Screening for duplications, deletions and a common intronic mutation detects 35% of second mutations in patients with USH2A monoallelic mutations on Sanger sequencing

详细信息    查看全文

• 作者：Heather B Steele-Stallard (11)
  Polona Le Quesne Stabej (11)
  Eva Lenassi (12) (13)
  Linda M Luxon (14) (15)
  Mireille Claustres (16) (17)
  Anne-Francoise Roux (16) (17)
  Andrew R Webster (12) (13)
  Maria Bitner-Glindzicz (11) (15) (18)
  
• 关键词：Usher syndrome ; USH2A ; Deletion ; Duplication ; Pseudoexon ; Multiplex ligation dependant probe amplification (MLPA) ; Array CGH
• 刊名：Orphanet Journal of Rare Diseases
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：8
• 期：1
• 全文大小：336KB
• 参考文献：1. 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.
  2. Saihan Z, Webster AR, Luxon L, Bitner-Glindzicz M: Update on Usher syndrome. / Curr Opin Neurol 2009, 22:19-7. CrossRef
  3. Riazuddin S, Belyantseva IA, Giese APJ, Lee K, Indzhykulian AA, Nandamuri SP, Yousaf R, Sinha GP, Lee S, Terrell D, Hegde RS, Ali RA, Anwar S, Andrade-Elizondo PB, Sirmaci A, Parise LV, Basit S, Wali A, Ayub M, Ansar M, Ahmad W, Khan SN, Akram J, Tekin M, Riazuddin S, Cook T, Buschbeck EK, Frolenkov GI, Leal SM, Friedman TB, Ahmed ZM: Alterations of the CIB2 calcium- and integrin-binding protein cause Usher syndrome type 1J and nonsyndromic deafness DFNB48. / Nat Genet 2012, 44:1265-271. CrossRef
  4. Ebermann I, Phillips JB, Liebau MC, Koenekoop RK, Schermer B, Lopez I, Sch?fer E, Roux A-F, Dafinger C, Bernd A, Zrenner E, Claustres M, Blanco B, Nürnberg G, Nürnberg P, Ruland R, Westerfield M, Benzing T, Bolz HJ: PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome. / J Clin Invest 2010, 120:1812-823. CrossRef
  5. Kimberling WJ, Hildebrand MS, Shearer AE, Jensen ML, Halder JA, Trzupek K, Cohn ES, Weleber RG, Stone EM, Smith RJH: Frequency of Usher syndrome in two pediatric populations: implications for genetic screening of deaf and hard of hearing children. / Genet Med 2010, 12:512-16. CrossRef
  6. Baux D, Larrieu L, Blanchet C, Hamel C, Ben Salah S, Vielle A, Gilbert-Dussardier B, Holder M, Calvas P, Philip N, Edery P, Bonneau D, Claustres M, Malcolm S, Roux A-F: Molecular and in silico analyses of the full-length isoform of usher in identify new pathogenic alleles in Usher type II patients. / Hum Mutat 2007, 28:781-89. CrossRef
  7. Le Quesne SP, Saihan Z, Rangesh N, Steele-Stallard HB, Ambrose J, Coffey A, Emmerson J, Haralambous E, Hughes Y, Steel KP, Luxon LM, Webster AR, Bitner-Glindzicz M: Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study. / J Med Genet 2012, 49:27-6. CrossRef
  8. Garcia-Garcia G, Aparisi MJ, Jaijo T, Rodrigo R, Leon AM, Avila-Fernandez A, Blanco-Kelly F, Bernal S, Navarro R, Diaz-Llopis M, Baiget M, Ayuso C, Millan JM, Aller E: Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations. / Orphanet J Rare Dis 2011, 6:65. CrossRef
  9. USH-Bases: / LSDBs for usher syndrome genes. https://grenada.lumc.nl/LOVD2/Usher_montpellier/USHbases.html
  10. Roux A-F, Faugère V, Vaché C, Baux D, Besnard T, Léonard S, Blanchet C, Hamel C, Mondain M, Gilbert-Dussardier B, Edery P, Lacombe D, Bonneau D, Holder-Espinasse M, Ambrosetti U, Journel H, David A, Lina-Granade G, Malcolm S, Claustres M: Four-year follow-up of diagnostic service in USH1 patients. / Invest Ophthalmol Vis Sci 2011, 52:4063-071. CrossRef
  11. Vaché C, Besnard T, le Berre P, García-García G, Baux D, Larrieu L, Abadie C, Blanchet C, Bolz HJ, Millan J, Hamel C, Malcolm S, Claustres M, Roux A-F: Usher syndrome type 2 caused by activation of an USH2A pseudoexon: implications for diagnosis and therapy. / Hum Mutat 2012, 33:104-08. CrossRef
  12. Nakanishi H, Ohtsubo M, Iwasaki S, Hotta Y, Mizuta K, Mineta H, Minoshima S: Hair roots as an mRNA source for mutation analysis of Usher syndrome-causing genes. / J Hum Genet 2010, 55:701-03. CrossRef
  13. Vaché C, Besnard T, Blanchet C, Baux D, Larrieu L, Faugère V, Mondain M, Hamel C, Malcolm S, Claustres M, Roux A-F: Nasal epithelial cells are a reliable source to study splicing variants in Usher syndrome. / Hum Mutat 2010, 31:734-41. CrossRef
  14. Aller E, Jaijo T, García-García G, Aparisi MJ, Blesa D, Díaz-Llopis M, Ayuso C, Millán JM: Identification of large rearrangements of the PCDH15 gene by combined MLPA and a CGH: large duplications are responsible for Usher syndrome. / Invest Ophthalmol Vis Sci 2010, 51:5480-485. CrossRef
