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Exome sequencing reveals CCDC111 mutation associated with high myopia

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Abstract

Myopia is a refractive error of the eye that is prevalent worldwide. The most extreme form, high myopia, is usually associated with other ocular disorders such as retinal detachment, macular degeneration, cataract, and glaucoma, and is one of leading causes of blindness. The etiology is complex and has not been fully elucidated. In this study, we identified a novel missense variant of the CCDC111 gene (NM_152683.2: c.265T > G; p.Y89D) in a high myopia family by exome sequencing. The variant was identified in 4 patients from an additional 270 sporadic high myopia patients, but not found in 270 controls. The amino acid is highly conserved across species, and variants giving rise to amino acid substitutions are predicted to be functionally damaging. The CCDC111 gene was ubiquitously expressed in primary cell cultures from human eye tissue, including corneal epithelial cells, choroidal melanoma cells, scleral fibroblasts, retinal epithelial cells, retinal Müller cells, and lens capsule epithelial cells. In summary, our results suggested that the CCDC111 may be a susceptibility gene for high myopia.

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References

  • Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249. doi:10.1038/nmeth0410-248

    Article  PubMed  CAS  Google Scholar 

  • Bilguvar K, Ozturk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoglu D, Tuysuz B, Caglayan AO, Gokben S, Kaymakcalan H, Barak T, Bakircioglu M, Yasuno K, Ho W, Sanders S, Zhu Y, Yilmaz S, Dincer A, Johnson MH, Bronen RA, Kocer N, Per H, Mane S, Pamir MN, Yalcinkaya C, Kumandas S, Topcu M, Ozmen M, Sestan N, Lifton RP, State MW, Gunel M (2010) Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 467:207–210. doi:10.1038/nature09327

    Article  PubMed  CAS  Google Scholar 

  • Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106:19096–19101. doi:10.1073/pnas.0910672106

    Article  PubMed  CAS  Google Scholar 

  • Fan Q, Barathi VA, Cheng CY, Zhou X, Meguro A, Nakata I, Khor CC, Goh LK, Li YJ, Lim W, Ho CE, Hawthorne F, Zheng Y, Chua D, Inoko H, Yamashiro K, Ohno-Matsui K, Matsuo K, Matsuda F, Vithana E, Seielstad M, Mizuki N, Beuerman RW, Tai ES, Yoshimura N, Aung T, Young TL, Wong TY, Teo YY, Saw SM (2012) Genetic variants on chromosome 1q41 influence ocular axial length and high myopia. PLoS Genet 8:e1002753. doi:10.1371/journal.pgen.1002753

    Article  PubMed  CAS  Google Scholar 

  • He M, Zheng Y, Xiang F (2009) Prevalence of myopia in urban and rural children in mainland China. Optom Vis Sci 86:40–44. doi:10.1097/OPX.0b013e3181940719

    Article  PubMed  Google Scholar 

  • Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, Steehouwer M, de Vries P, de Reuver R, Wieskamp N, Mortier G, Devriendt K, Amorim MZ, Revencu N, Kidd A, Barbosa M, Turner A, Smith J, Oley C, Henderson A, Hayes IM, Thompson EM, Brunner HG, de Vries BB, Veltman JA (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42:483–485. doi:10.1038/ng.581

    Article  PubMed  CAS  Google Scholar 

  • Hosaka A (1988) Population studies—myopia experience in Japan. Acta Ophthalmol Suppl 185:37–40

    PubMed  CAS  Google Scholar 

  • Hosgood HD 3rd, Zhang L, Shen M, Berndt SI, Vermeulen R, Li G, Yin S, Yeager M, Yuenger J, Rothman N, Chanock S, Smith M, Lan Q (2009) Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. Occup Environ Med 66:848–853. doi:10.1136/oem.2008.044024

    Article  PubMed  CAS  Google Scholar 

  • Hu DN (2003) Cell culture in ophthalmology: culture of specific cell types. Zhonghua Yan Ke Za Zhi 39:312–316

    PubMed  Google Scholar 

  • Hysi PG, Young TL, Mackey DA, Andrew T, Fernandez-Medarde A, Solouki AM, Hewitt AW, Macgregor S, Vingerling JR, Li YJ, Ikram MK, Fai LY, Sham PC, Manyes L, Porteros A, Lopes MC, Carbonaro F, Fahy SJ, Martin NG, van Duijn CM, Spector TD, Rahi JS, Santos E, Klaver CC, Hammond CJ (2010) A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25. Nat Genet 42:902–905. doi:10.1038/ng.664

