title: Identification of Novel and Recurrent Disease-Causing Mutations in Retinal Dystrophies Using Whole Exome Sequencing (WES): Benefits and Limitations.
abstract: Inherited retinal dystrophies (IRDs) are Mendelian diseases with tremendous genetic and phenotypic heterogeneity. Identification of the underlying genetic basis of these dystrophies is therefore challenging. In this study we employed whole exome sequencing (WES) in 11 families with IRDs and identified disease-causing variants in 8 of them. Sequence analysis of about 250 IRD-associated genes revealed 3 previously reported disease-associated variants in RHO, BEST1 and RP1. We further identified 5 novel pathogenic variants in RPGRIP1 (p.Ser964Profs*37), PRPF8 (p.Tyr2334Leufs*51), CDHR1 (p.Pro133Arg and c.439-17G>A) and PRPF31 (p.Glu183_Met193dup). In addition to confirming the power of WES in genetic diagnosis of IRDs, we document challenges in data analysis and show cases where the underlying genetic causes of IRDs were missed by WES and required additional techniques. For example, the mutation c.439-17G>A in CDHR1 would be rated unlikely applying the standard WES analysis. Only transcript analysis in patient fibroblasts confirmed the pathogenic nature of this variant that affected splicing of CDHR1 by activating a cryptic splice-acceptor site. In another example, a 33-base pair duplication in PRPF31 missed by WES could be identified only via targeted analysis by Sanger sequencing. We discuss the advantages and challenges of using WES to identify mutations in heterogeneous diseases like IRDs.
authors.affiliation: Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.
authors.forename: Amit
authors.initials: A
authors.lastname: Tiwari
authors.affiliation: Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.
authors.forename: Johannes
authors.initials: J
authors.lastname: Lemke
authors.affiliation: Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, D-50931, Cologne, Germany.
authors.forename: Janine
authors.initials: J
authors.lastname: Altmueller
authors.affiliation: Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, D-50931, Cologne, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Thiele
authors.affiliation: Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.
authors.forename: Esther
authors.initials: E
authors.lastname: Glaus
authors.affiliation: Department of Ophthalmology, University Hospital Zurich, Frauenklinikstrasse 24, CH-8091, Zürich, Switzerland.
authors.forename: Johannes
authors.initials: J
authors.lastname: Fleischhauer
authors.affiliation: Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, D-50931, Cologne, Germany.|Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch Str. 21, D-50931, Cologne, Germany.|Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, D-50931, Cologne, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Nürnberg
authors.affiliation: Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.
authors.forename: John
authors.initials: J
authors.lastname: Neidhardt
authors.affiliation: Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.|Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.|Neuroscience Center Zurich (ZNZ), University and ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Berger
mesh_terms: D002478:Cells, Cultured; D004252:DNA Mutational Analysis; D059472:Exome / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics*; D010375:Pedigree; D058499:Retinal Dystrophies / Q000235:genetics*; D017422:Sequence Analysis, DNA