title: Genome-wide association study with DNA pooling identifies variants at CNTNAP2 associated with pseudoexfoliation syndrome.
abstract: Genetic and nongenetic factors contribute to development of pseudoexfoliation (PEX) syndrome, a complex, age-related, generalized matrix process frequently associated with glaucoma. To identify specific genetic variants underlying its etiology, we performed a genome-wide association study (GWAS) using a DNA-pooling approach. Therefore, equimolar amounts of DNA samples of 80 subjects with PEX syndrome, 80 with PEX glaucoma (PEXG) and 80 controls were combined into separate pools and hybridized to 500K SNP arrays (Affymetrix). Array probe intensity data were analyzed and visualized with expressly developed software tools GPFrontend and GPGraphics in combination with GenePool software. For replication, independent German cohorts of 610 unrelated patients with PEX/PEXG and 364 controls as well as Italian cohorts of 249 patients and 190 controls were used. Of 19, 17 SNPs showing significant allele frequency difference in DNA pools were confirmed by individual genotyping. Further single genotyping at CNTNAP2 locus revealed association between PEX/PEXG for two SNPs, which was confirmed in an independent German but not the Italian cohort. Both SNPs remained significant in the combined German cohorts even after Bonferroni correction (rs2107856: P(c)=0.0108, rs2141388: P(c)=0.0072). CNTNAP2 was found to be ubiquitously expressed in all human ocular tissues, particularly in retina, and localized to cell membranes of epithelial, endothelial, smooth muscle, glial and neuronal cells. Confirming efficiency of GWAS with DNA-pooling approach by detection of the known LOXL1 locus, our study data show evidence for association of CNTNAP2 with PEX syndrome and PEXG in German patients.
authors.affiliation: Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany.
authors.forename: Mandy
authors.initials: M
authors.lastname: Krumbiegel
authors.forename: Francesca
authors.initials: F
authors.lastname: Pasutto
authors.forename: Ursula
authors.initials: U
authors.lastname: Schlötzer-Schrehardt
authors.forename: Steffen
authors.initials: S
authors.lastname: Uebe
authors.forename: Matthias
authors.initials: M
authors.lastname: Zenkel
authors.forename: Christian Y
authors.initials: CY
authors.lastname: Mardin
authors.forename: Nicole
authors.initials: N
authors.lastname: Weisschuh
authors.forename: Daniela
authors.initials: D
authors.lastname: Paoli
authors.forename: Eugen
authors.initials: E
authors.lastname: Gramer
authors.forename: Christian
authors.initials: C
authors.lastname: Becker
authors.forename: Arif B
authors.initials: AB
authors.lastname: Ekici
authors.forename: Bernhard H F
authors.initials: BH
authors.lastname: Weber
authors.forename: Peter
authors.initials: P
authors.lastname: Nürnberg
authors.forename: Friedrich E
authors.initials: FE
authors.lastname: Kruse
authors.forename: André
authors.initials: A
authors.lastname: Reis
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D016022:Case-Control Studies; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D017889:Exfoliation Syndrome / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study / Q000379:methods*; D005858:Germany; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software; D044465:White People / Q000235:genetics
chemical_list: C403049:CNTNAP2 protein, human; D008565:Membrane Proteins; D009419:Nerve Tissue Proteins; D004247:DNA
references.citation: Am J Pathol. 2008 Dec;173(6):1724-35
references.pmid: 18974306
references.citation: Genes Brain Behav. 2008 Jun;7(4):435-46
references.pmid: 18067574
references.citation: Science. 2007 Sep 7;317(5843):1397-400
references.pmid: 17690259
