Ophthalmology
Volume 118, Issue 1 , Pages 160-167.e3 , January 2011

Simultaneous Mutation Detection in 90 Retinal Disease Genes in Multiple Patients Using a Custom-designed 300-kb Retinal Resequencing Chip

  • Judith C. Booij, MD, PhD

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
  • ,
  • Arne Bakker, BSc

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
  • ,
  • Jamilia Kulumbetova, MD, PhD

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
  • ,
  • Youssef Moutaoukil, BSc

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
  • ,
  • Bert Smeets, PhD

      Affiliations

    • Clinical Genetics University Maastricht, The Netherlands
  • ,
  • Joke Verheij, MD, PhD

      Affiliations

    • Genetics, University Medical Center, Groningen, The Netherlands
  • ,
  • Hester Y. Kroes, MD, PhD

      Affiliations

    • Medical Genetics, University Medical Center Utrecht, The Netherlands
  • ,
  • Caroline C.W. Klaver, MD, PhD

      Affiliations

    • Ophthalmology, Erasmus Medical Centre Rotterdam, The Netherlands
  • ,
  • Mary van Schooneveld, MD, PhD

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
  • ,
  • Arthur A.B. Bergen, PhD

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
    • Clinical Genetics, Academic Medical Centre Amsterdam, The Netherlands
    • Ophthalmology, Academic Medical Centre Amsterdam, The Netherlands
    • Corresponding Author InformationCorrespondence: Arthur A. B. Bergen, NIN, Department of Clinical and Molecular Ophthalmogenetics, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
  • ,
  • Ralph J. Florijn, PhD

      Affiliations

    • Departments of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands

Received 19 October 2009 ,Revised 14 April 2010 ,Accepted 14 April 2010.

