A deep learning approach to explore the association of age-related macular degeneration polygenic risk score with retinal optical coherence tomography: A preliminary study.

PURPOSE: Age-related macular degeneration (AMD) is a complex eye disorder affecting millions worldwide. This article uses deep learning techniques to investigate the relationship between AMD, genetics and optical coherence tomography (OCT) scans. METHODS: The cohort consisted of 332 patients, of which 235 were diagnosed with AMD and 97 were controls with no signs of AMD. The genome-wide association studies summary statistics utilized to establish the polygenic risk score (PRS) in relation to AMD were derived from the GERA European study. A PRS estimation based on OCT volumes for both eyes was performed using a proprietary convolutional neural network (CNN) model supported by machine learning models. The method's performance was assessed using numerical evaluation metrics, and the Grad-CAM technique was used to evaluate the results by visualizing the features learned by the model. RESULTS: The best results were obtained with the CNN and the Extra Tree regressor (MAE = 0.55, MSE = 0.49, RMSE = 0.70, R2 = 0.34). Extending the feature vector with additional information on AMD diagnosis, age and smoking history improved the results slightly, with mainly AMD diagnosis used by the model (MAE = 0.54, MSE = 0.44, RMSE = 0.66, R2 = 0.42). Grad-CAM heatmap evaluation showed that the model decisions rely on retinal morphology factors relevant to AMD diagnosis. CONCLUSION: The developed method allows an efficient PRS estimation from OCT images. A new technique for analysing the association of OCT images with PRS of AMD, using a deep learning approach, may provide an opportunity to discover new associations between genotype-based AMD risk and retinal morphology.

Association of Genetic Risk for Age-Related Macular Degeneration with Morphological Features of the Retinal Microvascular Network.

BACKGROUND: Age-related macular degeneration (AMD) is a multifactorial disease encompassing a complex interaction between aging, environmental risk factors, and genetic susceptibility. The study aimed to determine whether there is a relationship between the polygenic risk score (PRS) in patients with AMD and the characteristics of the retinal vascular network visualized by optical coherence tomography angiography (OCTA). METHODS: 235 patients with AMD and 97 healthy controls were included. We used data from a previous AMD PRS study with the same group. The vascular features from different retina layers were compared between the control group and the patients with AMD. The association between features and PRS was then analyzed using univariate and multivariate approaches. RESULTS: Significant differences between the control group and AMD patients were found in the vessel diameter distribution (variance: p = 0.0193, skewness: p = 0.0457) and fractal dimension distribution (mean: p = 0.0024, variance: p = 0.0123). Both univariate and multivariate analyses showed no direct and significant association between the characteristics of the vascular network and AMD PRS. CONCLUSIONS: The vascular features of the retina do not constitute a biomarker of the risk of AMD. We have not identified a genotype-phenotype relationship, and the expression of AMD-related genes is perhaps not associated with the characteristics of the retinal vascular network.

Polygenic Risk Score and Rare Variant Burden Identified by Targeted Sequencing in a Group of Patients with Pigment Epithelial Detachment in Age-Related Macular Degeneration.

A subset of ophthalmic imaging examination results from 334 patients were subjected to reanalysis to identify a specific group of patients with pigment epithelial detachment (PED) in at least one eye. Overall, we found a subgroup of 47 patients manifesting PED and studied their genotypes in comparison to those of patients with age-related macular degeneration without PED and healthy controls. We established a polygenic risk score that allowed the explanation of 16.3% of the variation within the disease. The highest predictive value was achieved for a model consisting of six non-coding variants: rs760306 (BEST1), rs148662546 (BEST1), rs11569560 (C3), rs74600252 (GUCA1B), rs2240688 (PROM1), and rs185507582 (TCF4). The risk of PED occurrence was found to be the highest in the first tercile, showing a 7.89-fold higher risk compared to the third tercile for AMD without PED (95% CI: 2.87; 21.71, p < 0.001) and a 7.22-fold higher risk compared to the healthy controls (95% CI: 2.60; 20.06, p < 0.001). In addition, we focused on rare variants in targeted genes. The rare variants' burden was compared among the groups, but no statistical significance was observed in the number of rare variants, predicted functional effects, or pathogenicity classification.

Polygenic Risk Score Impact on Susceptibility to Age-Related Macular Degeneration in Polish Patients.

Age-related macular degeneration (AMD) is a common retina degenerative disease with a complex genetic and environmental background. This study aimed to determine the polygenic risk score (PRS) stratification between the AMD case and control patients. The PRS model was established on the targeted sequencing data of a cohort of 471 patients diagnosed with AMD and 167 healthy controls without symptoms of retinal degeneration. The highest predictive value to the target dataset was achieved for a 22-variant model with a p-value lower than threshold PT = 0.0123. The median PRS for cases was higher by 1.1 than for control samples (95% CI: (−1.19; −0.85)). The patients in the highest quantile had a significantly higher relative risk of developing AMD than those in the lowest reference quantile (OR = 35.13, 95% CI: (7.9; 156.1), p < 0.001). The diagnostic ability was investigated using ROC analysis with AUC = 0.76 (95% CI: (0.72; 0.80)). The polygenic susceptibility to AMD may be the starting point to expand AMD diagnostics based on rare highly penetrant variants and investigate associations with disease progression and treatment response in Polish patients in future studies.