Assessment of CFH and HTRA1 polymorphisms in age-related macular degeneration using classic and machine-learning approaches

2020 ◽  
Vol 41 (6) ◽  
pp. 539-547
Author(s):  
Antonieta Martínez-Velasco ◽  
Andric C. Perez-Ortiz ◽  
Bani Antonio-Aguirre ◽  
Lourdes Martínez-Villaseñor ◽  
Esmeralda Lira-Romero ◽  
...  
Keyword(s):  
Machine Learning ◽  
Macular Degeneration ◽  
Age Related Macular Degeneration ◽  
Learning Approaches ◽  
Age Related

scholarly journals GWAS-based Machine Learning for Prediction of Age-Related Macular Degeneration Risk

2019 ◽  
Author(s):  
Qi Yan ◽  
Yale Jiang ◽  
Heng Huang ◽  
Anand Swaroop ◽  
Emily Y. Chew ◽  
...  
Keyword(s):  
Machine Learning ◽  
Macular Degeneration ◽  
Genetic Information ◽  
Prediction Models ◽  
Age Related Macular Degeneration ◽  
Accurate Estimation ◽  
Learning Approaches ◽  
Age Related ◽  
Genome Wide ◽  
Normal Controls

ABSTRACTNumerous independent susceptibility variants have been identified for Age-related macular degeneration (AMD) by genome-wide association studies (GWAS). Since advanced AMD is currently incurable, an accurate prediction of a person’s AMD risk using genetic information is desirable for early diagnosis and clinical management. In this study, genotype data of 32,215 Caucasian individuals with age above 50 years from the International AMD Genomics Consortium in dbGAP were used to establish and validate prediction models for AMD risk using four different machine learning approaches: neural network, lasso regression, support vector machine, and random forest. A standard logistic regression model was also considered using a genetic risk score. To identify feature SNPs for AMD prediction models, we selected the genome-wide significant SNPs from GWAS. All methods achieved good performance for predicting normal controls versus advanced AMD cases (AUC=0.81∼0.82 in a separate test dataset) and normal controls versus any AMD (AUC=0.78∼0.79). By applying the state-of-art machine learning approaches on the large AMD GWAS data, the predictive models we established can provide an accurate estimation of an individual’s AMD risk profile across the person’s lifespan based on a comprehensive genetic information.

scholarly journals Imaging and artificial intelligence for progression of age-related macular degeneration

2021 ◽  
pp. 153537022110315
Author(s):  
Kathleen Romond ◽  
Minhaj Alam ◽  
Sasha Kravets ◽  
Luis de Sisternes ◽  
Theodore Leng ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Macular Degeneration ◽  
Vision Loss ◽  
External Validation ◽  
Geographic Atrophy ◽  
Age Related Macular Degeneration ◽  
Learning Approaches ◽  
Imaging Data ◽  
Age Related

Age-related macular degeneration (AMD) is a leading cause of severe vision loss. With our aging population, it may affect 288 million people globally by the year 2040. AMD progresses from an early and intermediate dry form to an advanced one, which manifests as choroidal neovascularization and geographic atrophy. Conversion to AMD-related exudation is known as progression to neovascular AMD, and presence of geographic atrophy is known as progression to advanced dry AMD. AMD progression predictions could enable timely monitoring, earlier detection and treatment, improving vision outcomes. Machine learning approaches, a subset of artificial intelligence applications, applied on imaging data are showing promising results in predicting progression. Extracted biomarkers, specifically from optical coherence tomography scans, are informative in predicting progression events. The purpose of this mini review is to provide an overview about current machine learning applications in artificial intelligence for predicting AMD progression, and describe the various methods, data-input types, and imaging modalities used to identify high-risk patients. With advances in computational capabilities, artificial intelligence applications are likely to transform patient care and management in AMD. External validation studies that improve generalizability to populations and devices, as well as evaluating systems in real-world clinical settings are needed to improve the clinical translations of artificial intelligence AMD applications.