References 

  1. Retnet. http://www.sph.uth.tmc.edu/Retnet/Accessed April 10, 2010
  2. Haim M. Epidemiology of retinitis pigmentosa in Denmark. Acta Ophthalmol Scand Suppl. 2002;1–34
  3. Booij JC, Florijn RJ, ten Brink JB, et al. Identification of mutations in the AIPL1, CRB1, GUCY2D, RPE65, and RPGRIP1 genes in patients with juvenile retinitis pigmentosa. J Med Genet. 2005;42:e67
  4. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16:1215
  5. Schageman JJ, Horton CJ, Niu S, et al. ELXR: a resource for rapid exon-directed sequence analysis. Genome Biol. 2004;5:R36
  6. Beiboer SH, Wieringa-Jelsma T, Maaskant-van Wijk PA, et al. Rapid genotyping of blood group antigens by multiplex polymerase chain reaction and DNA microarray hybridization. Transfusion. 2005;45:667–679
  7. Leveque M, Marlin S, Jonard L, et al. Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Eur J Hum Genet. 2007;15:1145–1155
  8. HGMD database. http://www.hgmd.cf.ac.uk/ac/hahaha.phpAccessed April 10, 2010
  9. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16:1215
  10. ELXRdb http:/elxr.swmed.edu/elxrdb_query.html.
  11. primer3 http://frodo.wi.mit.edu/primer3/.
  12. ServiceXS http://www.servicexs.com/
  13. Ensembl www.ensembl.org/index.html
  14. Beiboer SH, Wieringa-Jelsma T, Maaskant-van Wijk PA, et al. Rapid genotyping of blood group antigens by multiplex polymerase chain reaction and DNA microarray hybridization. Transfusion. 2005;45:667–679
  15. Leveque M, Marlin S, Jonard L, et al. Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Eur J Hum Genet. 2007;15:1145–1155
  16. HGMD database http://www.hgmd.cf.ac.uk/ac/hahaha.php.
  17. Genecards http://www.genecards.org/index.shtml.
  18. Stenirri S, Alaimo G, Manitto MP, et al. Are microarrays useful in the screening of ABCA4 mutations in Italian patients affected by macular degenerations?. Clin Chem Lab Med. 2008;46:1250–1255
  19. Schulz V, Hendig D, Henjakovic M, et al. Mutational analysis of the ABCC6 gene and the proximal ABCC6 gene promoter in German patients with pseudoxanthoma elasticum (PXE). Hum Mutat. 2006;27:831
  20. Le Saux O, Beck K, Sachsinger C, et al. A spectrum of ABCC6 mutations is responsible for pseudoxanthoma elasticum. Am J Hum Genet. 2001;69:749–764
  21. Cai L, Lumsden A, Guenther UP, et al. A novel Q378X mutation exists in the transmembrane transporter protein ABCC6 and its pseudogene: implications for mutation analysis in pseudoxanthoma elasticum. J Mol Med. 2001;79:536–546
  22. Bergen AA, Plomp AS, Schuurman EJ, et al. Mutations in ABCC6 cause pseudoxanthoma elasticum. Nat Genet. 2000;25:228–231
  23. Meloni I, Rubegni P, De AG, et al. Pseudoxanthoma elasticum: Point mutations in the ABCC6 gene and a large deletion including also ABCC1 and MYH11. Hum Mutat. 2001;18:85
  24. Li JB, Gerdes JM, Haycraft CJ, et al. Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell. 2004;117:541–552
  25. Stone EM. Leber congenital amaurosis - a model for efficient genetic testing of heterogeneous disorders: LXIV Edward Jackson Memorial Lecture. Am J Ophthalmol. 2007;144:791–811
  26. 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
  27. Dryja TP, Finn JT, Peng YW, et al. Mutations in the gene encoding the alpha subunit of the rod cGMP-gated channel in autosomal recessive retinitis pigmentosa. Proc Natl Acad Sci U S A. 1995;92:10177–10181
  28. den Hollander AI, Davis J, van der Velde-Visser SD, et al. CRB1 mutation spectrum in inherited retinal dystrophies. Hum Mutat. 2004;24:355–369
  29. den Hollander AI, ten Brink JB, de Kok YJ, et al. Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12). Nat Genet. 1999;23:217–221
  30. Ayyagari R, Zhang K, Hutchinson A, et al. Evaluation of the ELOVL4 gene in patients with age-related macular degeneration. Ophthalmic Genet. 2001;22:233–239
  31. Henderson RH, Waseem N, Searle R, et al. An assessment of the apex microarray technology in genotyping patients with Leber congenital amaurosis and early-onset severe retinal dystrophy. Invest Ophthalmol Vis Sci. 2007;48:5684–5689
  32. Petrukhin K, Koisti MJ, Bakall B, et al. Identification of the gene responsible for Best macular dystrophy. Nat Genet. 1998;19:241–247
  33. Lotery AJ, Munier FL, Fishman GA, et al. Allelic variation in the VMD2 gene in best disease and age-related macular degeneration. Invest Ophthalmol Vis Sci. 2000;41:1291–1296
  34. Swain P, Kumar S, Patel D, et al. Mutations associated with retinopathies alter mitogen-activated protein kinase-induced phosphorylation of neural retina leucine-zipper. Mol Vis. 2007;13:1114–1120
