iSyTE: Integrated systems tool for eye gene discovery

Investigative Ophthalmology and Visual Science

Volumn 53, Issue 3, 2012, Pages 1617-1627

  Lachke, Salil A ^a,b   Ho, Joshua W K ^a,c   Kryukov, Gregory V ^a,b,d   O'Connell, Daniel J ^a   Aboukhalil, Anton ^a,e   Bulyk, Martha L ^a,f   Park, Peter J ^a,c,g   Maas, Richard L ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

^c Harvard Medical School Center for Biomedical Informatics   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e Massachusetts Institute of Technology Cambridge   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONGENITAL CATARACT; CONTROLLED STUDY; EMBRYO; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; IN SITU HYBRIDIZATION; LENS; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ANIMAL; CATARACT; GENETICS; METHODOLOGY; PRENATAL DEVELOPMENT;

ANIMALS; CATARACT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; IN SITU HYBRIDIZATION; LENS, CRYSTALLINE; MICE; MICROARRAY ANALYSIS;

EID: 84860577992     PISSN: 01460404     EISSN: 15525783     Source Type: Journal    
DOI: 10.1167/iovs.11-8839     Document Type: Article

References (65)

1. Resnikoff S, Pascolini D, Etya'ale D, et al. Global data on visual impairment in the year 2002. Bull World Health Organ. 2004;82: 844-851.
2. Shiels A, Bennett TM, Hejtmancik JF. CatMap: putting cataract on the map. Mol Vis. 2010;16:2007-2015.
3. Hejtmancik JF. Congenital cataracts and their molecular genetics. Semin Cell Dev Biol. 2008;19:134-149.
4. Graw J. Mouse models of cataract. J Genet. 2009;88:469-486.
5. Rahi JS, Dezateaux C. Congenital and infantile cataract in the United Kingdom: underlying or associated factors. British Congenital Cataract Interest Group. Invest Ophthalmol Vis Sci. 2000;41: 2108-2114.
6. Rowan S, Sigger T, Lachke SA, et al. Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. Genes Dev. 2010;24:980-985.
7. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249-264.
8. Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004; 20:307-315.
9. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article310.2202/1544-6115.1027.
10. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B (Methodological). 1995;57:289-300.
11. Lachke SA, Maas RL. Building the developmental oculome: systems biology in vertebrate eye development and disease. Wiley Interdiscip Rev Syst Biol Med. 2010;2:305-323.
12. Matalova E, Fleischmannova J, Sharpe PT, Tucker AS. Tooth agenesis: from molecular genetics to molecular dentistry. J Dent Res. 2008;87:617-623.
13. Bohring A, Stamm T, Spaich C, et al. WNT10A mutations are a frequent cause of a broad spectrum of ectodermal dysplasias with sex-biased manifestation pattern in heterozygotes. Am J Hum Genet. 2009;85:97-105.
14. Xu PX, Woo I, Her H, Beier DR, Maas RL. Mouse Eya homologues of the Drosophila eyes absent gene require Pax6 for expression in lens and nasal placode. Development. 1997;124:219-231.
15. Donner AL, Lachke SA, Maas RL. Lens induction in vertebrates: variations on a conserved theme of signaling events. Semin Cell Dev Biol. 2006;17:676-685.
16. Ramachandran RD, Perumalsamy V, Hejtmancik JF. Autosomal recessive juvenile onset cataract associated with mutation in BFSP1. Hum Genet. 2007;121:475-482.
17. Jakobs PM, Hess JF, FitzGerald PG, et al. Autosomal-dominant congenital cataract associated with a deletion mutation in the human beaded filament protein gene BFSP2. Am J Hum Genet. 2000;66:1432-1436.
18. Shiels A, Bennett TM, Knopf HLS, et al. CHMP4B, a novel gene for autosomal dominant cataracts linked to chromosome 20q. Am J Hum Genet. 2007;81:596-606.
19. Litt M, Kramer P, LaMorticella DM, et al. Autosomal dominant congenital cataract associated with a missense mutation in the human alpha crystallin gene CRYAA. Hum Mol Genet. 1998;7:471-474.
20. Berry V, Francis P, Reddy MA, et al. Alpha-B crystallin gene (CRYAB) mutation causes dominant congenital posterior polar cataract in humans. Am J Hum Genet. 2001;69:1141-1145.
