Fine mapping linkage analysis identifies a novel susceptibility locus for myopia on chromosome 2q37 adjacent to but not overlapping MYP12

Molecular Vision

Volumn 15, Issue , 2009, Pages 722-730

  Schäche, Maria ^a,b   Chen, Christine Y ^a,b   Pertile, Kelly Kathleen ^a,b   Richardson, Andrea Jane ^a,b   Dirani, Mohamed ^a,b   Mitchell, Paul ^b,c   Baird, Paul Nigel ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b VISION COOPERATIVE RESEARCH CENTRE   (Australia)

^c UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ANKYRIN; EYE PROTEIN; MYOPIA PROTEIN 12; UNCLASSIFIED DRUG;

ARTICLE; AUSTRALIA; CHROMOSOME 2Q; CONTROLLED STUDY; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; INTRON; LINKAGE ANALYSIS; MAJOR CLINICAL STUDY; MYOPIA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 2; FAMILY; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; LINKAGE (GENETICS); LOD SCORE; MYOPIA; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA;

EID: 65349111883     PISSN: None     EISSN: 10900535     Source Type: Journal    
DOI: None     Document Type: Article

References (76)

1. Wang Q, Klein BEK, Klein R, Moss SE. Refractive Status in the Beaver Dam Eye Study. Invest Ophthalmol Vis Sci 1994; 35:4344-7.
2. He M, Huang W, Zheng Y, Huang L, Ellwein LB. Refractive error and visual impairment in school children in rural southern China. Ophthalmology 2007; 114:374-82.
3. Katz J, Tielsch JM, Sommer A. Prevalence and risk factors for refractive errors in an adult inner city population. Invest Ophthalmol Vis Sci 1997; 38:334-40.
4. Raju P, Ramesh SV, Arvind H, George R, Baskaran M, Paul PG, Kumaramanickavel G, McCarty C, Vijaya L. Prevalence of refractive errors in a rural South Indian population. Invest Ophthalmol Vis Sci 2004; 45:4268-72.
5. Saw SM, Gazzard G, Koh D, Farook M, Widjaja D, Lee J, Tan DTH. Prevalence rates of refractive errors in Sumatra, Indonesia. Invest Ophthalmol Vis Sci 2002; 43:3174-80.
6. Wu SY, Nemesure B, Leske MC. Refractive errors in a black adult population: The Barbados Eye Study. Invest Ophthalmol Vis Sci 1999; 40:2179-84.
7. Curtin BJ. The Myopias: basic science and clinical management. Philadelphia: Harper and Row; 1985.
8. Mitchell P, Wang JJ. Diabetes, fasting blood glucose and age-related maculopathy: The Blue Mountains Eye Study. Aust N Z J Ophthalmol 1999; 27:197-9.
9. Mutti DO, Zadnik K, Adams AJ. Myopia. The nature versus nurture debate goes on. Invest Ophthalmol Vis Sci 1996; 37:952-7.
10. Saw SM, Tan SB, Fung D, Chia KS, Koh D, Tan DTH, Stone RA. IQ and the association with myopia in children. Invest Ophthalmol Vis Sci 2004; 45:2943-8.
11. Hammond CJ, Snieder H, Gilbert CE, Spector TD. Genes and environment in refractive error: The twin eye study. Invest Ophthalmol Vis Sci 2001; 42:1232-6.
12. Dirani M, Chamberlain M, Shekar SN, Islam AF, Garoufalis P, Chen CY, Guymer RH, Baird PN. Heritability of refractive error and ocular biometrics: the Genes in Myopia (GEM) twin study. Invest Ophthalmol Vis Sci 2006; 47:4756-61.
13. Lyhne N, Sjolie AK, Kyvik KO, Green A. The importance of genes and environment for ocular refraction and its determiners: a population based study among 20-45 year old twins. Br J Ophthalmol 2001; 85:1470-6.
14. Wojciechowski R, Congdon N, Bowie H, Munoz B, Gilbert D, West SK. Heritability of refractive error and familial aggregation of myopia in an elderly American population. Invest Ophthalmol Vis Sci 2005; 46:1588-92.
15. Chen CY, Scurrah KJ, Stankovich J, Garoufalis P, Dirani M, Pertile KK, Richardson AJ, Mitchell P, Baird PN. Heritability and shared environment estimates for myopia and associated ocular biometric traits: the Genes in Myopia (GEM) family study. Hum Genet 2007; 121:511-20.
16. Mutti DO, Mitchell GL, Moeschberger ML, Jones LA, Zadnik K. Parental myopia, near work, school achievement, and children's refractive error. Invest Ophthalmol Vis Sci 2002; 43:3633-40.
