Gene panel sequencing in Brazilian patients with retinitis pigmentosa

Kárita Antunes Costa, Mariana Vallim Salles, Chris Whitebirch, Pei-Wen Chiang, Juliana Maria Ferraz Sallum

Research output: Contribution to journalArticle

Abstract

Background: Retinal dystrophies constitute a group of diseases characterized by clinical variability and pronounced genetic heterogeneity. Retinitis pigmentosa is the most common subtype of hereditary retinal dystrophy and is characterized by a progressive loss of peripheral field vision (Tunnel Vision), eventual loss of central vision, and progressive night blindness. The characteristics of the fundus changes include bone-spicule formations, attenuated blood vessels, reduced and/or abnormal electroretinograms, changes in structure imaged by optical coherence tomography, and subjective changes in visual function. The different syndromic and nonsyndromic forms of retinal dystrophies can be attributed to mutations in more than 250 genes. Molecular diagnosis for patients with retinitis pigmentosa has been hampered by extreme genetic and clinical heterogeneity between retinitis pigmentosa and other forms of retinal dystrophies. Next generation sequencing (NGS) technologies are among the most promising techniques to identify pathogenic variations in retinal dystrophies. Purpose: The purpose of this study was to discover the molecular diagnosis for Brazilian patients clinically diagnosed with a retinitis pigmentosa pattern of inheritance by using NGS technologies. Materials and methods: Sixteen patients with the clinical diagnosis of retinitis pigmentosa were included in the study. Their DNA was sequenced in a panel with 132 genes related to retinal dystrophies using the Illumina ® platform. Sequence analysis and variation calling was performed using Soft Genetics ®, NextGene, and Geneticist Assistant software. The criteria for pathogenicity analysis were established according to the results of prediction programs (Polyphen 2, Mutation taster and MetaCore™) and comparison of pathogenic variations found with databases. Results: The identified potentially pathogenic variations were all confirmed by Sanger sequencing. There were 89 variations predicted as pathogenic, but only 10 of them supported the conclusion of the molecular diagnosis. Five of the nine patients were autosomal dominant RP (56%), two (22%) were autosomal recessive RP, and two (22%) were X-linked RP. Nine of the 16 patients (56%) had probably positive or positive results. Conclusion: The Next Generation Sequencing used in this study allowed the molecular diagnosis to be confirmed in 56% of the patients and clarified the inheritance pattern of the patient's retinal dystrophies.

Original languageEnglish (US)
Article number33
JournalInternational Journal of Retina and Vitreous
Volume3
Issue number1
DOIs
StatePublished - Jan 1 2017

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Retinal Dystrophies
Retinitis Pigmentosa
Genes
Inheritance Patterns
Genetic Heterogeneity
Night Blindness
Technology
Mutation
Optical Coherence Tomography
Osteogenesis
Sequence Analysis
Blood Vessels
Virulence
Software
Databases
DNA

Keywords

  • Illumina platform
  • Molecular diagnosis
  • Next generation sequencing
  • Retinal dystrophies genes
  • Retinitis pigmentosa

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Gene panel sequencing in Brazilian patients with retinitis pigmentosa. / Costa, Kárita Antunes; Salles, Mariana Vallim; Whitebirch, Chris; Chiang, Pei-Wen; Sallum, Juliana Maria Ferraz.

In: International Journal of Retina and Vitreous, Vol. 3, No. 1, 33, 01.01.2017.

Research output: Contribution to journalArticle

Costa, Kárita Antunes ; Salles, Mariana Vallim ; Whitebirch, Chris ; Chiang, Pei-Wen ; Sallum, Juliana Maria Ferraz. / Gene panel sequencing in Brazilian patients with retinitis pigmentosa. In: International Journal of Retina and Vitreous. 2017 ; Vol. 3, No. 1.
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AB - Background: Retinal dystrophies constitute a group of diseases characterized by clinical variability and pronounced genetic heterogeneity. Retinitis pigmentosa is the most common subtype of hereditary retinal dystrophy and is characterized by a progressive loss of peripheral field vision (Tunnel Vision), eventual loss of central vision, and progressive night blindness. The characteristics of the fundus changes include bone-spicule formations, attenuated blood vessels, reduced and/or abnormal electroretinograms, changes in structure imaged by optical coherence tomography, and subjective changes in visual function. The different syndromic and nonsyndromic forms of retinal dystrophies can be attributed to mutations in more than 250 genes. Molecular diagnosis for patients with retinitis pigmentosa has been hampered by extreme genetic and clinical heterogeneity between retinitis pigmentosa and other forms of retinal dystrophies. Next generation sequencing (NGS) technologies are among the most promising techniques to identify pathogenic variations in retinal dystrophies. Purpose: The purpose of this study was to discover the molecular diagnosis for Brazilian patients clinically diagnosed with a retinitis pigmentosa pattern of inheritance by using NGS technologies. Materials and methods: Sixteen patients with the clinical diagnosis of retinitis pigmentosa were included in the study. Their DNA was sequenced in a panel with 132 genes related to retinal dystrophies using the Illumina ® platform. Sequence analysis and variation calling was performed using Soft Genetics ®, NextGene, and Geneticist Assistant software. The criteria for pathogenicity analysis were established according to the results of prediction programs (Polyphen 2, Mutation taster and MetaCore™) and comparison of pathogenic variations found with databases. Results: The identified potentially pathogenic variations were all confirmed by Sanger sequencing. There were 89 variations predicted as pathogenic, but only 10 of them supported the conclusion of the molecular diagnosis. Five of the nine patients were autosomal dominant RP (56%), two (22%) were autosomal recessive RP, and two (22%) were X-linked RP. Nine of the 16 patients (56%) had probably positive or positive results. Conclusion: The Next Generation Sequencing used in this study allowed the molecular diagnosis to be confirmed in 56% of the patients and clarified the inheritance pattern of the patient's retinal dystrophies.

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