21. Padma T, Ayyagari R, Murty JS, et al. Autosomal dominant zonular cataract with sutural opacities localized to chromosome 17q11-12. Am J Hum Genet. 1995;57:840-845.
22. Billingsley G, Santhiya ST, Paterson AD, et al. CRYBA4, a novel human cataract gene, is also involved in microphthalmia. Am J Hum Genet. 2006;79:702-709.
23. Mackay DS, Boskovska OB, Knopf HLS, Lampi KJ, Shiels A. A nonsense mutation in CRYBB1 associated with autosomal dominant cataract linked to human chromosome 22q. Am J Hum Genet. 2002;71:1216-1221.
24. Kramer P, Yount J, Mitchell T, et al. A second gene for cerulean cataracts maps to the beta crystallin region on chromosome 22. Genomics. 1996;35:539-542.
25. Riazuddin SA, Yasmeen A, Yao W, et al. Mutations in betaB3- crystallin associated with autosomal recessive cataract in two Pakistani families. Invest Ophthalmol Vis Sci. 2005;46:2100-2106.
26. Héon E, Liu S, Billingsley G, et al. Gene localization for aculeiform cataract, on chromosome 2q33-35. Am J Hum Genet. 1998;63:921-926.
27. Sun H, Ma Z, Li Y, et al. Gamma-S crystallin gene (CRYGS) mutation causes dominant progressive cortical cataract in humans. J Med Genet. 2005;42:706-710.
28. Zhang T, Hua R, Xiao W, et al. Mutations of the EPHA2 receptor tyrosine kinase gene cause autosomal dominant congenital cataract. Hum Mutat. 2009;30:E603-E611.
29. Chen J, Ma Z, Jiao X, et al. Mutations in FYCO1 cause autosomalrecessive congenital cataracts. Am J Hum Genet. 2011;88:827-838.
30. Pras E, Raz J, Yahalom V, et al. A nonsense mutation in the glucosaminyl (N-acetyl) transferase 2 gene (GCNT2): association with autosomal recessive congenital cataracts. Invest Ophthalmol Vis Sci. 2004;45:1940-1945.
31. Mackay D, Ionides A, Kibar Z, et al. Connexin46 mutations in autosomal dominant congenital cataract. Am J Hum Genet. 1999; 64:1357-1364.
32. Shiels A, Mackay D, Ionides A, et al. A missense mutation in the human connexin50 gene (GJA8) underlies autosomal dominant "zonular pulverulent" cataract, on chromosome 1q. Am J Hum Genet. 1998;62:526-532.
33. Bu L, Jin Y, Shi Y, et al. Mutant DNA-binding domain of HSF4 is associated with autosomal dominant lamellar and Marner cataract. Nat Genet. 2002;31:276-278.
34. Pras E, Levy-Nissenbaum E, Bakhan T, et al. A missense mutation in the LIM2 gene is associated with autosomal recessive presenile cataract in an inbred Iraqi Jewish family. Am J Hum Genet. 2002; 70:1363-1367.
35. Jamieson RV, Perveen R, Kerr B, et al. Domain disruption and mutation of the bZIP transcription factor, MAF, associated with cataract, ocular anterior segment dysgenesis and coloboma. Hum Mol Genet. 2002;11:33-42.
36. Berry V, Francis P, Kaushal S, Moore A, Bhattacharya S. Missense mutations in MIP underlie autosomal dominant "polymorphic" and lamellar cataracts linked to 12q. Nat Genet. 2000;25:15-17.
37. Khan K, Rudkin A, Parry DA, et al. Homozygous mutations in PXDN cause congenital cataract, corneal opacity, and developmental glaucoma. Am J Hum Genet. 2011;89:464-473.
38. Lachke SA, Alkuraya FS, Kneeland SC, et al. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science. 2011;331:1571-1576.
39. Lachke SA, Higgins AW, Inagaki M, et al. The cell adhesion gene PVRL3 is associated with congenital ocular defects. Hum Genet. 2012;131:235-250.
40. Bateman JB, Richter L, Flodman P, et al. A new locus for autosomal dominant cataract on chromosome 19: linkage analyses and screening of candidate genes. Invest Ophthalmol Vis Sci. 2006;47:3441-3449.
41. Hattersley K, Laurie KJ, Liebelt JE, et al. A novel syndrome of paediatric cataract, dysmorphism, ectodermal features, and developmental delay in Australian Aboriginal family maps to 1p35.3-p36.32. BMC Med Genet. 2010;11:165.
