June 2013
Volume 54, Issue 15
Free
ARVO Annual Meeting Abstract  |   June 2013
Carriers of degenerative retinal diseases can be easily identified using target capture next generation sequencing
Author Affiliations & Notes
  • Shirel Weiss
    The Krieger Eye Research Laboratory, Felsenstein Medical Research Center- Tel Aviv University,, Petah Tiqwa, Israel
    Sackler Faculty of Medicine, Tel Aviv University, Petach Tiqwa, Israel
  • Eran Eyal
    Bioinformatics Laboratory, Cancer Research Center, Chaim Sheba Medical Center, Tel HaShomer, Ramat Gan, Israel
  • Mali Salmon-Divon
    Bioinformatics Laboratory, Cancer Research Center, Chaim Sheba Medical Center, Tel HaShomer, Ramat Gan, Israel
  • Yoram Cohen
    Sackler Faculty of Medicine, Tel Aviv University, Petach Tiqwa, Israel
    Department of Gynecology, The Gynecology Research Laboratory, Chaim Sheba Medical Center, Tel HaShomer, Ramat Gan, Israel
  • Nitza Goldenberg-Cohen
    The Krieger Eye Research Laboratory, Felsenstein Medical Research Center- Tel Aviv University,, Petah Tiqwa, Israel
    Pediatric Ophthalmology Unit, Schneider Children’s Medical Center of Israel, Petach Tiqwa, Israel
  • Footnotes
    Commercial Relationships Shirel Weiss, None; Eran Eyal, None; Mali Salmon-Divon, None; Yoram Cohen, None; Nitza Goldenberg-Cohen, None
  • Footnotes
    Support None
Investigative Ophthalmology & Visual Science June 2013, Vol.54, 3371. doi:https://doi.org/
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      Shirel Weiss, Eran Eyal, Mali Salmon-Divon, Yoram Cohen, Nitza Goldenberg-Cohen; Carriers of degenerative retinal diseases can be easily identified using target capture next generation sequencing. Invest. Ophthalmol. Vis. Sci. 2013;54(15):3371. doi: https://doi.org/.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose: Retinal degeneration ranks high among the many genetic causes of blindness. Mutations in multiple genes are responsible for a wide variety of retinal dystrophy phenotypes, such as autosomal recessive Stargardt disease, cone-rod dystrophy and retinitis pigmentosa. Here, we report on the development of a new test to find all possible disease-associated variants in the coding sequences of 25 recessive degenerative retinal diseases, based on target enrichment and next generation sequencing (NGS).

Methods: 372 exonic regions from 25 target genes were enriched by hybrid capture, sequenced by NGS to a depth of up to 0.36 gigabases, and assessed with stringent bioinformatic filters.

Results: Two DNA samples of control subjects not known to suffer from retinal degeneration or any other eye disease were investigated, and 1 mutation diagnosed Leber Congenital Amuorosis (LCA) patient. An average target coverage of 179x (ranging from 151-218x) was achieved. 66.6% (45-93%) of nucleotides had at least 7x coverage, and 59.6% (39-86%) had at least 20x coverage. The enrichment factor which is the ratio of the coverage of the targeted region versus the coverage of the genome outside the target region was found to be 2331 (1768-3068). In the initial experiment we found, 191 (153-229) SNPS and 8 (5-11) indels ,138 (136-141) with median coverage > 37x, 95.5% of these (151-230) have been previously reported in dbSNP (v.132). 21 (19-24) aberrations were found in coding regions, of them 10 (9-12) resulted in changes of the protein sequence. Using the more sensitive blast alignment algorithm, we detected 10bps deletion in the CRB1 gene of the LCA patient located in a deeply covered region.

Conclusions: Given the difficulties in clinical diagnosis of similar phenotypes, this method proved efficient. It revealed the specific genetic mutations underlying retinal diseases, potentially lowering the costs of testing, and enabling broad screening for carriers and affected patients. If made available to the general population, NGS may be an economical and superior method of diagnosis, genetic consultation and treatment for patients.

Keywords: 688 retina • 537 gene screening • 696 retinal degenerations: hereditary  
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