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

Hui Huang, Yanhua Chen, Huishuang Chen, Yuanyuan Ma, Pei-Wen Chiang, Jing Zhong, Xuyang Liu, Asan, Jing Wu, Yan Su, Xin Li, Jianlian Deng, Yingping Huang, Xinxin Zhang, Yang Li, Ning Fan, Ying Wang, Lihui Tang, Jinting Shen, Meiyan ChenXiuqing Zhang, Deng Te, Santasree Banerjee, Hui Liu, Ming Qi, Xin Yi

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere0185237
JournalPLoS One
Volume13
Issue number4
DOIs
StatePublished - Apr 1 2018

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Retinitis Pigmentosa
eye diseases
Genes
Eye Diseases
genes
mutation
gene therapy
genetic disorders
Gene therapy
Mutation
Inborn Genetic Diseases
Genetic Heterogeneity
Genetic Testing
exons
Genetic Therapy
eyes
Exons
sampling
methodology
Testing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa. / Huang, Hui; Chen, Yanhua; Chen, Huishuang; Ma, Yuanyuan; Chiang, Pei-Wen; Zhong, Jing; Liu, Xuyang; Asan; Wu, Jing; Su, Yan; Li, Xin; Deng, Jianlian; Huang, Yingping; Zhang, Xinxin; Li, Yang; Fan, Ning; Wang, Ying; Tang, Lihui; Shen, Jinting; Chen, Meiyan; Zhang, Xiuqing; Te, Deng; Banerjee, Santasree; Liu, Hui; Qi, Ming; Yi, Xin.

In: PLoS One, Vol. 13, No. 4, e0185237, 01.04.2018.

Research output: Contribution to journalArticle

Huang, H, Chen, Y, Chen, H, Ma, Y, Chiang, P-W, Zhong, J, Liu, X, Asan, Wu, J, Su, Y, Li, X, Deng, J, Huang, Y, Zhang, X, Li, Y, Fan, N, Wang, Y, Tang, L, Shen, J, Chen, M, Zhang, X, Te, D, Banerjee, S, Liu, H, Qi, M & Yi, X 2018, 'Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa', PLoS One, vol. 13, no. 4, e0185237. https://doi.org/10.1371/journal.pone.0185237
Huang, Hui ; Chen, Yanhua ; Chen, Huishuang ; Ma, Yuanyuan ; Chiang, Pei-Wen ; Zhong, Jing ; Liu, Xuyang ; Asan ; Wu, Jing ; Su, Yan ; Li, Xin ; Deng, Jianlian ; Huang, Yingping ; Zhang, Xinxin ; Li, Yang ; Fan, Ning ; Wang, Ying ; Tang, Lihui ; Shen, Jinting ; Chen, Meiyan ; Zhang, Xiuqing ; Te, Deng ; Banerjee, Santasree ; Liu, Hui ; Qi, Ming ; Yi, Xin. / Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa. In: PLoS One. 2018 ; Vol. 13, No. 4.
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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.",
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AU - Chen, Yanhua

AU - Chen, Huishuang

AU - Ma, Yuanyuan

AU - Chiang, Pei-Wen

AU - Zhong, Jing

AU - Liu, Xuyang

AU - Asan,

AU - Wu, Jing

AU - Su, Yan

AU - Li, Xin

AU - Deng, Jianlian

AU - Huang, Yingping

AU - Zhang, Xinxin

AU - Li, Yang

AU - Fan, Ning

AU - Wang, Ying

AU - Tang, Lihui

AU - Shen, Jinting

AU - Chen, Meiyan

AU - Zhang, Xiuqing

AU - Te, Deng

AU - Banerjee, Santasree

AU - Liu, Hui

AU - Qi, Ming

AU - Yi, Xin

PY - 2018/4/1

Y1 - 2018/4/1

N2 - 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.

AB - 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.

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