Targeted exon sequencing in usher syndrome type I

Investigative Ophthalmology and Visual Science

Volumn 55, Issue 12, 2014, Pages 8488-8496

  Bujakowska, Kinga M ^a   Consugar, Mark ^a   Place, Emily ^a   Harper, Shyana ^a   Lena, Jaclyn ^a   Taub, Daniel G ^a   White, Joseph ^a   Navarro Gomez, Daniel ^a   Difranco, Carol Weigel ^a   Farkas, Michael H ^a   Gai, Xiaowu ^a   Berson, Eliot L ^a   Pierce, Eric A ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Genetics; Hearing loss; Molecular diagnostic; Nextgeneration sequencing; Retina; Retinitis pigmentosa; Selective exon capture; Usher syndrome

Indexed keywords

CADHERIN 23; MEMBRANE PROTEIN; MYOSIN VIIA; PROTOCADHERIN 15; TRANSCRIPTOME; UNCLASSIFIED DRUG; USHER SYNDROME TYPE 1G PROTEIN; MYOSIN;

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA SEQUENCE; ELECTRORETINOGRAPHY; EYE EXAMINATION; FEMALE; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC HETEROGENEITY; HUMAN; HYBRIDIZATION; INFANT; MAJOR CLINICAL STUDY; MALE; RETINA DEGENERATION; RNA SPLICING; TARGETED EXON SEQUENCING; USHER SYNDROME; ADULT; COHORT ANALYSIS; EXON; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; METABOLISM; MUTATION; NUCLEOTIDE SEQUENCE; PEDIGREE; PROCEDURES;

ADULT; COHORT STUDIES; DNA MUTATIONAL ANALYSIS; EXONS; GENE EXPRESSION PROFILING; GENETIC VARIATION; HUMANS; MUTATION; MYOSINS; PEDIGREE; SEQUENCE ANALYSIS, DNA; USHER SYNDROMES;

EID: 84920066317     PISSN: 01460404     EISSN: 15525783     Source Type: Journal    
DOI: 10.1167/iovs.14-15169     Document Type: Article

References (55)

