Exome Sequencing of 47 Chinese Families with Cone-Rod Dystrophy: Mutations in 25 Known Causative Genes

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Huang, Li ^a   Zhang, Qingyan ^b   Li, Shiqiang ^a   Guan, Liping ^b   Xiao, Xueshan ^a   Zhang, Jianguo ^b   Jia, Xiaoyun ^a   Sun, Wenmin ^a   Zhu, Zhihong ^b   Gao, Yang ^a   Yin, Ye ^b   Wang, Panfeng ^a   Guo, Xiangming ^a   Wang, Jun ^b   Zhang, Qingjiong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ABCA4 GENE; ARTICLE; CACNA1F GENE; CHILD; CHINESE; CNGB3 GENE; COHORT ANALYSIS; EXOME; FAMILY STUDY; FEMALE; GENE; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; HEMIZYGOSITY; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; LEUKOCYTE; MAJOR CLINICAL STUDY; MALE; PATHOGENESIS; PDE6C GENE; PHENOTYPE; PRESCHOOL CHILD; RETINA CONE ROD DYSTROPHY; RETINA DYSTROPHY; RPGR GENE; RPGRIP1 GENE; SCHOOL CHILD; SEQUENCE ANALYSIS;

ATP-BINDING CASSETTE TRANSPORTERS; CALCIUM CHANNELS, L-TYPE; CHINA; CYCLIC NUCLEOTIDE PHOSPHODIESTERASES, TYPE 6; CYCLIC NUCLEOTIDE-GATED CATION CHANNELS; EXOME; EYE PROTEINS; HUMANS; MUTATION; PEDIGREE; PROTEINS; RETINITIS PIGMENTOSA;

EID: 84878934289     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065546     Document Type: Article

References (50)

