Clinical utility of the ABCR400 microarray: Basing a genetic service on a commercial gene chip

Archives of Ophthalmology

Volumn 127, Issue 4, 2009, Pages 549-554

  Roberts, Lisa J ^a   Ramesar, Rajkumar S ^a   Greenberg, Jacquie ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ABCA4 PROTEIN; CARRIER PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CONED DYSTROPHY; CONTROLLED STUDY; DIAGNOSTIC PROCEDURE; EYE EXAMINATION; EYE FUNDUS FLAVIMACULATUS; GENE IDENTIFICATION; GENE MUTATION; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RETINOPATHY; STARGARDT DISEASE;

ATP-BINDING CASSETTE TRANSPORTERS; DNA MUTATIONAL ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENETIC SCREENING; GENETIC SERVICES; GENOTYPE; HUMANS; MALE; MOLECULAR DIAGNOSTIC TECHNIQUES; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEDIGREE; RETINAL DEGENERATION; RISK ASSESSMENT;

EID: 65249142781     PISSN: 00039950     EISSN: 15383601     Source Type: Journal    
DOI: 10.1001/archophthalmol.2009.47     Document Type: Article

References (32)

1. Allikmets R, Singh N, Sun H, etal. A photoreceptor cell-specific ATP-bincling transporter gene(ABCR) is mutated in recessive Stargardt macular dystrophy. Nat Genet. 1997;15(3):236-246.
2. Weng J, MataNL,Azarian SM,Tzekov RT, Birch DG, Travis GH. Insights into the function of Rim protein in photoreceptors and etiology of Stargardt's disease from the phenotype in abcr knockout mice. Cell. 1999;98(1):13-23.
3. Klevering BJ, Maugeri A, Wagner A, et al. Three families displaying the combination of Stargardt's disease with cone-rod dystrophy or retinitis pigmentosa. Ophthalmology. 2004;111(3):546-553.
4. Jaakson K, Zernant J, Kulm M, etal. Genotyping microarray(gene chip) for the ABCR(ABCA4) gene. Hum Mutat. 2003;22(5):395-403.
5. Valverde D, Riveiro-Alvarez R, Aguirre-Lamban J, etal. Spectrum of the ABCA4 gene mutations implicated in severe retinopathies in Spanish patients. Invest Ophthalmol Vis Sci. 2007;48(3):985-990.
6. Hargitai J, Zernant J, Somfai GM, et al. Correlation of clinical and genetic findings in Hungarian patients with Stargardt disease. Invest Ophthalmol Vis Sci. 2005;46(12):4402-4408.
7. Grosse SD, Khoury MJ. What is the clinical utility of genetic testing? Genet Med. 2006;8(7):448-450.
8. September AV, VorsterAA, Ramesar RS, Greenberg LJ. Mutation spectrum and founder chromosomes for the ABCA4 gene in South African patients with Star- gardt disease. Invest Ophthalmol Vis Sci. 2004;45(6):1705-1711.
9. GerberS, RozetJM, van de PolTJ, etal. Complete exon-intron structure of the retina- specific ATP binding transportergene(ABCR) allows the identification of novel mutations underlying Stargardt disease. Genomics. 1998;48(1):139-142.
10. Briggs CE, Rucinski D, Rosenfeld PJ, HiroseT, Berson EL, DryjaTP. Mutations in ABCR(ABCA4) in patients with Stargardt macular degeneration or cone-rod degeneration. Invest Ophthalmol Vis Sci. 2001;42(10):2229-2236.
11. Webster AR, Heon E, Lotery AJ, et al. An analysis of allelic variation in the ABCA4 gene. Invest Ophthalmol Vis Sci. 2001;42(6):1179-1189.
12. Klevering BJ, Deutman AF, Maugeri A, Cremers FP, Hoyng CB.The spectrum of retinal phenotypes caused by mutations in the ABCA4 gene. Graefes Arch Clin Exp Ophthalmol. 2005;243(2):90-100.
13. Downs K, Zacks DN, Caruso R, et al. Molecular testing for hereditary retinal disease as part of clinical care. Arch Ophthalmol. 2007;125(2):252-258.
14. Stone EM. Genetic testing for inherited eye disease. Arch Ophthalmol. 2007;125(2):205-212.
15. Radu RA, Han Y, Bui TV, et al. Reductions in serum vitamin A arrest accumulation of toxic retinal fluorophores: a potential therapy fortreatment of lipofuscin- based retinal diseases. Invest Ophthalmol Vis Sci. 2005;46(12):4393-4401.
16. Lin HJ, Wan L, Tsai Y, etal. TheTGFB1 gene coclon 10 polymorphism contributes to the genetic predisposition to high myopia. Mol Vis. 2006;12:698-703.
17. Hayashi T, Inoko H, Nishizaki R, Ohno S, Mizuki N. Exclusion of transforming growth factor-p1 as a candidate gene for myopia in the Japanese. Jpn J Ophthalmol. 2007;51(2):96-99.
18. DNA extraction using a variation of the Puregene method(salt precipitation). http: //leedsdna.info/HUGO/2000/manual/manual.htm#-Toc491595043. Accessed July 16, 2008.
19. de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D. Efficiency and powerin genetic association studies. Nat Genet. 2005;37(11):1217-1223.
20. Yip SP, Pun SF, Leung KH, Lee SY. Rapid, simultaneous genotyping of five common Southeast Asian β-thalassemia mutations by multiplex minisequencing and denaturing HPLC. ClinChem. 2003;49(10):1656-1659.
21. Wu WM, Tsai HJ, Pang JH, Wang HS, Hong HS, Lee YS. Touchdown thermo- cycling program enables a robust single nucleotide polymorphism typing method based on allele-specific real-time polymerase chain reaction. AnalBiochem. 2005; 339(2):290-296.
22. Wang J, Chuang K, Ahluwalia M, etal. High-throughput SNP genotyping by single- tube PCR with Tm-shift primers. Biotechniques. 2005;39(6):885-893.
23. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21(2):263-265.
24. Cordell HJ, Clayton DG. A unified stepwise regression procedure forevaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am J Hum Genet. 2002;70(1):124- 141.
25. Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006;7(10):781-791.
26. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. JRStatSocB. 1995;57(1):289-300.
27. Qin ZS, Niu T, Liu JS. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet. 2002;71(5):1242-1247.
28. Nielsen DM, Ehm MG, Weir BS. Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus. Am J Hum Genet. 1998; 63(5):1531-1540.
29. International HapMap Consortium. The International HapMap Project. Nature. 2003; 426(6968):789-796.
30. Halldorsson BV, Istrail S, De La Vega FM. Optimal selection of SNP markers for disease association studies. Hum Hered. 2004;58(3-4):190-202.
31. Bax L, Yu LM, Ikeda N, Tsuruta H, Moons KG. Development and validation of MIX: comprehensive free software for meta-analysis of causal research data. BMC Med Res Methodol. 2006;6:50.
32. Saw SM, Chua WH, Wu HM, Yap E, Chia KS, Stone RA. Myopia: gene- environment interaction. Ann Acad Med Singapore. 2000;29(3):290-297.