scholarly journals The Relevance of Cataract as a Risk Factor for Age-Related Macular Degeneration: A Machine Learning Approach

2019 ◽  
Vol 9 (24) ◽  
pp. 5550
Author(s):  
Antonieta Martínez-Velasco ◽  
Lourdes Martínez-Villaseñor ◽  
Luis Miralles-Pechuán ◽  
Andric C. Perez-Ortiz ◽  
Juan C. Zenteno ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factor ◽  
Macular Degeneration ◽  
Significant Risk ◽  
Age Related Macular Degeneration ◽  
Supervised Machine Learning ◽  
Current Debate ◽  
Learning Approach ◽  
Age Related ◽  
Machine Learning Approach

Age-related macular degeneration (AMD) is the leading cause of visual dysfunction and irreversible blindness in developed countries and a rising cause in underdeveloped countries. There is a current debate on whether or not cataracts are significant risk factors for AMD development. In particular, research regarding this association is so far inconclusive. For this reason, we aimed to employ here a machine-learning approach to analyze the relevance and importance of cataracts as a risk factor for AMD in a large cohort of Hispanics from Mexico. We conducted a nested case control study of 119 cataract cases and 137 healthy unmatched controls focusing on clinical data from electronic medical records. Additionally, we studied two single nucleotide polymorphisms in the CFH gene previously associated with the disease in various populations as positive control for our method. We next determined the most relevant variables and found the bivariate association between cataracts and AMD. Later, we used supervised machine-learning methods to replicate these findings without bias. To improve the interpretability, we detected the five most relevant features and displayed them using a bar graph and a rule-based tree. Our findings suggest that bilateral cataracts are not a significant risk factor for AMD development among Hispanics from Mexico.

scholarly journals Machine Learning to Analyze the Prognostic Value of Current Imaging Biomarkers in Neovascular Age-Related Macular Degeneration

2018 ◽  
Vol 2 (1) ◽  
pp. 24-30 ◽  
Author(s):  
Ursula Schmidt-Erfurth ◽  
Hrvoje Bogunovic ◽  
Amir Sadeghipour ◽  
Thomas Schlegl ◽  
Georg Langs ◽  
...  
Keyword(s):  
Machine Learning ◽  
Macular Degeneration ◽  
Prognostic Value ◽  
Age Related Macular Degeneration ◽  
Imaging Biomarkers ◽  
Age Related

scholarly journals Optimized Prediction Models from Fundus Imaging and Genetics for Late Age-Related Macular Degeneration

2021 ◽  
Vol 11 (11) ◽  
pp. 1127
Author(s):  
Arun Govindaiah ◽  
Abdul Baten ◽  
R. Theodore Smith ◽  
Siva Balasubramanian ◽  
Alauddin Bhuiyan
Keyword(s):  
Machine Learning ◽  
Macular Degeneration ◽  
Retinal Image ◽  
Prediction Models ◽  
Retinal Imaging ◽  
Image Data ◽  
Age Related Macular Degeneration ◽  
Learning Models ◽  
Age Related ◽  
Machine Learning Models

Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. In this study, we compare the performance of retinal fundus images and genetic-information-based machine learning models for the prediction of late AMD. Using data from the Age-related Eye Disease Study, we built machine learning models with various combinations of genetic, socio-demographic/clinical, and retinal image data to predict late AMD using its severity and category in a single visit, in 2, 5, and 10 years. We compared their performance in sensitivity, specificity, accuracy, and unweighted kappa. The 2-year model based on retinal image and socio-demographic (S-D) parameters achieved a sensitivity of 91.34%, specificity of 84.49% while the same for genetic and S-D-parameters-based model was 79.79% and 66.84%. For the 5-year model, the retinal image and S-D-parameters-based model also outperformed the genetic and S-D parameters-based model. The two 10-year models achieved similar sensitivities of 74.24% and 75.79%, respectively, but the retinal image and S-D-parameters-based model was otherwise superior. The retinal-image-based models were not further improved by adding genetic data. Retinal imaging and S-D data can build an excellent machine learning predictor of developing late AMD over 2–5 years; the retinal imaging model appears to be the preferred prognostic tool for efficient patient management.