1. Sohocki MM, Perrault I, Leroy BP, Payne AM, Dharmaraj S, et al. (2000) Prevalence of AIPL1 mutations in inherited retinal degenerative disease. Mol Genet Metab 70: 142-150.
2. Freund CL, Gregory-Evans CY, Furukawa T, Papaioannou M, Looser J, et al. (1997) Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. Cell 91: 543-553.
3. Payne AM, Downes SM, Bessant DA, Taylor R, Holder GE, et al. (1998) A mutation in guanylate cyclase activator 1A (GUCA1A) in an autosomal dominant cone dystrophy pedigree mapping to a new locus on chromosome 6p21.1. Hum Mol Genet 7: 273-277.
4. Kelsell RE, Gregory-Evans K, Payne AM, Perrault I, Kaplan J, et al. (1998) Mutations in the retinal guanylate cyclase (RETGC-1) gene in dominant cone-rod dystrophy. Hum Mol Genet 7: 1179-1184.
5. Kohn L, Kadzhaev K, Burstedt MS, Haraldsson S, Hallberg B, et al. (2007) Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families. Eur J Hum Genet 15: 664-671.
6. Yang Z, Chen Y, Lillo C, Chien J, Yu Z, et al. (2008) Mutant prominin 1 found in patients with macular degeneration disrupts photoreceptor disk morphogenesis in mice. J Clin Invest 118: 2908-2916.
7. Fishman GA, Stone EM, Alexander KR, Gilbert LD, Derlacki DJ, et al. (1997) Serine-27-phenylalanine mutation within the peripherin/RDS gene in a family with cone dystrophy. Ophthalmology 104: 299-306.
8. Kelsell RE, Gregory-Evans K, Gregory-Evans CY, Holder GE, Jay MR, et al. (1998) Localization of a gene (CORD7) for a dominant cone-rod dystrophy to chromosome 6q. Am J Hum Genet 63: 274-279.
9. Abid A, Ismail M, Mehdi SQ, Khaliq S, (2006) Identification of novel mutations in the SEMA4A gene associated with retinal degenerative diseases. J Med Genet 43: 378-381.
10. Kobayashi A, Higashide T, Hamasaki D, Kubota S, Sakuma H, et al. (2000) HRG4 (UNC119) mutation found in cone-rod dystrophy causes retinal degeneration in a transgenic model. Invest Ophthalmol Vis Sci 41: 3268-3277.
11. Cremers FP, van de Pol DJ, van Driel M, den Hollander AI, van Haren FJ, et al. (1998) Autosomal recessive retinitis pigmentosa and cone-rod dystrophy caused by splice site mutations in the Stargardt's disease gene ABCR. Hum Mol Genet 7: 355-362.
12. Parry DA, Toomes C, Bida L, Danciger M, Towns KV, et al. (2009) Loss of the metalloprotease ADAM9 leads to cone-rod dystrophy in humans and retinal degeneration in mice. Am J Hum Genet 84: 683-691.
13. Estrada-Cuzcano A, Neveling K, Kohl S, Banin E, Rotenstreich Y, et al. (2012) Mutations in C8orf37, encoding a ciliary protein, are associated with autosomal-recessive retinal dystrophies with early macular involvement. Am J Hum Genet 90: 102-109.
14. Wycisk KA, Budde B, Feil S, Skosyrski S, Buzzi F, et al. (2006) Structural and functional abnormalities of retinal ribbon synapses due to Cacna2d4 mutation. Invest Ophthalmol Vis Sci 47: 3523-3530.
15. Ostergaard E, Batbayli M, Duno M, Vilhelmsen K, Rosenberg T, (2010) Mutations in PCDH21 cause autosomal recessive cone-rod dystrophy. J Med Genet 47: 665-669.
16. Littink KW, Koenekoop RK, van den Born LI, Collin RW, Moruz L, et al. (2010) Homozygosity mapping in patients with cone-rod dystrophy: novel mutations and clinical characterizations. Invest Ophthalmol Vis Sci 51: 5943-5951.
17. Michaelides M, Aligianis IA, Ainsworth JR, Good P, Mollon JD, et al. (2004) Progressive cone dystrophy associated with mutation in CNGB3. Invest Ophthalmol Vis Sci 45: 1975-1982.
18. Polok B, Escher P, Ambresin A, Chouery E, Bolay S, et al. (2009) Mutations in CNNM4 cause recessive cone-rod dystrophy with amelogenesis imperfecta. Am J Hum Genet 84: 259-265.
19. Wu H, Cowing JA, Michaelides M, Wilkie SE, Jeffery G, et al. (2006) Mutations in the gene KCNV2 encoding a voltage-gated potassium channel subunit cause "cone dystrophy with supernormal rod electroretinogram" in humans. Am J Hum Genet 79: 574-579.
20. Thiadens AA, den Hollander AI, Roosing S, Nabuurs SB, Zekveld-Vroon RC, et al. (2009) Homozygosity mapping reveals PDE6C mutations in patients with early-onset cone photoreceptor disorders. Am J Hum Genet 85: 240-247.
21. Wang QL, Chen S, Esumi N, Swain PK, Haines HS, et al. (2004) QRX, a novel homeobox gene, modulates photoreceptor gene expression. Hum Mol Genet 13: 1025-1040.
