Journal article
DNA copy number variants of known glaucoma genes in relation to primary open-angle glaucoma
Investigative ophthalmology & visual science, Vol.55(12), pp.8251-8258
11/20/2014
DOI: 10.1167/iovs.14-15712
PMCID: PMC4271633
PMID: 25414181
Abstract
We examined the role of DNA copy number variants (CNVs) of known glaucoma genes in relation to primary open angle glaucoma (POAG). Our study included DNA samples from two studies (NEIGHBOR and GLAUGEN). All the samples were genotyped with the Illumina Human660W_Quad_v1 BeadChip. After removing non-blood-derived and amplified DNA samples, we applied quality control steps based on the mean Log R Ratio and the mean B allele frequency. Subsequently, data from 3057 DNA samples (1599 cases and 1458 controls) were analyzed with PennCNV software. We defined CNVs as those ≥5 kilobases (kb) in size and interrogated by ≥5 consecutive probes. We further limited our investigation to CNVs in known POAG-related genes, including CDKN2B-AS1, TMCO1, SIX1/SIX6, CAV1/CAV2, the LRP12-ZFPM2 region, GAS7, ATOH7, FNDC3B, CYP1B1, MYOC, OPTN, WDR36, SRBD1, TBK1, and GALC. Genomic duplications of CDKN2B-AS1 and TMCO1 were each found in a single case. Two cases carried duplications in the GAS7 region. Genomic deletions of SIX6 and ATOH7 were each identified in one case. One case carried a TBK1 deletion and another case carried a TBK1 duplication. No controls had duplications or deletions in these six genes. A single control had a duplication in the MYOC region. Deletions of GALC were observed in five cases and two controls. The CNV analysis of a large set of cases and controls revealed the presence of rare CNVs in known POAG susceptibility genes. Our data suggest that these rare CNVs may contribute to POAG pathogenesis and merit functional evaluation.
Details
- Title: Subtitle
- DNA copy number variants of known glaucoma genes in relation to primary open-angle glaucoma
- Creators
- Yutao Liu - Duke UniversityMelanie E Garrett - Duke UniversityBrian L Yaspan - Genentech, Inc., San Francisco, California, United StatesJessica Cooke Bailey - Case Western Reserve UniversityStephanie J Loomis - Massachusetts Eye and Ear InfirmaryMurray Brilliant - Marshfield ClinicDonald L Budenz - University of North Carolina at Chapel HillWilliam G Christen - Brigham and Women's HospitalJohn H Fingert - University of Iowa, Ophthalmology and Visual SciencesDouglas Gaasterland - Eye Doctors of Washington, Chevy Chase, Maryland, United StatesTerry Gaasterland - Scripps Genome Center, University of California at San Diego, San Diego, California, United StatesJae H Kang - Brigham and Women's HospitalRichard K Lee - Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United StatesPaul Lichter - Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United StatesSayoko E Moroi - Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United StatesAnthony Realini - Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, United StatesJulia E Richards - Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United StatesJoel S Schuman - Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United StatesWilliam K Scott - University of Miami HospitalKuldev Singh - Department of Ophthalmology, Stanford University, Palo Alto, California, United StatesArthur J Sit - Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United StatesDouglas Vollrath - Department of Ophthalmology, Stanford University, Palo Alto, California, United StatesRobert Weinreb - Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United StatesGadi Wollstein - Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United StatesDonald J Zack - Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United StatesKang Zhang - Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United StatesMargaret A Pericak-Vance - Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United StatesJonathan L Haines - Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United StatesLouis R Pasquale - Massachusetts Eye and Ear InfirmaryJaney L Wiggs - Department of Ophthalmology, Massachusetts Eye & Ear, Boston, Massachusetts, United StatesR Rand Allingham - Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United StatesAllison E Ashley-Koch - Department of Medicine, Duke University Medical Center, Durham, North Carolina, United StatesMichael A Hauser - Duke University
- Resource Type
- Journal article
- Publication Details
- Investigative ophthalmology & visual science, Vol.55(12), pp.8251-8258
- Publisher
- United States
- DOI
- 10.1167/iovs.14-15712
- PMID
- 25414181
- PMCID
- PMC4271633
- ISSN
- 0146-0404
- eISSN
- 1552-5783
- Grant note
- EY013178 / NEI NIH HHS EY18660 / NEI NIH HHS R56 EY011671 / NEI NIH HHS CA87969 / NCI NIH HHS EY011671 / NEI NIH HHS P30 EY014104 / NEI NIH HHS EY008208 / NEI NIH HHS R01 HL073389 / NHLBI NIH HHS R01 HL035464 / NHLBI NIH HHS R01 EY023512 / NEI NIH HHS HL073389 / NHLBI NIH HHS HHSN268200782096C / NHGRI NIH HHS U01 CA049449 / NCI NIH HHS T32EY021453 / NEI NIH HHS EY144428 / NEI NIH HHS R01 EY018660 / NEI NIH HHS EY09611 / NEI NIH HHS EY010886 / NEI NIH HHS R01 EY015872 / NEI NIH HHS R01EY023242 / NEI NIH HHS P30-EY005722 / NEI NIH HHS U10 EY012118 / NEI NIH HHS U01 HG004446 / NHGRI NIH HHS HG005259-01 / NHGRI NIH HHS P01 CA087969 / NCI NIH HHS R01EY022305 / NEI NIH HHS R01 EY009611 / NEI NIH HHS HG004424 / NHGRI NIH HHS EY009847 / NEI NIH HHS EY144448 / NEI NIH HHS HL35464 / NHLBI NIH HHS R01 EY009847 / NEI NIH HHS EY015473 / NEI NIH HHS U01 HG004424 / NHGRI NIH HHS CA49449 / NCI NIH HHS R01 EY009580 / NEI NIH HHS R01 EY022306 / NEI NIH HHS HG004446 / NHGRI NIH HHS R01 EY013178 / NEI NIH HHS R01 EY019126 / NEI NIH HHS HG004608 / NHGRI NIH HHS R01 EY011405 / NEI NIH HHS EY009149 / NEI NIH HHS T32 EY021453 / NEI NIH HHS R01 EY011671 / NEI NIH HHS R01 EY023242 / NEI NIH HHS EY023512 / NEI NIH HHS R03 EY015682 / NEI NIH HHS R01 EY022305 / NEI NIH HHS R01 EY015473 / NEI NIH HHS R01 EY015543 / NEI NIH HHS R01 EY008208 / NEI NIH HHS HHSN268200782096C / NHLBI NIH HHS UL1 TR000427 / NCATS NIH HHS EY13315 / NEI NIH HHS EY011008 / NEI NIH HHS EY015872 / NEI NIH HHS EY006827 / NEI NIH HHS UM1 CA167552 / NCI NIH HHS EY015682 / NEI NIH HHS U01 HG004608 / NHGRI NIH HHS EY012118 / NEI NIH HHS U01 HG004728 / NHGRI NIH HHS P30 EY005722 / NEI NIH HHS R01 EY013315 / NEI NIH HHS EY015543 / NEI NIH HHS EY09580 / NEI NIH HHS R01 CA049449 / NCI NIH HHS R01 EY010886 / NEI NIH HHS R01 EY011008 / NEI NIH HHS EY019126 / NEI NIH HHS R01 EY012118 / NEI NIH HHS HG004728 / NHGRI NIH HHS
- Language
- English
- Date published
- 11/20/2014
- Academic Unit
- Ophthalmology and Visual Sciences
- Record Identifier
- 9983979971202771
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