  35. Spritz RA, Lee ST, Fukai K, et al. Novel mutations of the P gene in type II oculocutaneous albinism (OCA2). Hum Mutat. 1997;10:175–177
  36. Lee ST, Nicholls RD, Bundey S, et al. Mutations of the P gene in oculocutaneous albinism, ocular albinism, and Prader-Willi syndrome plus albinism. N Engl J Med. 1994;330:529–534
  37. Pesch UE, Leo-Kottler B, Mayer S, et al. OPA1 mutations in patients with autosomal dominant optic atrophy and evidence for semi-dominant inheritance. Hum Mol Genet. 2001;10:1359–1368
  38. Ferre M, Bonneau D, Milea D, et al. Molecular screening of 980 cases of suspected hereditary optic neuropathy with a report on 77 novel OPA1 mutations. Hum Mutat. 2009;30:E692–E705
  39. Dryja TP, Rucinski DE, Chen SH, Berson EL. Frequency of mutations in the gene encoding the alpha subunit of rod cGMP-phosphodiesterase in autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 1999;40:1859–1865
  40. McLaughlin ME, Ehrhart TL, Berson EL, Dryja TP. Mutation spectrum of the gene encoding the beta subunit of rod phosphodiesterase among patients with autosomal recessive retinitis pigmentosa. Proc Natl Acad Sci U S A. 1995;92:3249–3253
  41. Chakarova CF, Hims MM, Bolz H, et al. Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Hum Mol Genet. 2002;11:87–92
  42. Gendia blindness chip http://www.gendia.net/t18_note4.html.
  43. Morimura H, Saindelle-Ribeaudeau F, Berson EL, Dryja TP. Mutations in RGR, encoding a light-sensitive opsin homologue, in patients with retinitis pigmentosa. Nat Genet. 1999;23:393–394
  44. Payne A, Vithana E, Khaliq S, et al. RP1 protein truncating mutations predominate at the RP1 adRP locus. Invest Ophthalmol Vis Sci. 2000;41:4069–4073
  45. Gerber S, Perrault I, Hanein S, et al. Complete exon-intron structure of the RPGR-interacting protein (RPGRIP1) gene allows the identification of mutations underlying Leber congenital amaurosis. Eur J Hum Genet. 2001;9:561–571
  46. Hayashi T, Omoto S, Takeuchi T, et al. Four Japanese male patients with juvenile retinoschisis: only three have mutations in the RS1 gene. Am J Ophthalmol. 2004;138:788–798
  47. Hotta Y, Fujiki K, Hayakawa M, et al. Japanese juvenile retinoschisis is caused by mutations of the XLRS1 gene. Hum Genet. 1998;103:142–144
  48. Spritz RA, Strunk KM, Giebel LB, King RA. Detection of mutations in the tyrosinase gene in a patient with type IA oculocutaneous albinism. N Engl J Med. 1990;322:1724–1728
  49. Najera C, Beneyto M, Blanca J, et al. Mutations in myosin VIIA (MYO7A) and usherin (USH2A) in Spanish patients with Usher syndrome types I and II, respectively. Hum Mutat. 2002;20:76–77
  50. Aller E, Najera C, Millan JM, et al. Genetic analysis of 2299delG and C759F mutations (USH2A) in patients with visual and/or auditory impairments. Eur J Hum Genet. 2004;12:407–410
  51. Weston MD, Eudy JD, Fujita S, et al. Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. Am J Hum Genet. 2000;66:1199–1210
  52. Ouyang XM, Hejtmancik JF, Jacobson SG, et al. Mutational spectrum in Usher syndrome type II. Clin Genet. 2004;65:288–293
  53. Bitner-Glindzicz M, Lindley KJ, Rutland P, et al. A recessive contiguous gene deletion causing infantile hyperinsulinism, enteropathy and deafness identifies the Usher type 1C gene. Nat Genet. 2000;26:56–60
  54. Cremers FP, Kimberling WJ, Kulm M, et al. Development of a genotyping microarray for Usher syndrome. J Med Genet. 2007;44:153–160
  55. Ahmed ZM, Riazuddin S, Riazuddin S, Wilcox ER. The molecular genetics of Usher syndrome. Clin Genet. 2003;63:431–444
  56. Gendia http://www.gendia.net/t18_note7.html.
  57. van Wijk E, Pennings RJ, te BH, et al. Identification of 51 novel exons of the Usher syndrome type 2A (USH2A) gene that encode multiple conserved functional domains and that are mutated in patients with Usher syndrome type II. Am J Hum Genet. 2004;74:738–744

 Manuscript no. 2009-1455.

 Financial Disclosure(s): The author(s) have no proprietary or commercial interest in any materials discussed in this article.

 Funded by the Algemene Nederlandse Vereniging ter Voorkoming van Blindheid, Landelijke Stichting voor Blinden en Slechtzienden, Rotterdamse Vereniging Blindenbelangen, Stichting Blindenpenning, Stichting Oogfonds Nederland, and Gelderse Blindenstichting.

PII: S0161-6420(10)00450-1

doi: 10.1016/j.ophtha.2010.04.022

Ophthalmology
Volume 118, Issue 1 , Pages 160-167.e3 , January 2011