Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa

PLoS One. 2018 Apr 11;13(4):e0185237. doi: 10.1371/journal.pone.0185237. eCollection 2018.

Abstract

Background: Inherited eye diseases are major causes of vision loss in both children and adults. Inherited eye diseases are characterized by clinical variability and pronounced genetic heterogeneity. Genetic testing may provide an accurate diagnosis for ophthalmic genetic disorders and allow gene therapy for specific diseases.

Methods: A targeted gene capture panel was designed to capture exons of 283 inherited eye disease genes including 58 known causative retinitis pigmentosa (RP) genes. 180 samples were tested with this panel, 68 were previously tested by Sanger sequencing. Systematic evaluation of our method and comprehensive molecular diagnosis were carried on 99 RP patients.

Results: 96.85% targeted regions were covered by at least 20 folds, the accuracy of variants detection was 99.994%. In 4 of the 68 samples previously tested by Sanger sequencing, mutations of other diseases not consisting with the clinical diagnosis were detected by next-generation sequencing (NGS) not Sanger. Among the 99 RP patients, 64 (64.6%) were detected with pathogenic mutations, while in 3 patients, it was inconsistent between molecular diagnosis and their initial clinical diagnosis. After revisiting, one patient's clinical diagnosis was reclassified. In addition, 3 patients were found carrying large deletions.

Conclusions: We have systematically evaluated our method and compared it with Sanger sequencing, and have identified a large number of novel mutations in a cohort of 99 RP patients. The results showed a sufficient accuracy of our method and suggested the importance of molecular diagnosis in clinical diagnosis.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Child
  • Cost-Benefit Analysis
  • Female
  • Humans
  • Male
  • Molecular Diagnostic Techniques / economics
  • Molecular Diagnostic Techniques / methods*
  • Mutation
  • Retinitis Pigmentosa / diagnosis*
  • Retinitis Pigmentosa / genetics*
  • Sequence Analysis*

Grant support

This research was supported by the Shenzhen Municipal Government of China (NO.CXZZ20130517144604091, NO.GJHZ20130417140916986), the Shenzhen Key Laboratory of Genomics (NO.CXB200903110066A) and the Guangdong Enterprise Key Laboratory of Human Disease Genomics (NO.2011A060906007).