Xiaozhen Liu1,2, Tianchang Tao3, Lin Zhao1,2, Genlin Li3, Liping Yang1,2. 1. Department of Ophthalmology, Peking University Third Hospital, Beijing, China. 2. Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China. 3. Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China.
Abstract
IMPORTANCE: Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND: Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN: Retrospective analysis. PARTICIPANTS: Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS: A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES: The diagnostic rate. RESULTS: (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE: Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
IMPORTANCE: Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND: Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN: Retrospective analysis. PARTICIPANTS: Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS: A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES: The diagnostic rate. RESULTS: (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE: Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
Authors: Sena A Gocuk; Yuanzhang Jiao; Alexis Ceecee Britten-Jones; Nathan M Kerr; Lyndell Lim; Simon Skalicky; Richard Stawell; Lauren N Ayton; Heather G Mack Journal: Clin Ophthalmol Date: 2022-04-13