22. Wada Y, Abe T, Sato H, Tamai M, (2001) A novel Gly35Ser mutation in the RDH5 gene in a Japanese family with fundus albipunctatus associated with cone dystrophy. Arch Ophthalmol 119: 1059-1063.
23. Hameed A, Abid A, Aziz A, Ismail M, Mehdi SQ, et al. (2003) Evidence of RPGRIP1 gene mutations associated with recessive cone-rod dystrophy. J Med Genet 40: 616-619.
24. Jalkanen R, Mantyjarvi M, Tobias R, Isosomppi J, Sankila EM, et al. (2006) X linked cone-rod dystrophy, CORDX3, is caused by a mutation in the CACNA1F gene. J Med Genet 43: 699-704.
25. Demirci FY, Rigatti BW, Wen G, Radak AL, Mah TS, et al. (2002) X-linked cone-rod dystrophy (locus COD1): identification of mutations in RPGR exon ORF15. Am J Hum Genet 70: 1049-1053.
26. Huang L, Xiao X, Li S, Jia X, Wang P, et al. (2012) CRX variants in cone-rod dystrophy and mutation overview. Biochem Biophys Res Commun 426: 498-503.
27. Huang L, Li S, Xiao X, Jia X, Sun W, et al. (2013) Novel GUCA1A mutation identified in a Chinese family with cone-rod dystrophy. Neurosci Lett 541: 179-183.
28. Xiao X, Guo X, Jia X, Li S, Wang P, et al. (2011) A recurrent mutation in GUCY2D associated with autosomal dominant cone dystrophy in a Chinese family. Mol Vis 17: 3271-3278.
29. Huang L, Li S, Xiao X, Jia X, Wang P, et al. (2013) Screening for variants in 20 genes in 130 unrelated patients with cone-rod dystrophy. Mol Med Rep 7: 1779-1785.
30. Wang Q, Wang P, Li S, Xiao X, Jia X, et al. (2010) Mitochondrial DNA haplogroup distribution in Chaoshanese with and without myopia. Mol Vis 16: 303-309.
31. Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, et al. (2010) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42: 969-972.
32. Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
33. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
34. Li R, Li Y, Fang X, Yang H, Wang J, et al. (2009) SNP detection for massively parallel whole-genome resequencing. Genome Res 19: 1124-1132.
35. Rozen S, Skaletsky H, (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
36. Li L, Xiao X, Li S, Jia X, Wang P, et al. (2011) Detection of variants in 15 genes in 87 unrelated Chinese patients with Leber congenital amaurosis. PLoS One 6: e19458.
37. den Dunnen JT, Antonarakis SE, (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat 15: 7-12.
38. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
39. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
40. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
41. Reese MG, Eeckman FH, Kulp D, Haussler D, (1997) Improved splice site detection in Genie. J Comput Biol 4: 311-323.
42. den Hollander AI, Black A, Bennett J, Cremers FP, (2010) Lighting a candle in the dark: advances in genetics and gene therapy of recessive retinal dystrophies. J Clin Invest 120: 3042-3053.
43. Kohl S, Kitiratschky V, Papke M, Schaich S, Sauer A, et al. (2012) Genes and mutations in autosomal dominant cone and cone-rod dystrophy. Adv Exp Med Biol 723: 337-343.
44. Ito S, Nakamura M, Nuno Y, Ohnishi Y, Nishida T, et al. (2004) Novel complex GUCY2D mutation in Japanese family with cone-rod dystrophy. Invest Ophthalmol Vis Sci 45: 1480-1485.
45. Garcia-Hoyos M, Auz-Alexandre CL, Almoguera B, Cantalapiedra D, Riveiro-Alvarez R, et al. (2011) Mutation analysis at codon 838 of the Guanylate Cyclase 2D gene in Spanish families with autosomal dominant cone, cone-rod, and macular dystrophies. Mol Vis 17: 1103-1109.
46. Kitiratschky VB, Behnen P, Kellner U, Heckenlively JR, Zrenner E, et al. (2009) Mutations in the GUCA1A gene involved in hereditary cone dystrophies impair calcium-mediated regulation of guanylate cyclase. Hum Mutat 30: E782-796.
47. Ducroq D, Rozet JM, Gerber S, Perrault I, Barbet D, et al. (2002) The ABCA4 gene in autosomal recessive cone-rod dystrophies. Am J Hum Genet 71: 1480-1482.
48. Fishman GA, Stone EM, Eliason DA, Taylor CM, Lindeman M, et al. (2003) ABCA4 gene sequence variations in patients with autosomal recessive cone-rod dystrophy. Arch Ophthalmol 121: 851-855.
49. Thiadens AA, Phan TM, Zekveld-Vroon RC, Leroy BP, van den Born LI, et al. (2012) Clinical course, genetic etiology, and visual outcome in cone and cone-rod dystrophy. Ophthalmology 119: 819-826.
50. Maugeri A, Klevering BJ, Rohrschneider K, Blankenagel A, Brunner HG, et al. (2000) Mutations in the ABCA4 (ABCR) gene are the major cause of autosomal recessive cone-rod dystrophy. Am J Hum Genet 67: 960-966.