    Article  PubMed  CAS  Google Scholar 

  • Iyer LM, Koonin EV, Leipe DD, Aravind L (2005) Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res 33:3875–3896. doi:10.1093/nar/gki702

    Article  PubMed  CAS  Google Scholar 

  • Katz J, Tielsch JM, Sommer A (1997) Prevalence and risk factors for refractive errors in an adult inner city population. Invest Ophthalmol Vis Sci 38:334–340

    PubMed  CAS  Google Scholar 

  • Kempen JH, Mitchell P, Lee KE, Tielsch JM, Broman AT, Taylor HR, Ikram MK, Congdon NG, O’Colmain BJ, Eye Diseases Prevalence Research G (2004) The prevalence of refractive errors among adults in the United States, Western Europe, and Australia. Arch Ophthalmol 122:495–505. doi:10.1001/archopht.122.4.495

    Article  PubMed  Google Scholar 

  • 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. doi:10.1038/nprot.2009.86

    Article  PubMed  CAS  Google Scholar 

  • Lam CY, Tam PO, Fan DS, Fan BJ, Wang DY, Lee CW, Pang CP, Lam DS (2008) A genome-wide scan maps a novel high myopia locus to 5p15. Invest Ophthalmol Vis Sci 49:3768–3778. doi:iovs.07-1126

    Article  PubMed  Google Scholar 

  • Li Z, Qu J, Xu X, Zhou X, Zou H, Wang N, Li T, Hu X, Zhao Q, Chen P, Li W, Huang K, Yang J, He Z, Ji J, Wang T, Li J, Li Y, Liu J, Zeng Z, Feng G, He L, Shi Y (2011) A genome-wide association study reveals association between common variants in an intergenic region of 4q25 and high-grade myopia in the Chinese Han population. Hum Mol Genet 20:2861–2868. doi:10.1093/hmg/ddr169

    Article  PubMed  CAS  Google Scholar 

  • Ma JH, Shen SH, Zhang GW, Zhao DS, Xu C, Pan CM, Jiang H, Wang ZQ, Song HD (2010) Identification of a locus for autosomal dominant high myopia on chromosome 5p13.3-p15.1 in a Chinese family. Mol Vis 16:2043–2054

    PubMed  CAS  Google Scholar 

  • Morgan IG, Ohno-Matsui K, Saw SM (2012) Myopia. Lancet 379:1739–1748. doi:10.1016/S0140-6736(12)60272-4

    Article  PubMed  Google Scholar 

  • Nakanishi H, Yamada R, Gotoh N, Hayashi H, Yamashiro K, Shimada N, Ohno-Matsui K, Mochizuki M, Saito M, Iida T, Matsuo K, Tajima K, Yoshimura N, Matsuda F (2009) A genome-wide association analysis identified a novel susceptible locus for pathological myopia at 11q24.1. PLoS Genet 5:e1000660. doi:10.1371/journal.pgen.1000660

    Article  PubMed  Google Scholar 

  • Nallasamy S, Paluru PC, Devoto M, Wasserman NF, Zhou J, Young TL (2007) Genetic linkage study of high-grade myopia in a Hutterite population from South Dakota. Mol Vis 13:229–236. doi:v13/a26

    PubMed  CAS  Google Scholar 

  • Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272–276. doi:10.1038/nature08250

    Article  PubMed  CAS  Google Scholar 

  • Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ (2010) Exome sequencing identifies the cause of a Mendelian disorder. Nat Genet 42:30–35. doi:10.1038/ng.499

    Article  PubMed  CAS  Google Scholar 

  • Paget S, Julia S, Vitezica ZG, Soler V, Malecaze F, Calvas P (2008) Linkage analysis of high myopia susceptibility locus in 26 families. Mol Vis 14:2566–2574

    PubMed  CAS  Google Scholar 

  • Paluru P, Ronan SM, Heon E, Devoto M, Wildenberg SC, Scavello G, Holleschau A, Makitie O, Cole WG, King RA, Young TL (2003) New locus for autosomal dominant high myopia maps to the long arm of chromosome 17. Invest Ophthalmol Vis Sci 44:1830–1836

    Article  PubMed  Google Scholar 

  • Paluru PC, Nallasamy S, Devoto M, Rappaport EF, Young TL (2005) Identification of a novel locus on 2q for autosomal dominant high-grade myopia. Invest Ophthalmol Vis Sci 46:2300–2307. doi:46/7/2300

    Article  PubMed  Google Scholar 

  • Sawada A, Tomidokoro A, Araie M, Iwase A, Yamamoto T (2008) Refractive errors in an elderly Japanese population: the Tajimi study. Ophthalmology 115(363–370):e363. doi:S0161-6420(07)00379-X

