Dataset Information

Rare variants in optic disc area gene CARD10 enriched in primary open-angle glaucoma.

ABSTRACT: Genome-wide association studies (GWAS) have identified association of common alleles with primary open-angle glaucoma (POAG) and its quantitative endophenotypes near numerous genes. This study aims to determine whether rare pathogenic variants in these disease-associated genes contribute to POAG.Participants fulfilled strict inclusion criteria of advanced POAG at a young age of diagnosis. Myocilin mutation carriers were excluded using direct sequencing. Whole exome sequencing was performed on 187 glaucoma cases and 103 local screened nonglaucoma controls then joint-called with exomes of 993 previously sequenced Australian controls. GWAS-associated genes were assessed for enrichment of rare predicted pathogenic variants in POAG. Significantly enriched genes were compared against Exome Aggregation Consortium (ExAC) public control.Eighty-six GWAS disease or trait-associated glaucoma genes were captured and sequenced. CARD10 showed enrichment after Bonferroni correction for rare variants in glaucoma cases (OR = 13.2, P = 6.94 × 10-5) with mutations identified in 4.28% of our POAG cohort compared to 0.27% in controls. CARD10 was significantly associated with optic disc parameters in previous GWAS. The whole GWAS gene set showed no enrichment in POAG overall (OR = 1.12, P = 0.51).We report here an enrichment of rare predicted pathogenic coding variants within a GWAS-associated locus in POAG (CARD10). These findings indicate that both common and rare pathogenic coding variants in CARD10 may contribute to POAG pathogenesis.

SUBMITTER: Zhou T

PROVIDER: S-EPMC5118207 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Rare variants in optic disc area gene <i>CARD10</i> enriched in primary open-angle glaucoma.

Zhou Tiger T Souzeau Emmanuelle E Sharma Shiwani S Siggs Owen M OM Goldberg Ivan I Healey Paul R PR Graham Stuart S Hewitt Alex W AW Mackey David A DA Casson Robert J RJ Landers John J Mills Richard R Ellis Jonathan J Leo Paul P Brown Matthew A MA MacGregor Stuart S Burdon Kathryn P KP Craig Jamie E JE

Molecular genetics & genomic medicine 20161003 6

<h4>Background</h4>Genome-wide association studies (GWAS) have identified association of common alleles with primary open-angle glaucoma (POAG) and its quantitative endophenotypes near numerous genes. This study aims to determine whether rare pathogenic variants in these disease-associated genes contribute to POAG.<h4>Methods</h4>Participants fulfilled strict inclusion criteria of advanced POAG at a young age of diagnosis. Myocilin mutation carriers were excluded using direct sequencing. Whole e ...[more]

PMID: 27896285

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Project description:PurposePrimary open-angle glaucoma (POAG) is one of the leading causes of irreversible blindness in the United States and worldwide. Although deep learning methods have been proposed to diagnose POAG, these methods all used a single image as input. Contrastingly, glaucoma specialists typically compare the follow-up image with the baseline image to diagnose incident glaucoma. To simulate this process, we proposed a Siamese neural network, POAGNet, to detect POAG from optic disc photographs.DesignThe POAGNet, an algorithm for glaucoma diagnosis, is developed using optic disc photographs.ParticipantsThe POAGNet was trained and evaluated on 2 data sets: (1) 37 339 optic disc photographs from 1636 Ocular Hypertension Treatment Study (OHTS) participants and (2) 3684 optic disc photographs from the Sequential fundus Images for Glaucoma (SIG) data set. Gold standard labels were obtained using reading center grades.MethodsWe proposed a Siamese network model, POAGNet, to simulate the clinical process of identifying POAG from optic disc photographs. The POAGNet consists of 2 side outputs for deep supervision and uses convolution to measure the similarity between 2 networks.Main outcome measuresThe main outcome measures are the area under the receiver operating characteristic curve, accuracy, sensitivity, and specificity.ResultsIn POAG diagnosis, extensive experiments show that POAGNet performed better than the best state-of-the-art model on the OHTS test set (area under the curve [AUC] 0.9587 versus 0.8750). It also outperformed the baseline models on the SIG test set (AUC 0.7518 versus 0.6434). To assess the transferability of POAGNet, we also validated the impact of cross-data set variability on our model. The model trained on OHTS achieved an AUC of 0.7490 on SIG, comparable to the previous model trained on the same data set. When using the combination of SIG and OHTS for training, our model achieved superior AUC to the single-data model (AUC 0.8165 versus 0.7518). These demonstrate the relative generalizability of POAGNet.ConclusionsBy simulating the clinical grading process, POAGNet demonstrated high accuracy in POAG diagnosis. These results highlight the potential of deep learning to assist and enhance clinical POAG diagnosis. The POAGNet is publicly available on https://github.com/bionlplab/poagnet.