  15. Besnard T, Vaché C, Baux D, Larrieu L, Abadie C, Blanchet C, Odent S, Blanchet P, Calvas P, Hamel C, Dollfus H, Lina-Granade G, Lespinasse J, David A, Isidor B, Morin G, Malcolm S, Tuffery-Giraud S, Claustres M, Roux A-F: Non-USH2A mutations in USH2 patients. / Hum Mutat 2012, 33:504-10. CrossRef
  16. / MRC-Holland - MLPA procedure - introduction. http://www.mlpa.com/WebForms/WebFormMain.aspx?Tag=wl2zCji\rCGANQgZPuTixsEyIW1MscfzuKj2NDFYc\g
  17. / Softgenetics - software power tools for genetic analysis. http://www.softgenetics.com/GeneMarker.html
  18. Bonnet C, Grati M, Marlin S, Levilliers J, Hardelin J-P, Parodi M, Niasme-Grare M, Zelenika D, Délépine M, Feldmann D, Jonard L, El-Amraoui A, Weil D, Delobel B, Vincent C, Dollfus H, Eliot M-M, David A, Calais C, Vigneron J, Montaut-Verient B, Bonneau D, Dubin J, Thauvin C, Duvillard A, Francannet C, Mom T, Lacombe D, Duriez F, Drouin-Garraud V, Thuillier-Obstoy M-F, Sigaudy S, Frances A-M, Collignon P, Challe G, Couderc R, Lathrop M, Sahel J-A, Weissenbach J, Petit C, Denoyelle F: Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis. / Orphanet J Rare Dis 2011, 6:21. CrossRef
  19. Abu-Safieh L, Al-Anazi S, Al-Abdi L, Hashem M, Alkuraya H, Alamr M, Sirelkhatim MO, Al-Hassnan Z, Alkuraya B, Mohamed JY, Al-Salem A, Alrashed M, Faqeih E, Softah A, Al-Hashem A, Wali S, Rahbeeni Z, Alsayed M, Khan AO, Al-Gazali L, Taschner PEM, Al-Hazzaa S, Alkuraya FS: In search of triallelism in Bardet-Biedl syndrome. / Eur J Hum Genet 2012, 20:420-27. CrossRef
  20. Jaijo T, Aller E, García-García G, Aparisi MJ, Bernal S, Avila-Fernández A, Barragán I, Baiget M, Ayuso C, Anti?olo G, Díaz-Llopis M, Külm M, Beneyto M, Nájera C, Millán JM: Microarray-based mutation analysis of 183 Spanish families with Usher syndrome. / Invest Ophthalmol Vis Sci 2010, 51:1311-317. CrossRef
  21. Xu W, Dai H, Lu T, Zhang X, Dong B, Li Y: Seven novel mutations in the long isoform of the USH2A gene in Chinese families with nonsyndromic retinitis pigmentosa and Usher syndrome Type II. / Mol Vis 2011, 17:1537-552.
  22. Saihan Z, Stabej PLQ, Robson AG, Rangesh N, Holder GE, Moore AT, Steel KP, Luxon LM, Bitner-Glindzicz M, Webster AR: Mutations in the USH1C gene associated with sector retinitis pigmentosa and hearing loss. / Retina 2011, 31:1708-716. CrossRef
  23. Hirami Y, Osakada F, Takahashi K, Okita K, Yamanaka S, Ikeda H, Yoshimura N, Takahashi M: Generation of retinal cells from mouse and human induced pluripotent stem cells. / Neurosci Lett 2009, 458:126-31. let.2009.04.035">CrossRef
  24. Jin Z-B, Okamoto S, Osakada F, Homma K, Assawachananont J, Hirami Y, Iwata T, Takahashi M: Modeling retinal degeneration using patient-specific induced pluripotent stem cells. / PLoS ONE 2011, 6:e17084. CrossRef
  25. Zahabi A, Shahbazi E, Ahmadieh H, Hassani S-N, Totonchi M, Taei A, Masoudi N, Ebrahimi M, Aghdami N, Seifinejad A, Mehrnejad F, Daftarian N, Salekdeh GH, Baharvand H: A new efficient protocol for directed differentiation of retinal pigmented epithelial cells from normal and retinal disease induced pluripotent stem cells. / Stem Cells Dev 2012, 21:2262-272. CrossRef
  26. Zou J, Luo L, Shen Z, Chiodo VA, Ambati BK, Hauswirth WW, Yang J: Whirlin replacement restores the formation of the USH2 protein complex in whirlin knockout photoreceptors. / Invest Ophthalmol Vis Sci 2011, 52:2343-351. CrossRef
  27. Goldmann T, Overlack N, M?ller F, Belakhov V, van Wyk M, Baasov T, Wolfrum U, Nagel-Wolfrum K: A comparative evaluation of NB30, NB54 and PTC124 in translational read-through efficacy for treatment of an USH1C nonsense mutation. / EMBO Mol Med 2012.
  28. Overlack N, Goldmann T, Wolfrum U, Nagel-Wolfrum K: Gene repair of an Usher syndrome causing mutation by zinc-finger nuclease mediated homologous recombination. / Invest Ophthalmol Vis Sci 2012, 53:4140-146. CrossRef
  29. Williams DS: Usher syndrome: animal models, retinal function of Usher proteins, and prospects for gene therapy. / Vision Res 2008, 48:433-41. CrossRef
  30. Sahly I, Dufour E, Schietroma C, Michel V, Bahloul A, Perfettini I, Pepermans E, Estivalet A, Carette D, Aghaie A, Ebermann I, Lelli A, Iribarne M, Hardelin J-P, Weil D, Sahel J-A, El-Amraoui A, Petit C: Localization of Usher 1 proteins to the photoreceptor calyceal processes, which are absent from mice. / J Cell Biol 2012, 199:381-99. CrossRef
  