17. Nallasamy S, Paluru P, Devoto M, Wasserman NF, Zhou J, Young TL. Genetic linkage of high-grade myopia in a Hutterite population from South Dakota. Mol Vis 2007; 13:229-36.
18. Zhang Q, Guo X, Xiao X, Jia X, Li S, Hejtmancik JF. A new locus for autosomal dominant high myopia maps to 4q22-q27 between D4S1578 and D4S1612. Mol Vis 2005; 11:554-60.
19. Zhang Q, Guo X, Xiao X, Jia X, Li S, Hejtmancik JF. Novel locus for X linked recessive high myopia maps to Xq23-q25 but outside MYP1. J Med Genet 2006; 43:e20.
20. Wojciechowski R, Moy C, Ciner E, Ibay G, Reider L, Bailey-Wilson JE, Stambolian D. Genomewide scan in Ashkenazi Jewish families demonstrates evidence of linkage of ocular refraction to a QTL on chromosome 1p36. Hum Genet 2006; 119:389-99.
21. Naiglin L, Gazagne C, Dallongeville F, Thalamas C, Idder A, Rascol O, Malecaze F, Calvas P. A genome wide scan for familial high myopia suggests a novel locus on chromosome 7q36. J Med Genet 2002; 39:118-24.
22. Paluru P, Ronan SM, Heon E, Devoto M, Wildenberg SC, Scavello G, Holleschau A, Makitie O, Cole WG, King RA, Young TL. New locus for autosomal dominant high myopia maps to the long arm of chromosome 17. Invest Ophthalmol Vis Sci 2003; 44:1830-6.
23. Paluru PC, Nallasamy S, Devoto M, Rappaport EF, Young TL. Identification of a novel locus on 2q for autosomal dominant high-grade myopia. Invest Ophthalmol Vis Sci 2005; 46:2300-7.
24. Young TL, Ronan SM, Drahozal LA, Wildenberg SC, Alvear AB, Oetting WS, Atwood LD, Wilkin DJ, King RA. Evidence that a locus for familial high myopia maps to chromosome 18p. Am J Hum Genet 1998; 63:109-19.
25. Young TL, Ronan SM, Alvear AB, Wildenberg SC, Oetting WS, Atwood LD, Wilkin DJ, King RA. A second locus for familial high myopia maps to chromosome 12q. Am J Hum Genet 1998; 63:1419-24.
26. Young TL, Atwood LD, Ronan SM, Dewan AT, Alvear AB, Peterson J, Holleschau A, King RA. Further refinement of the MYP2 locus for autosomal dominant high myopia by linkage disequilibrium analysis. Ophthalmic Genet 2001; 22:69-75.
27. Nishizaki R, Ota M, Inoko H, Meguro A, Shiota T, Okada E, Mok J, Oka A, Ohno S, Mizuki N. New susceptibility locus for high myopia is linked to the uromodulin-like 1 (UMODL1) gene region on chromosome 21q22.3. Eye 2009; 23:222-9.
28. Lam CY, Tam PO, Fan DS, Fan BJ, Wang DY, Lee CW, Pang CP, Lam DS. Genome-wide Scan Maps a Novel High Myopia Locus to 5p15. Invest Ophthalmol Vis Sci 2008; 49:3768-78.
29. Hammond CJ, Andrew T, Mak YT, Spector TD. A susceptibility locus for myopia in the normal population is linked to the PAX6 gene region on chromosome 11: A genomewide scan of dizygotic twins. Am J Hum Genet 2004; 75:294-304.
30. Stambolian D, Ibay G, Reider L, Dana D, Moy C, Schlifka M, Holmes T, Ciner E, Bailey-Wilson JE. Genomewide Linkage Scan for Myopia Susceptibility Loci among Ashkenazi Jewish Families Shows Evidence of Linkage on Chromosome 22q12. Am J Hum Genet 2004; 75:448-59.
31. Ciner E, Wojciechowski R, Ibay G, Bailey-Wilson JE, Stambolian D. Genomewide scan of ocular refraction in African-American families shows significant linkage to chromosome 7p15. Genet Epidemiol 2008; 32:454-63.
32. Zhang Q, Li S, Xiao X, Guo X. Confirmation of a genetic locus for X-linked recessive high myopia outside MYP1. J Hum Genet 2007; 52:469-72.
33. Lam DSC, Tam POS, Fan DS, Baum L, Leung YF, Pang CP. Familial high myopia linkage to chromosome 18p. Ophthalmologica 2003; 217:115-8.
34. Stambolian D, Ciner EB, Reider LC, Moy C, Dana D, Owens R, Schlifka M, Holmes T, Ibay G, Bailey-Wilson JE. Genome-wide scan for myopia in the Old Order Amish. Am J Ophthalmol 2005; 140:469-76.
35. Farbrother JE, Kirov G, Owen MJ, Pong-Wong R, Haley CS, Guggenheim JA. Linkage analysis of the genetic loci for high myopia on 18p, 12q, and 17q in 51 UK families. Invest Ophthalmol Vis Sci 2004; 45:2879-85.
