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Assessment of CFH and HTRA1 polymorphisms in age-related macular degeneration using classic and machine-learning
Antonieta Martínez-Velasco1, Andric C Perez-Ortiz2,3, Bani Antonio-Aguirre2
1Facultad De Ingeniería, Universidad Panamericana , Ciudad De México, Mexico.
Insights
Genetic variants in the HTRA1 gene are strongly linked to age-related macular degeneration (AMD) in Mexican Hispanics. This finding highlights HTRA1 as a significant risk factor, particularly for geographic atrophy (GA).
Area of Science:
- Genetics
- Ophthalmology
- Population Health
Background:
- Age-related macular degeneration (AMD) poses a significant risk due to genetic factors like CFH and HTRA1.
- Previous studies indicate these genes' importance in various populations.
Purpose of the Study:
- To investigate the association of specific single nucleotide polymorphisms (SNPs) in CFH and HTRA1 genes with AMD risk.
- To evaluate these associations in a Hispanic population from Mexico.
Main Methods:
- A hospital-based case-control study involving 122 AMD cases and 249 controls.
- Genotyping of CFH (rs1329428, rs203687) and HTRA1 (rs11200638) SNPs using Taqman probes.
- Analysis using logistic regression models and machine learning (ML) algorithms.
Main Results:
- The HTRA1 rs11200638 polymorphism showed a significant association with AMD in this population.
- Carriers of A/G and A/A genotypes had 2.32 and 7.81 times higher odds of AMD, respectively.
- This SNP was also significantly associated with an increased risk of geographic atrophy (GA) in a recessive inheritance model.
Conclusions:
- HTRA1 genetic variants are strongly associated with AMD in Mexican Hispanics, particularly with GA.
- Machine learning methods confirmed the findings from traditional statistical analyses, demonstrating their utility in genetic association studies.
Background:
CFH and HTRA1 are pivotal genes driving increased risk for age-related macular degeneration (AMD) among several populations. Here, we performed a hospital-based case-control study to evaluate the effects of three single nucleotide polymorphisms (SNPs) among Hispanics from Mexico.
Materials And Methods:
122 cases and 249 controls were genotyped using Taqman probes. Experienced ophthalmologists diagnosed AMD following the American Association of Ophthalmology guidelines. We studied CFH (rs1329428, rs203687) and HTRA1 (rs11200638) SNPs thoroughly by logistic regression models (assuming different modes of inheritance) and machine learning-based methods (ML).
Results:
HTRA1 rs11200638 is the most significant polymorphism associated with AMD in our studied population. In a multivariate regression model adjusted for clinically and statistically meaningful covariates, the A/G and A/A genotypes increased the odds of disease by a factor of 2.32 and 7.81, respectively (P < .05) suggesting a multiplicative effect of the polymorphic A allele. Furthermore, this observation remains statistically meaningful in the allelic, dominant, and recessive models, and ML algorithms. When stratifying by phenotype, this polymorphism was significantly associated with increased odds for geographic atrophy (GA) in a recessive mode of inheritance (12.4, p < .05).
Conclusions:
In sum, this work supports a strong association between HTRA1 genetic variants and AMD in Hispanics from Mexico, especially with GA. Moreover, ML was able to replicate the results of conventional biostatistics methods unbiasedly.
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