scholarly journals Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases

2021 ◽  
Author(s):  
Manik Kuchroo ◽  
Marcello DiStasio ◽  
Eda Calapkulu ◽  
Maryam Ige ◽  
Le Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Multiple Sclerosis ◽  
Alzheimer’S Disease ◽  
Macular Degeneration ◽  
Single Cell ◽  
Topological Analysis ◽  
Age Related Macular Degeneration ◽  
Learning Approach ◽  
Age Related ◽  
Machine Learning Approach

1One Sentence SummaryA novel topological machine learning approach applied to single-nucleus RNA sequencing from human retinas with age-related macular degeneration identifies interacting disease phase-specific glial activation states shared with Alzheimer’s disease and multiple sclerosis.2AbstractNeurodegeneration occurs in a wide range of diseases, including age-related macular degeneration (AMD), Alzheimer’s disease (AD), and multiple sclerosis (MS), each with distinct inciting events. To determine whether glial transcriptional states are shared across phases of degeneration, we sequenced 50,498 nuclei from the retinas of seven AMD patients and six healthy controls, generating the first single-cell transcriptomic atlas of AMD. We identified groupings of cells implicated in disease pathogenesis by applying a novel topologically-inspired machine learning approach called ‘diffusion condensation.’ By calculating diffusion homology features and performing persistence analysis, diffusion condensation identified activated glial states enriched in the early phases of AMD, AD, and MS as well as an AMD-specific proangiogenic astrocyte state promoting pathogenic neovascularization in advanced AMD. Finally, by mapping the expression of disease-associated genes to glial states, we identified key signaling interactions creating hypotheses for therapeutic intervention. Our topological analysis identified an integrated disease-phase specific glial landscape that is shared across neurodegenerative conditions affecting the central nervous system.

scholarly journals Automated analysis of retinal imaging using machine learning techniques for computer vision

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1573 ◽  
Author(s):  
Jeffrey De Fauw ◽  
Pearse Keane ◽  
Nenad Tomasev ◽  
Daniel Visentin ◽  
George van den Driessche ◽  
...  
Keyword(s):  
Machine Learning ◽  
Diabetic Retinopathy ◽  
Macular Degeneration ◽  
Human Error ◽  
Machine Learning Algorithms ◽  
Age Related Macular Degeneration ◽  
Machine Learning Techniques ◽  
Sound Waves ◽  
Age Related ◽  
Fundus Photographs

There are almost two million people in the United Kingdom living with sight loss, including around 360,000 people who are registered as blind or partially sighted. Sight threatening diseases, such as diabetic retinopathy and age related macular degeneration have contributed to the 40% increase in outpatient attendances in the last decade but are amenable to early detection and monitoring. With early and appropriate intervention, blindness may be prevented in many cases. Ophthalmic imaging provides a way to diagnose and objectively assess the progression of a number of pathologies including neovascular (“wet”) age-related macular degeneration (wet AMD) and diabetic retinopathy. Two methods of imaging are commonly used: digital photographs of the fundus (the ‘back’ of the eye) and Optical Coherence Tomography (OCT, a modality that uses light waves in a similar way to how ultrasound uses sound waves). Changes in population demographics and expectations and the changing pattern of chronic diseases creates a rising demand for such imaging. Meanwhile, interrogation of such images is time consuming, costly, and prone to human error. The application of novel analysis methods may provide a solution to these challenges. This research will focus on applying novel machine learning algorithms to automatic analysis of both digital fundus photographs and OCT in Moorfields Eye Hospital NHS Foundation Trust patients. Through analysis of the images used in ophthalmology, along with relevant clinical and demographic information, Google DeepMind Health will investigate the feasibility of automated grading of digital fundus photographs and OCT and provide novel quantitative measures for specific disease features and for monitoring the therapeutic success.

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