autosomal dominant), ADNIV (autosomal dominant neovascular inflammatory vitreoretinopathy), AR (autosomal recessive), AR-1 (autosomal recessive-1 allele identified), ARMS (amplification refractory mutation system), AZOOR (acute zonal occult outer retinopathy), BBS (Bardet-Biedl syndrome), BWA (Burrows Wheeler aligner), CRISPR (clustered regularly interspaced short palindromic repeats), CSNB (congential stationary night blindness), CSSD (congenital stationary synaptic dysfunction), DDND (developmental delay and/or neuromuscular degeneration), ECORD (early childhood onset retinal dystrophy), EPP (estimate of pathogenic probability), ERG (electroretinogram), EV (erosive vitreoretinopathy), ExAC (Exome Aggregation Consortium), FEVR (familial exudative vitreoretinopathy), FGR (false genotype rate), GATK (genome analysis toolkit), HMA (homocystinuria with macular atrophy), HPCD (helicoid peripapillary chorioretinal degeneration), ISCEV (International Society for Clinical Electrophysiology of Vision), IVS (intervening sequence), LB (lysogeny broth), L/M Opsin (long/medium wave length opsin), LCA (Leber congenital amaurosis), LCHAD (long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency), LHON (Leber hereditary optic neuropathy), MCLMR (microcephaly congenital lymphedema and chorioretinopathy), MDPD (mutation detection probability distribution), MIDD (maternally inherited diabetes and deafness), MIS (missense), Mito (mitochondrial), NGS (next-generation sequencing), PCR (polymerase chain reaction), PV (plausible variants), RP (retinitis pigmentosa), RPE (retinal pigment epithelium), SECORD (severe early childhood onset retinal dystrophy), TA Cloning (thymine and adenine cloning), TERM (terminating), VVD (vision variation database), XL (X-linked)
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