36. Stambolian D, Ibay G, Reider L, Dana D, Moy C, Schlifka M, Holmes TM, Ciner E, Bailey-Wilson JE. Genome-wide scan of additional Jewish families confirms linkage of a myopia susceptibility locus to chromosome 22q12. Mol Vis 2006; 12:1499-505.
37. Klein AP, Duggal P, Lee KE, Klein R, Bailey-Wilson JE, Klein BE. Confirmation of linkage to ocular refraction on chromosome 22q and identification of a novel linkage region on 1q. Arch Ophthalmol 2007; 125:80-5.
38. Nurnberg G, Jacobi FK, Broghammer M, Becker C, Blin N, Nurnberg P, Stephani U, Pusch CM. Refinement of the MYP3 locus on human chromosome 12 in a German family with Mendelian autosomal dominant high-grade myopia by SNP array mapping. Int J Mol Med 2008; 21:429-38.
39. Chen CY, Stankovich J, Scurrah KJ, Garoufalis P, Dirani M, Pertile KK, Richardson AJ, Baird PN. Linkage replication of the MYP12 locus in common myopia. Invest Ophthalmol Vis Sci 2007; 48:4433-9.
40. Garoufalis P, Chen CYC, Dirani M, Couper TA, Taylor HR, Baird PN. Methodology and recruitment of probands and their families for the Genes in Myopia (GEM) Study. Ophthalmic Epidemiol 2005; 12:383-92.
41. Richardson AJ, Narendran N, Guymer RH, Vu H, Baird PN. Blood storage at 4 degrees C-factors involved in DNA yield and quality. J Lab Clin Med 2006; 147:290-4.
42. Wong TY, Foster PJ, Hee J, Ng TP, Tielsch JM, Chew SJ, Johnson GJ, Seah SKL. Prevalence and risk factors for refractive errors in adult Chinese in Singapore. Invest Ophthalmol Vis Sci 2000; 41:2486-94.
43. Guzowski M, Wang JJ, Rochtchina E, Rose KA, Mitchell P. Five-year refractive changes in an older population - The Blue Mountains Eye Study. Ophthalmology 2003; 110:1364-70.
44. Mutti DO, Zadnik K. Age-related decreases in the prevalence of myopia: Longitudinal change or cohort effect? Invest Ophthalmol Vis Sci 2000; 41:2103-7.
45. Wensor M, McCarty CA, Taylor HR. Prevalence and risk factors of myopia in Victoria, Australia. Arch Ophthalmol 1999; 117:658-63.
46. Rose K, Smith W, Morgan I, Mitchell P. The increasing prevalence of myopia: implications for Australia. Clin Experiment Ophthalmol 2001; 29:116-20.
47. Junghans B, Kiely PM, Crewther DP, Crewther SG. Referral rates for a functional vision screening among a large cosmopolitan sample of Australian children. Ophthalmic Physiol Opt 2002; 22:10-25.
48. Attebo K, Ivers RQ, Mitchell P. Refractive errors in an older population - The blue mountains eye study. Ophthalmology 1999; 106:1066-72.
49. Taylor HR, Livingston PM, Stanislavsky YL, McCarty CA. Visual impairment in Australia: Distance visual acuity, near vision, and visual field findings of the Melbourne Visual Impairment Project. Am J Ophthalmol 1997; 123:328-37.
50. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K. A high-resolution recombination map of the human genome. Nat Genet 2002; 31:241-7.
51. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002; 30:97-101.
52. Thiele H, Nurnberg P. HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics 2005; 21:1730-2.
53. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. Ensembl 2008. Nucleic Acids Res 2008; 36:D707-14.
54. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002; 12:996-1006.
55. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876-82.
56. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Sun W, Wang H, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449:851-61.
57. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81:559-75.
58. Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet 2003; 361:865-72.
59. Lam DSC, Lee WS, Leung YF, Tam POS, Fan DSP, Fan BJ, Pang CP. TGF beta-induced factor: A candidate gene for high myopia. Invest Ophthalmol Vis Sci 2003; 44:1012-5.