• 作者单位：Heather B Steele-Stallard (11)
  Polona Le Quesne Stabej (11)
  Eva Lenassi (12) (13)
  Linda M Luxon (14) (15)
  Mireille Claustres (16) (17)
  Anne-Francoise Roux (16) (17)
  Andrew R Webster (12) (13)
  Maria Bitner-Glindzicz (11) (15) (18)
  
  11. UCL Institute of Child Health, London, UK
  12. UCL Institute of Ophthalmology, London, UK
  13. Moorfields Eye Hospital, London, UK
  14. Audiovestibular Medicine, National Hospital for Neurology and Neurosurgery, London, UK
  15. UCL Ear Institute, London, UK
  16. CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
  17. Inserm, U827, Montpellier, F-34000, France
  18. Great Ormond Street Hospital, London, UK
  

文摘

Background Usher Syndrome is the leading cause of inherited deaf-blindness. It is divided into three subtypes, of which the most common is Usher type 2, and the USH2A gene accounts for 75-80% of cases. Despite recent sequencing strategies, in our cohort a significant proportion of individuals with Usher type 2 have just one heterozygous disease-causing mutation in USH2A, or no convincing disease-causing mutations across nine Usher genes. The purpose of this study was to improve the molecular diagnosis in these families by screening USH2A for duplications, heterozygous deletions and a common pathogenic deep intronic variant USH2A: c.7595-2144A>G. Methods Forty-nine Usher type 2 or atypical Usher families who had missing mutations (mono-allelic USH2A or no mutations following Sanger sequencing of nine Usher genes) were screened for duplications/deletions using the USH2A SALSA MLPA reagent kit (MRC-Holland). Identification of USH2A: c.7595-2144A>G was achieved by Sanger sequencing. Mutations were confirmed by a combination of reverse transcription PCR using RNA extracted from nasal epithelial cells or fibroblasts, and by array comparative genomic hybridisation with sequencing across the genomic breakpoints. Results Eight mutations were identified in 23 Usher type 2 families (35%) with one previously identified heterozygous disease-causing mutation in USH2A. These consisted of five heterozygous deletions, one duplication, and two heterozygous instances of the pathogenic variant USH2A: c.7595-2144A>G. No variants were found in the 15 Usher type 2 families with no previously identified disease-causing mutations. In 11 atypical families, none of whom had any previously identified convincing disease-causing mutations, the mutation USH2A: c.7595-2144A>G was identified in a heterozygous state in one family. All five deletions and the heterozygous duplication we report here are novel. This is the first time that a duplication in USH2A has been reported as a cause of Usher syndrome. Conclusions We found that 8 of 23 (35%) of ‘missing-mutations in Usher type 2 probands with only a single heterozygous USH2A mutation detected with Sanger sequencing could be attributed to deletions, duplications or a pathogenic deep intronic variant. Future mutation detection strategies and genetic counselling will need to take into account the prevalence of these types of mutations in order to provide a more comprehensive diagnostic service.