references.citation: Genome Res. 2009 Nov;19(11):2075-80
references.pmid: 19801603
references.citation: J Neurosci. 2008 Dec 24;28(52):14213-22
references.pmid: 19109503
references.citation: J Hum Genet. 2009 May;54(5):289-97
references.pmid: 19343041
references.citation: Exp Eye Res. 2009 Oct;89(4):479-85
references.pmid: 19442659
references.citation: Mol Vis. 2008 Jul 21;14:1338-43
references.pmid: 18648524
references.citation: Am J Hum Genet. 2008 Jan;82(1):165-73
references.pmid: 18179895
references.citation: Acta Ophthalmol Scand. 2007 May;85(3):257-61
references.pmid: 17488453
references.citation: Invest Ophthalmol Vis Sci. 2008 Apr;49(4):1459-63
references.pmid: 18385063
references.citation: J Cell Biol. 1997 Dec 15;139(6):1495-506
references.pmid: 9396755
references.citation: Invest Ophthalmol Vis Sci. 2009 Jun;50(6):2796-801
references.pmid: 19182256
references.citation: J Neurosci Res. 2001 Jul 15;65(2):139-49
references.pmid: 11438983
references.citation: Mol Psychiatry. 2008 Mar;13(3):261-6
references.pmid: 17646849
references.citation: Invest Ophthalmol Vis Sci. 2007 Apr;48(4):1447-57
references.pmid: 17389470
references.citation: Mol Vis. 2008 Jun 05;14:1037-40
references.pmid: 18552979
references.citation: Genomics. 2003 Jul;82(1):1-9
references.pmid: 12809671
references.citation: Invest Ophthalmol Vis Sci. 2002 May;43(5):1475-87
references.pmid: 11980863
references.citation: Am J Hum Genet. 2008 Jan;82(1):160-4
references.pmid: 18179894
references.citation: Am J Ophthalmol. 2006 May;141(5):921-937
references.pmid: 16678509
references.citation: Mol Vis. 2008 May 09;14:857-61
references.pmid: 18483563
references.citation: J Glaucoma. 2010 Oct-Nov;19(8):561-5
references.pmid: 20543710
references.citation: Nucleic Acids Res. 2008 Apr;36(6):e35
references.pmid: 18276640
references.citation: Genomics. 1998 Jul 1;51(1):27-34
references.pmid: 9693030
references.citation: BMC Med Genet. 2008 Feb 06;9:5
references.pmid: 18254956
references.citation: N Engl J Med. 2006 Mar 30;354(13):1370-7
references.pmid: 16571880
references.citation: Mol Vis. 2008 Sep 22;14:1727-36
references.pmid: 18806885
references.citation: Mol Vis. 2008 Feb 09;14:318-22
references.pmid: 18334947
references.citation: PLoS One. 2008;3(10):e3490
references.pmid: 18941528
references.citation: Mol Vis. 2008 Jan 29;14:146-9
references.pmid: 18334928
references.citation: Ophthalmic Genet. 1998 Dec;19(4):175-85
references.pmid: 9895242
references.citation: Mol Vis. 2008;14:2381-9
references.pmid: 19098994
references.citation: Am J Ophthalmol. 2008 Mar;145(3):582-585
references.pmid: 18201684
references.citation: Mol Vis. 2008 Mar 17;14:533-41
references.pmid: 18385788
references.citation: Mol Psychiatry. 2005 Apr;10(4):384-92
references.pmid: 15452586
references.citation: Bioinformatics. 2005 Jan 15;21(2):263-5
references.pmid: 15297300
references.citation: Hum Genomics. 2004 Nov;1(6):421-34
references.pmid: 15606997
references.citation: Am J Hum Genet. 2009 Nov;85(5):655-66
references.pmid: 19896112
references.citation: Ophthalmic Genet. 2001 Sep;22(3):171-85
references.pmid: 11559859
references.citation: Invest Ophthalmol Vis Sci. 2006 May;47(5):1982-90
references.pmid: 16639006
references.citation: Surv Ophthalmol. 2001 Jan-Feb;45(4):265-315
references.pmid: 11166342
references.citation: Am J Med Genet B Neuropsychiatr Genet. 2006 Dec 5;141B(8):844-53
references.pmid: 16894614
references.citation: Am J Hum Genet. 2007 Jan;80(1):126-39
references.pmid: 17160900
references.citation: Am J Hum Genet. 2008 Jan;82(1):150-9
references.pmid: 18179893
references.citation: Neuron. 1999 Dec;24(4):1037-47
references.pmid: 10624965
references.citation: Exp Eye Res. 2005 Jun;80(6):871-5
references.pmid: 15939044