1. Weil D, Blanchard S, Kaplan J, et al. Defective myosin VIIA gene responsible for Usher syndrome type 1B. Nature. 1995; 374:60-61.
2. Verpy E, Leibovici M, Zwaenepoel I, et al. A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C. Nat Genet. 2000;26:51-55.
3. Bolz H, von Brederlow B, Ramırez A, et al. Mutation of CDH23, encoding a new member of the cadherin gene family, causes Usher syndrome type 1D. Nat Genet. 2001;27:108-112.
4. Ahmed ZM, Riazuddin S, Bernstein SL, et al. Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F. Am J Hum Genet. 2001;69:25-34.
5. Weil D, El-Amraoui A, Masmoudi S, et al. Usher syndrome type I G (USH1G) is caused by mutations in the gene encoding SANS, a protein that associates with the USH1C protein, harmonin. Hum Mol Genet. 2003;12:463-471.
6. Riazuddin S, Belyantseva IA, Giese APJ, et al. Alterations of the CIB2 calciumand integrin-binding protein cause Usher syndrome type 1J and nonsyndromic deafness DFNB48. Nat Genet. 2012;44:1265-1271.
7. Hartong DT, Berson EL, Dryja TP. Retinitis pigmentosa. Lancet. 2006;368:1795-1809.
8. Rosenberg T, Haim M, Hauch AM, Parving A. The prevalence of Usher syndrome and other retinal dystrophy-hearing impairment associations. Clin Genet. 1997;51:314-321.
9. Hope CI, Bundey S, Proops D. Fielder a R. Usher syndrome in the city of Birmingham-prevalence and clinical classification. Br J Ophthalmol. 1997;81:46-53.
10. Millán JM, Aller E, Jaijo T, Blanco-Kelly F, Gimenez-Pardo A, Ayuso C. An update on the genetics of usher syndrome. J Ophthalmol. 2011;2011:417217.
11. Boughman JA, Vernon M, Shaver KA. Usher syndrome: definition and estimate of prevalence from two high-risk populations. J Chronic Dis. 1983;36:595-603.
12. Sahly I, Dufour E, Schietroma C, et al. Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. J Cell Biol. 2012;199;381-399.
13. Williams D. Usher syndrome: animal models, retinal function of Usher proteins, and prospects for gene therapy. Vision Res. 2008;48;433-441.
14. Miyasaka Y, Suzuki S, Ohshiba Y, et al. Compound heterozygosity of the functionally null Cdh23v-ngt and hypomorphic Cdh23ahl alleles leads to early-onset progressive hearing loss in mice. J Exp Anim Sci. 2013;62:333-346.
15. Liu X, Udovichenko IP, Brown SD, Steel KP, Williams DS. Myosin VIIa participates in opsin transport through the photoreceptor cilium. J Neurosci. 1999;19:6267-6274.
16. Libby RT, Steel KP. Electroretinographic anomalies in mice with mutations in Myo7a, the gene involved in human Usher syndrome type 1B. Invest Ophthalmol Vis Sci. 2001;42:770-778.
17. Di Palma F, Holme RH, Bryda EC, et al. Mutations in Cdh23, encoding a new type of cadherin, cause stereocilia disorganization in waltzer, the mouse model for Usher syndrome type 1D. Nat Genet. 2001;27:103-107.
18. Johnson KR, Gagnon LH, Webb LS, et al. Mouse models of USH1C and DFNB18: phenotypic and molecular analyses of two new spontaneous mutations of the Ush1c gene. Hum Mol Genet. 2003;12:3075-3086.
19. Ahmed ZM, Kjellstrom S, Haywood-Watson RJL, et al. Double homozygous waltzer and Ames waltzer mice provide no evidence of retinal degeneration. Mol Vis. 2008;14;2227-2236.
20. Lentz J, Gordon W, Farris HE, et al. Deafness and retinal degeneration in a novel USH1C knock-in mouse model. Dev Neurobiol. 2010;70:253-267.
21. Fromer M, Moran JL, Chambert K, et al. Discovery and statistical genotyping of copy-number variation from wholeexome sequencing depth. Am J Hum Genet. 2012;91:597-607.
22. Farkas M, Grant G, White J, Sousa M, Consugar M, Pierce E. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics. 2013;14:486.
23. Berson EL, Rosner B, Sandberg MA, et al. A randomized trial of vitamin A and vitamin E supplementation for retinitis pigmentosa. Arch Ophthalmol. 1993;111:1462-1463.
24. Falk MJ, Zhang Q, Nakamaru-Ogiso E, et al. NMNAT1 mutations cause Leber congenital amaurosis. Nat Genet. 2012;44:1040-1045.
25. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-1760.
26. Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078-2079.
27. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc. 1995;57:289-300.
28. McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;9:1297-1303.
