title: Application of Whole Exome Sequencing in Six Families with an Initial Diagnosis of Autosomal Dominant Retinitis Pigmentosa: Lessons Learned.
abstract: This study aimed to identify the genetics underlying dominant forms of inherited retinal dystrophies using whole exome sequencing (WES) in six families extensively screened for known mutations or genes. Thirty-eight individuals were subjected to WES. Causative variants were searched among single nucleotide variants (SNVs) and insertion/deletion variants (indels) and whenever no potential candidate emerged, copy number variant (CNV) analysis was performed. Variants or regions harboring a candidate variant were prioritized and segregation of the variant with the disease was further assessed using Sanger sequencing in case of SNVs and indels, and quantitative PCR (qPCR) for CNVs. SNV and indel analysis led to the identification of a previously reported mutation in PRPH2. Two additional mutations linked to different forms of retinal dystrophies were identified in two families: a known frameshift deletion in RPGR, a gene responsible for X-linked retinitis pigmentosa and p.Ser163Arg in C1QTNF5 associated with Late-Onset Retinal Degeneration. A novel heterozygous deletion spanning the entire region of PRPF31 was also identified in the affected members of a fourth family, which was confirmed with qPCR. This study allowed the identification of the genetic cause of the retinal dystrophy and the establishment of a correct diagnosis in four families, including a large heterozygous deletion in PRPF31, typically considered one of the pitfalls of this method. Since all findings in this study are restricted to known genes, we propose that targeted sequencing using gene-panel is an optimal first approach for the genetic screening and that once known genetic causes are ruled out, WES might be used to uncover new genes involved in inherited retinal dystrophies.
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Berta
authors.initials: B
authors.lastname: Almoguera
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jiankang
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Genetics and Genomics, IIS-Fundacion Jimenez Diaz, 28040, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Fernandez-San Jose
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Yichuan
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: March
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Renata
authors.initials: R
authors.lastname: Pellegrino
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Ryan
authors.initials: R
authors.lastname: Golhar
authors.affiliation: Department of Genetics and Genomics, IIS-Fundacion Jimenez Diaz, 28040, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Corton
authors.affiliation: Department of Genetics and Genomics, IIS-Fundacion Jimenez Diaz, 28040, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
authors.forename: Fiona
authors.initials: F
authors.lastname: Blanco-Kelly
authors.affiliation: Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain; Department of Ophthalmology, Fundacion Jimenez Diaz, 28040, Madrid, Spain.
authors.forename: Maria Isabel
authors.initials: MI
authors.lastname: López-Molina
authors.affiliation: Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain; Department of Ophthalmology, Fundacion Jimenez Diaz, 28040, Madrid, Spain.
authors.forename: Blanca
authors.initials: B
authors.lastname: García-Sandoval
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Yiran
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Tian
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuanzhu
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Guan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Brendan
authors.initials: B
authors.lastname: Keating
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America.
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
authors.affiliation: Department of Genetics and Genomics, IIS-Fundacion Jimenez Diaz, 28040, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Ayuso
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D004252:DNA Mutational Analysis; D004596:Electroretinography; D059472:Exome; D005136:Eye Proteins / Q000235:genetics; D005192:Family Health; D005260:Female; D006579:Heterozygote; D006801:Humans; D054643:INDEL Mutation; D008297:Male; D008875:Middle Aged; D016366:Open Reading Frames; D010375:Pedigree; D064531:Peripherins / Q000235:genetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012162:Retinal Degeneration / Q000235:genetics; D012174:Retinitis Pigmentosa / Q000175:diagnosis / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013030:Spain; D055815:Young Adult
chemical_list: D005136:Eye Proteins; C454222:PRPF31 protein, human; C578997:PRPH2 protein, human; D064531:Peripherins