title: Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene.
abstract: We performed whole genome sequencing in 16 unrelated patients with autosomal recessive retinitis pigmentosa (ARRP), a disease characterized by progressive retinal degeneration and caused by mutations in over 50 genes, in search of pathogenic DNA variants. Eight patients were from North America, whereas eight were Japanese, a population for which ARRP seems to have different genetic drivers. Using a specific workflow, we assessed both the coding and noncoding regions of the human genome, including the evaluation of highly polymorphic SNPs, structural and copy number variations, as well as 69 control genomes sequenced by the same procedures. We detected homozygous or compound heterozygous mutations in 7 genes associated with ARRP (USH2A, RDH12, CNGB1, EYS, PDE6B, DFNB31, and CERKL) in eight patients, three Japanese and five Americans. Fourteen of the 16 mutant alleles identified were previously unknown. Among these, there was a 2.3-kb deletion in USH2A and an inverted duplication of ~446 kb in EYS, which would have likely escaped conventional screening techniques or exome sequencing. Moreover, in another Japanese patient, we identified a homozygous frameshift (p.L206fs), absent in more than 2,500 chromosomes from ethnically matched controls, in the ciliary gene NEK2, encoding a serine/threonine-protein kinase. Inactivation of this gene in zebrafish induced retinal photoreceptor defects that were rescued by human NEK2 mRNA. In addition to identifying a previously undescribed ARRP gene, our study highlights the importance of rare structural DNA variations in Mendelian diseases and advocates the need for screening approaches that transcend the analysis of the coding sequences of the human genome.
authors.affiliation: Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland.
authors.forename: Koji M
authors.initials: KM
authors.lastname: Nishiguchi
authors.forename: Richard G
authors.initials: RG
authors.lastname: Tearle
authors.forename: Yangfan P
authors.initials: YP
authors.lastname: Liu
authors.forename: Edwin C
authors.initials: EC
authors.lastname: Oh
authors.forename: Noriko
authors.initials: N
authors.lastname: Miyake
authors.forename: Paola
authors.initials: P
authors.lastname: Benaglio
authors.forename: Shyana
authors.initials: S
authors.lastname: Harper
authors.forename: Hanna
authors.initials: H
authors.lastname: Koskiniemi-Kuendig
authors.forename: Giulia
authors.initials: G
authors.lastname: Venturini
authors.forename: Dror
authors.initials: D
authors.lastname: Sharon
authors.forename: Robert K
authors.initials: RK
authors.lastname: Koenekoop
authors.forename: Makoto
authors.initials: M
authors.lastname: Nakamura
authors.forename: Mineo
authors.initials: M
authors.lastname: Kondo
authors.forename: Shinji
authors.initials: S
authors.lastname: Ueno
authors.forename: Tetsuhiro R
authors.initials: TR
authors.lastname: Yasuma
authors.forename: Jacques S
authors.initials: JS
authors.lastname: Beckmann
authors.forename: Shiro
authors.initials: S
authors.lastname: Ikegawa
authors.forename: Naomichi
authors.initials: N
authors.lastname: Matsumoto
authors.forename: Hiroko
authors.initials: H
authors.lastname: Terasaki
authors.forename: Eliot L
authors.initials: EL
authors.lastname: Berson
authors.forename: Nicholas
authors.initials: N
authors.lastname: Katsanis
authors.forename: Carlo
authors.initials: C
authors.lastname: Rivolta
mesh_terms: D000818:Animals; D001483:Base Sequence; D016368:Frameshift Mutation / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics*; D005826:Genetics, Medical; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study; D006801:Humans; D007564:Japan; D008969:Molecular Sequence Data; D000072379:NIMA-Related Kinases; D017346:Protein Serine-Threonine Kinases / Q000235:genetics*; D012174:Retinitis Pigmentosa / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014481:United States; D015027:Zebrafish
chemical_list: C089441:NEK2 protein, human; D000072379:NIMA-Related Kinases; D017346:Protein Serine-Threonine Kinases
keywords: ciliopathy; medical genetics; ophthalmology; retinal blindness
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