29. NHLBI GO Exome Sequencing Project. Exome variant server. Available at: http://evs.gs.washington.edu/EVS/. Accessed June 30, 2014.
30. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812-3814.
31. Desmet F-O, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37:e67.
32. Reese M, Eeckman F, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol. 1997;4:311-323.
33. Bharadwaj AK, Kasztejna JP, Huq S, Berson EL, Dryja TP. Evaluation of the myosin VIIA gene and visual function in patients with Usher syndrome type I. Exp Eye Res. 2000;71; 173-181.
34. Cosgrove D, Zallocchi M. Usher protein functions in hair cells and photoreceptors. Int J Biochem Cell Biol. 2014;46;80-89.
35. Besnard T, Garc ıa-Garcıa G, Baux D, et al. Experience of targeted Usher exome sequencing as a clinical test. Mol Genet genomic Med. 2014;2;30-43.
36. Jaijo T, Aller E, Garc ıa-Garcıa G, et al. Microarray-based mutation analysis of 183 Spanish families with Usher syndrome. Invest Ophthalmol Vis Sci. 2010;51:1311-1317.
37. Katsanis N, Ansley SJ, Badano JL, et al. Triallelic inheritance in Bardet-Biedl syndrome, a Mendelian recessive disorder. Science. 2001:293;2256-2259.
38. Badano JL, Leitch CC, Ansley SJ, et al. Dissection of epistasis in oligogenic Bardet-Biedl syndrome. Nature. 2006;439:326-330.
39. Badano JL, Kim JC, Hoskins BE, et al. Heterozygous mutations in BBS1, BBS2 and BBS6 have a potential epistatic effect on Bardet-Biedl patients with two mutations at a second BBS locus. Hum Mol Genet. 2003;12:1651-1659.
40. Coppieters F, Casteels I, Meire F, et al. Genetic screening of LCA in Belgium: predominance of CEP290 and identification of potential modifier alleles in AHI1 of CEP290-related phenotypes. Hum Mutat. 2010;31:E1709-E1766.
41. Poloschek CM, Bach M, Lagreze WA, et al. ABCA4 and ROM1: implications for modification of the PRPH2-associated macular dystrophy phenotype. Invest Ophthalmol Vis Sci. 2010;51; 4253-4265.
42. Samardzija M, Wenzel A, Naash M, Remé CE, Grimm C. RPE65 as a modifier gene for inherited retinal degeneration. Eur J Neurosci. 2006;23:1028-1034.
43. Niederriter AR, Davis EE, Golzio C, Oh EC, Tsai I-C, Katsanis N. In vivo modeling of the morbid human genome using Danio rerio. J Vis Exp. 2013;78:e50338.
44. Vozzi D, Aaspõllu A, Athanasakis E, et al. Molecular epidemiology of Usher syndrome in Italy. Mol Vis. 2011;17:1662-1668.
45. Ebermann I, Lopez I, Bitner-Glindzicz M, Brown C, Koenekoop RK, Bolz HJ. Deafblindness in French Canadians from Quebec: a predominant founder mutation in the USH1C gene provides the first genetic link with the Acadian population. Genome Biol. 2007;8:R47.
46. Zwaenepoel I, Verpy E, Blanchard S, et al. Identification of three novel mutations in the USH1C gene and detection of thirty-one polymorphisms used for haplotype analysis. Hum Mutat. 2001;17:34-41.
47. Den Hollander AI, Koenekoop RK, Yzer S, et al. Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis. Am J Hum Genet. 2006;79:556-561.
48. Webb TR, Parfitt DA, Gardner JC, et al. Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23). Hum Mol Genet. 2012;21:3647-3654.
49. Braun TA, Mullins RF, Wagner AH, et al. Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease. Hum Mol Genet. 2013;22:5136-5145.
50. Nishiguchi KM, Tearle RG, Liu YP, et al. Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene. Proc Natl Acad Sci U S A. 2013;110:16139-16144.
51. Jacobson SG, Cideciyan AV, Aleman TS, et al. Usher syndromes due to MYO7A, PCDH15, USH2A or GPR98 mutations share retinal disease mechanism. Hum Mol Genet. 2008;17;2405-1415.
52. Khattar V, Hathiram B. The clinical test for the sensory interaction of balance. Int J Otorhinolaryngol Clin. 2012;4: 41-45.
53. Horak FB, Wrisley DM, Frank J. The Balance Evaluation Systems Test (BESTest) to differentiate balance deficits. Phys Ther. 2009;89:484-498.
54. Lopes VS, Boye SE, Louie CM, et al. Retinal gene therapy with a large MYO7A cDNA using adeno-associated virus. Gene Ther. 2013;20:824-833.
55. Hashimoto T, Gibbs D, Lillo C, et al. Lentiviral gene replacement therapy of retinas in a mouse model for Usher syndrome type 1B. Gene Ther. 2007;14:584-594.