60. Tsai YY, Chiang CC, Lin HJ, Lin JM, Wan L, Tsai FJA. PAX6 gene polymorphism is associated with genetic predisposition to extreme myopia. Eye 2008; 22:576-81.
61. Inamori Y, Ota M, Inoko H, Okada E, Nishizaki R, Shiota T, Mok J, Oka A, Ohno S, Mizuki N. The COL1A1 gene and high myopia susceptibility in Japanese. Hum Genet 2007; 122:151-7.
62. Han W, Yap MKH, Wang J, Yip SP. Family-based association analysis of hepatocyte growth factor (HGF) gene polymorphisms in high myopia. Invest Ophthalmol Vis Sci 2006; 47:2291-9.
63. Mutti DO, Cooper ME, O'Brien S, Jones LA, Mariazita ML, Murray JC, Zadnik K. Candidate gene and locus analysis of myopia. Mol Vis 2007; 13:1012-9.
64. Pertile KK, Schache M, Islam FM, Chen CY, Dirani M, Mitchell P, Baird PN. Assessment of TGIF as a candidate gene for myopia. Invest Ophthalmol Vis Sci 2008; 49:49-54.
65. Hasumi Y, Inoko H, Mano S, Ota M, Okada E, Kulski JK, Nishizaki R, Mok J, Oka A, Kumagai N, Nishida T, Ohno S, Mizuki N. Analysis of single nucleotide polymorphisms at 13 loci within the transforming growth factor-induced factor gene shows no association with high myopia in Japanese subjects. Immunogenetics 2006; 58:947-53.
66. Li J, Zhang QJ, Xiao XS, Li JZ, Zhang FS, Li SQ, Li W, Li T, Jia XY, Guo L, Guo XM. The SNPs analysis of encoding sequence of interacting factor gene in Chinese population. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2003; 20:454-6.
67. Liang CL, Hung KS, Tsai YY, Chang W, Wang HS, Juo SH. Systematic assessment if the tagged polymorphisms of the COL1A1 gene for high myopia. J Hum Genet 2007; 52:374-7.
68. Simpson CL, Hysi P, Bhattacharya SS, Hammond CJ, Webster A, Peckham CS, Sham PC, Rahi JS. The Roles of PAX6 and SOX2 in Myopia: lessons from the 1958 British Birth Cohort. Invest Ophthalmol Vis Sci 2007; 48:4421-5.
69. Hewitt AW, Kearns LS, Jamieson RV, Williamson KA, van Heyningen V, Mackey DA. PAX6 mutations may be associated with high myopia. Ophthalmic Genet 2007; 28:179-82.
70. Scavello GS, Paluru PC, Ganter WR, Young TL. Sequence variants in the transforming growth beta-induced factor (TGIF) gene are not associated with high myopia. Invest Ophthalmol Vis Sci 2004; 45:2091-7.
71. Scavello GS Jr, Paluru PC, Zhou J, White PS, Rappaport EF, Young TL. Genomic structure and organization of the high grade Myopia-2 locus (MYP2) critical region: mutation screening of 9 positional candidate genes. Mol Vis 2005; 11:97-110.
72. Zhou J, Young TL. Evaluation of Lipin 2 as a candidate gene for autosomal dominant 1 high-grade myopia. Gene 2005; 352:10-9.
73. Paluru PC, Scavello GS, Ganter WR, Young TL. Exclusion of lumican and fibromodulin as candidate genes in MYP3 linked high grade myopia. Mol Vis 2004; 10:917-22.
74. Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn JN, Daly MJ, Hughes TE, Groop L, Altshuler D, Almgren P, Florez JC, Meyer J, Ardlie K, Bengtsson Bostrom K, Isomaa B, Lettre G, Lindblad U, Lyon HN, Melander O, Newton-Cheh C, Nilsson P, Orho-Melander M, Rastam L, Speliotes EK, Taskinen MR, Tuomi T, Guiducci C, Berglund A, Carlson J, Gianniny L, Hackett R, Hall L, Holmkvist J, Laurila E, Sjogren M, Sterner M, Surti A, Svensson M, Tewhey R, Blumenstiel B, Parkin M, Defelice M, Barry R, Brodeur W, Camarata J, Chia N, Fava M, Gibbons J, Handsaker B, Healy C, Nguyen K, Gates C, Sougnez C, Gage D, Nizzari M, Gabriel SB, Chirn GW, Ma Q, Parikh H, Richardson D, Ricke D, Purcell S. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 2007; 316:1331-6.
75. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover RN, Thomas G, Chanock SJ. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007; 39:870-4.
76. Kottgen A, Kao WH, Hwang SJ, Boerwinkle E, Yang Q, Levy D, Benjamin EJ, Larson MG, Astor BC, Coresh J, Fox CS. Genome-wide association study for renal traits in the Framingham Heart and Atherosclerosis Risk in Communities Studies. BMC Med Genet 2008; 9:49.