42. Puk O, Löster J, Dalke C, et al. Mutation in a novel connexin-like gene (Gjf1) in the mouse affects early lens development and causes a variable small-eye phenotype. Invest Ophthalmol Vis Sci. 2008;49:1525-1532.
43. Lassen N, Bateman JB, Estey T, et al. Multiple and additive functions of ALDH3A1 and ALDH1A1: cataract phenotype and ocular oxidative damage in Aldh3a1(-/-)/Aldh1a1(-/-) knock-out mice. J Biol Chem. 2007;282:25668-25676.
44. Eiberg H, Lund AM, Warburg M, Rosenberg T. Assignment of congenital cataract Volkmann type (CCV) to chromosome 1p36. Hum Genet. 1995;96:33-38.
45. Butt T, Yao W, Kaul H, et al. Localization of autosomal recessive congenital cataracts in consanguineous Pakistani families to a new locus on chromosome 1p. Mol Vis. 2007;13:1635-1640.
46. Wang L, Lin H, Shen Y, et al. A new locus for inherited nuclear cataract mapped to the long arm of chromosome 1. Mol Vis. 2007;13:1357-1362.
47. Gao L, Qin W, Cui H, et al. A novel locus of coralliform cataract mapped to chromosome 2p24-pter. J Hum Genet. 2005;50:305-310.
48. Khaliq S, Hameed A, Ismail M, Anwar K, Mehdi SQ. A novel locus for autosomal dominant nuclear cataract mapped to chromosome 2p12 in a Pakistani family. Invest Ophthalmol Vis Sci. 2002;43: 2083-2087.
49. Abouzeid H, Meire FM, Osman I, et al. A new locus for congenital cataract, microcornea, microphthalmia, and atypical iris coloboma maps to chromosome 2. Ophthalmology. 2009;116:154-162.
50. Sabir N, Riazuddin SA, Butt T, et al. Mapping of a new locus associated with autosomal recessive congenital cataract to chromosome 3q. Mol Vis. 2010;16:2634-2638.
51. Kaul H, Riazudddin SA, Yasmeen A, et al. A new locus for autosomal recessive congenital cataract identified in a Pakistani family. Mol Vis. 2010;16:240-245.
52. Sabir N, Riazuddin SA, Kaul H, et al. Mapping of a novel locus associated with autosomal recessive congenital cataract to chromosome 8p. Mol Vis. 2010;16:2911-2915.
53. Dash DP, Silvestri G, Hughes AE. Fine mapping of the keratoconus with cataract locus on chromosome 15q and candidate gene analysis. Mol Vis. 2006;12:499-505.
54. Berry V, Ionides AC, Moore AT, et al. A locus for autosomal dominant anterior polar cataract on chromosome 17p. Hum Mol Genet. 1996;5:415-419.
55. Armitage MM, Kivlin JD, Ferrell RE. A progressive early onset cataract gene maps to human chromosome 17q24. Nat Genet. 1995;9:37-40.
56. Zhao R, Yang Y, He X, et al. An autosomal dominant cataract locus mapped to 19q13-qter in a Chinese family. Mol Vis. 2011;17:265-269.
57. Zhang S, Liu M, Dong JM, et al. Identification of a genetic locus for autosomal dominant infantile cataract on chromosome 20p12.1-p11.23 in a Chinese family. Mol Vis. 2008;14:1893-1897.
58. Craig JE, Friend KL, Gecz J, et al. A novel locus for X-linked congenital cataract on Xq24. Mol Vis. 2008;14:721-726.
59. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell. 2001;107:579-589.
60. Diehn JJ, Diehn M, Marmor MF, Brown PO. Differential gene expression in anatomical compartments of the human eye. Genome Biol. 2005;6:R74.
61. Brown JD, Dutta S, Bharti K, et al. Expression profiling during ocular development identifies 2 Nlz genes with a critical role in optic fissure closure. Proc Natl Acad Sci U S A. 2009;106:1462-1467.
62. de Boer BA, Ruijter JM, Voorbraak FPJM, Moorman AFM. More than a decade of developmental gene expression atlases: where are we now? Nucleic Acids Res. 2009;37:7349-7359.
63. Fernald GH, Capriotti E, Daneshjou R, Karczewski KJ, Altman RB. Bioinformatics challenges for personalized medicine. Bioinformatics. 2011;27:1741-1748.
64. Ernst S, Kirchner S, Krellner C, et al. Emerging local Kondo screening and spatial coherence in the heavy-fermion metal YbRh2Si2. Nature. 2011;474:362-366.
65. Ozgül RK, Siemiatkowska AM, Yucel D, et al. Exome sequencing and cis-regulatory mapping identify mutations in MAK, a gene encoding a regulator of ciliary length, as a cause of retinitis pigmentosa. Am J Hum Genet. 2011;89:253-264.