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Genome-wide analysis identifies common CNVs associated with primary open angle glaucoma


Copy number variation (CNV) is one of the major factors contributing to genomic diversity and diseases. Glaucoma is a major neurodegenerative disease causing irreversible vision loss across the globe. We wanted to analyze the impact of common CNVs in a genome-wide scale in patients of primary open angle glaucoma (POAG) collected from the West Bengal, India.


Genome-wide data was generated on 364 POAG cases and 365 controls on Illumina 660W-Quad arrays and CNVs were called using PennCNV. Copy number variant regions (CNVRs) were analyzed for association. A publicly available dataset of POAG cohort of 866 cases and 495 controls from Caucasian origin (GLAUGEN study) was used as a validation cohort. Representative CNVs were validated using real-time PCR.


We analyzed genome-wide CNV from 1928 samples. After association analysis we found 308 significantly associated (p<0.05) CNVRs in the Indian data. These POAG associated CNVRs were enriched in nervous system development. 113 CNVRs (37%) were significantly associated with the Caucasian data set. These contain 5 genes previously reported in eye diseases, namely, IDUA, FOXE3, NDUF7, PRPF6 and WNT3. We also found 6 associated CNVRs in previously known glaucoma loci.


We have shown that common CNVRs are significantly associated in both datasets irrespective of the population background. We have also identified candidate genes/regions which are uniquely present in POAG cases and absent in controls. Our data might provide new insights into role of CNV in pathogenesis of POAG.

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Correspondence to Arijit Mukhopadhyay.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated.

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Kaurani, L., Vishal, M., Kumar, D. et al. Genome-wide analysis identifies common CNVs associated with primary open angle glaucoma. Mol Cytogenet 7 (Suppl 1), P131 (2014).

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