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Invest Ophthalmol Vis Sci. 2015 Aug;56(9):5087-93. doi: 10.1167/iovs.15-17305.

Accurate Imputation-Based Screening of Gln368Ter Myocilin Variant in Primary Open-Angle Glaucoma.

Author information

1
Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia.
2
Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia 3Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.
3
Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia 4Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia.
4
Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia.
5
Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia 5School of Medicine, University of Queensland, Herston Campus, Brisbane, Queensland, Australia.
6
Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia 6Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia.
7
Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia 7South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.

Abstract

PURPOSE:

Myocilin (MYOC) is a well-established primary open-angle glaucoma (POAG) risk gene, with rare variants known to have high penetrance. The most common clinically relevant risk variant, Gln368Ter, has an allele frequency of 0.1% to 0.3% in populations of European ancestry. Detection of rare MYOC variants has traditionally been conducted using Sanger sequencing. Here we report the use of genotyping arrays and imputation to assess whether rare variants including Gln368Ter can be reliably detected.

METHODS:

A total of 1155 cases with advanced POAG and 1992 unscreened controls genotyped on common variant arrays participated in this study. Accuracy of imputation of Gln368Ter variants was compared with direct sequencing. A genome-wide association study was performed using additive model adjusted for sex and the first six principal components.

RESULTS:

We found that although the arrays we used were designed to tag common variants, we could reliably impute the Gln368Ter variant (rs74315329). When tested in 1155 POAG cases and 1992 controls, rs74315329 was strongly associated with risk (odds ratio = 15.53, P = 1.07 × 10-9). All POAG samples underwent full sequencing of the MYOC gene, and we found a sensitivity of 100%, specificity of 99.91%, positive predictive value of 95.65%, and negative predictive value of 100% between imputation and sequencing. Gln368Ter was also accurately imputed in a further set of 1801 individuals without POAG. Among the total set of 3793 (1992 + 1801) individuals without POAG, six were predicted (probability > 95%) to carry the risk variant.

CONCLUSIONS:

We demonstrate that some clinically important rare variants can be reliably detected using arrays and imputation. These results have important implications for the detection of clinically relevant incidental findings in ongoing and future studies using arrays.

PMID:
26237198
PMCID:
PMC4525674
DOI:
10.1167/iovs.15-17305
[Indexed for MEDLINE]
Free PMC Article

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