    Article  Google Scholar 

  • Schwartz M, Haim M, Skarsholm D (1990) X-linked myopia: Bornholm eye disease. Linkage to DNA markers on the distal part of Xq. Clin Genet 38:281–286

    Article  PubMed  CAS  Google Scholar 

  • Shi Y, Gong B, Chen L, Zuo X, Liu X, Tam PO, Zhou X, Zhao P, Lu F, Qu J, Sun L, Zhao F, Chen H, Zhang Y, Zhang D, Lin Y, Lin H, Ma S, Cheng J, Yang J, Huang L, Zhang M, Zhang X, Pang CP, Yang Z (2013) A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population. Hum Mol Genet. doi:10.1093/hmg/ddt066

  • Shi Y, Li Y, Zhang D, Zhang H, Li Y, Lu F, Liu X, He F, Gong B, Cai L, Li R, Liao S, Ma S, Lin H, Cheng J, Zheng H, Shan Y, Chen B, Hu J, Jin X, Zhao P, Chen Y, Zhang Y, Lin Y, Li X, Fan Y, Yang H, Wang J, Yang Z (2011a) Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet 7:e1002084. doi:10.1371/journal.pgen.1002084

    Article  PubMed  CAS  Google Scholar 

  • Shi Y, Qu J, Zhang D, Zhao P, Zhang Q, Tam PO, Sun L, Zuo X, Zhou X, Xiao X, Hu J, Li Y, Cai L, Liu X, Lu F, Liao S, Chen B, He F, Gong B, Lin H, Ma S, Cheng J, Zhang J, Chen Y, Zhao F, Yang X, Chen Y, Yang C, Lam DS, Li X, Shi F, Wu Z, Lin Y, Yang J, Li S, Ren Y, Xue A, Fan Y, Li D, Pang CP, Zhang X, Yang Z (2011b) Genetic variants at 13q12.12 are associated with high myopia in the Han Chinese population. Am J Hum Genet 88:805–813. doi:10.1016/j.ajhg.2011.04.022

    Article  PubMed  CAS  Google Scholar 

  • Solouki AM, Verhoeven VJ, van Duijn CM, Verkerk AJ, Ikram MK, Hysi PG, Despriet DD, van Koolwijk LM, Ho L, Ramdas WD, Czudowska M, Kuijpers RW, Amin N, Struchalin M, Aulchenko YS, van Rij G, Riemslag FC, Young TL, Mackey DA, Spector TD, Gorgels TG, Willemse-Assink JJ, Isaacs A, Kramer R, Swagemakers SM, Bergen AA, van Oosterhout AA, Oostra BA, Rivadeneira F, Uitterlinden AG, Hofman A, de Jong PT, Hammond CJ, Vingerling JR, Klaver CC (2010) A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14. Nat Genet 42:897–901. doi:10.1038/ng.663

    Article  PubMed  CAS  Google Scholar 

  • Stambolian D, Wojciechowski R, Oexle K, Pirastu M, Li X, Raffel L, Cotch MF, Chew E, Klein B, Klein R, Wong T, Simpson CL, Klaver C, van Duijn C, Verhoeven V, Baird P, Vitart V, Paterson A, Mitchell P, Saw SM, Fossarello M, Kazmierkiewicz K, Murgia F, Portas L, Schache M, Richardson A, Xie J, Wang JJ, Rochtchina E, Group DER, Viswanathan A, Hayward C, Wright A, Polasek O, Campbell H, Rudan I, Oostra B, Uitterlinden A, Hofman A, Rivadeneira F, Amin N, Karssen L, Vingerling J, Hosseini SM, Doring A, Bettecken T, Vatavuk Z, Gieger C, Wichmann HE, Wilson J, Fleck B, Foster P, Topouzis F, McGuffin P, Sim X, Inouye M, Holliday E, Attia J, Scott R, Rotter J, Meitinger T, Bailey-Wilson J (2013) Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error. Hum Mol Genet. doi:10.1093/hmg/ddt116

