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

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Molecular Cytogenetics20147 (Suppl 1) :P131

  • Published:


  • Glaucoma
  • Copy Number Variation
  • Open Angle Glaucoma
  • Validation Cohort
  • Nervous System Development


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.

Authors’ Affiliations

Genomics & Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Delhi, India
Molecular & Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
G. N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics & Integrative Biology, Delhi, India
Mathematics Department, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India
Academy of Scientific and Innovative Research (AcSIR), Delhi, India
S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
Drishti Pradip Eye Clinic, Kolkata, India


© Kaurani et al; licensee BioMed Central Ltd. 2014

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