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Abstract #59541 Published in IGR 16-3
DNA Copy Number Variants of Known Glaucoma Genes in Relation to Primary Open-Angle Glaucoma
Liu Y; Garrett ME; Yaspan BL; Cooke Bailey JN; Loomis SJ; Brilliant M; Budenz DL; Christen WG; Fingert J; Gaasterland D; Gaasterland T; Kang JH; Lee RK; Lichter PR; Moroi SE; Realini T; Richards J; Schuman JS; Scott WK; Singh K; Sit AJ; Vollrath D; WeinreInvestigative Ophthalmology and Visual Science 2014; 0:
PURPOSE: To examine the role of DNA copy number variants (CNVs) of known glaucoma genes in relation to primary open angle glaucoma (POAG). METHODS: 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 ≥ 5kb 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. RESULTS: 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 aTBK1 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. CONCLUSIONS: 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.
Cellular Biology and Anatomy, Georgia Regents University, 1460 Laney Walker Blvd, CB1101, Augusta, GA, 30912, United States yutliu@gru.edu.
Full articleClassification:
3.4.2 Gene studies (Part of: 3 Laboratory methods > 3.4 Molecular genetics)