Project description:PurposeTo investigate whether lamina cribrosa (LC) defects are associated with optic disc morphology in primary open angle glaucoma (POAG) eyes with high myopia.MethodsA total of 129 POAG patients and 55 age-matched control subjects with high myopia were evaluated. Three-dimensional scan images obtained by swept source optical coherence tomography were used to detect LC defects. Radial B-scans and infrared images obtained by spectral domain optical coherence tomography were used to measure ?-peripapillary atrophy (PPA) lengths with and without Bruch's membrane (BM) (temporal, nasal, superior, and inferior), tilt angle (vertical and horizontal), and disc diameter (transverse and longitudinal). Peripapillary intrachoroidal cavitations (PICCs), disc area, ovality index, and cyclotorsion of the optic disc were analyzed as well.ResultsLC defects were found in 70 of 129 (54.2%) POAG eyes and 1 of 55 (1.8%) control eyes (P < 0.001). Age, sex, spherical equivalent, axial length, intraocular pressure, and central corneal thickness were not significantly different among POAG eyes with LC defects, POAG eyes without LC defects, and control eyes. Temporal PPA lengths without BM in all three groups correlated significantly with vertical and horizontal tilt angles, although no PPA length with BM correlated significantly with any tilt angle. PICCs were detected more frequently in POAG eyes with LC defects than those without LC defects (P = 0.01) and control eyes (P = 0.02). POAG eyes with LC defects showed a smaller ovality index (P = 0.004), longer temporal PPA without BM (P < 0.001), and larger vertical/horizontal tilt angles (vertical, P < 0.001; horizontal, P = 0.01), and transverse diameter (P = 0.01). In multivariate analysis for the presence of LC defects, presence of POAG (P < 0.001) and vertical tilt angle (P < 0.001) were identified as significant.ConclusionsThe presence of LC defects was associated with myopic optic disc morphology in POAG eyes with high myopia.

Project description:PurposeThe influence of myopia on glaucoma progression remains unknown, possibly because of the multifactorial nature of glaucoma and difficulty in assessing a solo contribution of myopia. The purpose of this study is to investigate the association of myopia with visual field (VF) progression in glaucoma using a paired-eye design to minimize the influence of confounding systemic factors that are diverse among individuals.MethodsThis retrospective study evaluated 144 eyes of 72 subjects with open-angle glaucoma, with similar intra-ocular pressure between paired eyes, spherical equivalent (SE) ≤ -2 diopter (D), and axial length ≥ 24 mm. Paired eyes with faster and slower VF progression were grouped separately, according to the global VF progression rate assessed by automated pointwise linear regression analysis. The SE, axial length, tilt ratio and torsion angle of optic discs, Bruch's membrane (BM) opening area, and gamma zone parapapillary atrophy (PPA) width were compared between the two groups. Factors associated with faster VF progression were determined by logistic regression analysis.ResultsThe mean follow-up duration was 8.9 ± 4.4 years. The mean value of SE and axial length were -6.31 ± 1.88 D and 26.05 ± 1.12 mm, respectively. The mean global visual field progression rate was -0.32 ± 0.38 dB/y. Tilt ratio, BM opening area, and gamma zone PPA width were significantly greater in the eyes with faster VF progression than those with slower progression. In multivariate analysis, these factors were significantly associated with faster VF progression (all P < 0.05), while SE and axial length were not associated with it.ConclusionIn myopic glaucoma subjects, tilt of the optic disc and temporal shifting and enlargement of the BM opening were associated with faster rate of VF progression between paired eyes. This suggests that myopia influences VF progression in glaucomatous eyes via optic disc deformations rather than via refractive error itself.

Dataset Information

Rare variants in optic disc area gene CARD10 enriched in primary open-angle glaucoma.

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Rare variants in optic disc area gene <i>CARD10</i> enriched in primary open-angle glaucoma.

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