  • Verhoeven VJ, Hysi PG, Wojciechowski R, Fan Q, Guggenheim JA, Hohn R, Macgregor S, Hewitt AW, Nag A, Cheng CY, Yonova-Doing E, Zhou X, Ikram MK, Buitendijk GH, McMahon G, Kemp JP, Pourcain BS, Simpson CL, Makela KM, Lehtimaki T, Kahonen M, Paterson AD, Hosseini SM, Wong HS, Xu L, Jonas JB, Parssinen O, Wedenoja J, Yip SP, Ho DW, Pang CP, Chen LJ, Burdon KP, Craig JE, Klein BE, Klein R, Haller T, Metspalu A, Khor CC, Tai ES, Aung T, Vithana E, Tay WT, Barathi VA, Chen P, Li R, Liao J, Zheng Y, Ong RT, Doring A, Evans DM, Timpson NJ, Verkerk AJ, Meitinger T, Raitakari O, Hawthorne F, Spector TD, Karssen LC, Pirastu M, Murgia F, Ang W, Mishra A, Montgomery GW, Pennell CE, Cumberland PM, Cotlarciuc I, Mitchell P, Wang JJ, Schache M, Janmahasathian S, Jr RP, Lass JH, Chew E, Iyengar SK, Gorgels TG, Rudan I, Hayward C, Wright AF, Polasek O, Vatavuk Z, Wilson JF, Fleck B, Zeller T, Mirshahi A, Muller C, Uitterlinden AG, Rivadeneira F, Vingerling JR, Hofman A, Oostra BA, Amin N, Bergen AA, Teo YY, The Diabetes C, Complications Trial/Epidemiology of Diabetes I, Complications Research G, Consortium for Refractive Error and Myopia, Wellcome Trust Case Control C, The Fuchs’ Genetics Multi-Center Study G et al (2013) Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet 45(3):314–318. doi:10.1038/ng.2554

    Article  PubMed  CAS  Google Scholar 

  • Vitale S, Sperduto RD, Ferris FL 3rd (2009) Increased prevalence of myopia in the United States between 1971–1972 and 1999–2004. Arch Ophthalmol 127:1632–1639. doi:10.1001/archophthalmol.2009.303

    Article  PubMed  Google Scholar 

  • Wang JL, Yang X, Xia K, Hu ZM, Weng L, Jin X, Jiang H, Zhang P, Shen L, Guo JF, Li N, Li YR, Lei LF, Zhou J, Du J, Zhou YF, Pan Q, Wang J, Wang J, Li RQ, Tang BS (2010) TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 133:3510–3518. doi:10.1093/brain/awq323

    Article  PubMed  Google Scholar 

  • Yang Z, Xiao X, Li S, Zhang Q (2009) Clinical and linkage study on a consanguineous Chinese family with autosomal recessive high myopia. Mol Vis 15:312–318

    PubMed  CAS  Google Scholar 

  • Young TL, Ronan SM, Alvear AB, Wildenberg SC, Oetting WS, Atwood LD, Wilkin DJ, King RA (1998a) A second locus for familial high myopia maps to chromosome 12q. Am J Hum Genet 63:1419–1424. doi:10.1086/302111

    Article  PubMed  CAS  Google Scholar 

  • Young TL, Ronan SM, Drahozal LA, Wildenberg SC, Alvear AB, Oetting WS, Atwood LD, Wilkin DJ, King RA (1998b) Evidence that a locus for familial high myopia maps to chromosome 18p. Am J Hum Genet 63:109–119. doi:10.1086/301907

    Article  PubMed  CAS  Google Scholar 

  • Zhang Q, Guo X, Xiao X, Jia X, Li S, Hejtmancik JF (2005) A new locus for autosomal dominant high myopia maps to 4q22-q27 between D4S1578 and D4S1612. Mol Vis 11:554–560. doi:v11/a65

    PubMed  CAS  Google Scholar 

  • Zhang Q, Guo X, Xiao X, Jia X, Li S, Hejtmancik JF (2006) Novel locus for X linked recessive high myopia maps to Xq23-q25 but outside MYP1. J Med Genet 43:e20. doi:10.1136/jmg.2005.037853

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors wish to thank the participants from the study who made this work possible. This study was sponsored by the National Basic Research Program of China (973 Project, No: 2011CB504604), the National Natural Science Foundation of China (81170880, and 81070751), the Zhejiang Provincial Natural Science Foundation of China (Z2100065), the Zhejiang Provincial Program for the Cultivation of High-level Innovative Health Talents, and the Program for New Century Excellent Talents in the University, National Ministry of Education Grant NCET-10–0977.

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Correspondence to Jia Qu or Xiangtian Zhou.

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This study was approved by the research review board at Wenzhou Medical College. Informed consent was obtained from each subject and each was treated in accordance with the tenets of the Declaration of Helsinki.

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Zhao, F., Wu, J., Xue, A. et al. Exome sequencing reveals CCDC111 mutation associated with high myopia. Hum Genet 132, 913–921 (2013). https://doi.org/10.1007/s00439-013-1303-6

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