scholarly journals Learning from Fifteen Years of Genome-Wide Association Studies in Age-Related Macular Degeneration

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2267
Author(s):  
Tobias Strunz ◽  
Christina Kiel ◽  
Bastian L. Sauerbeck ◽  
Bernhard H. F. Weber
Keyword(s):  
Macular Degeneration ◽  
Association Studies ◽  
Age Related Macular Degeneration ◽  
Gwas Data ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Age Related ◽  
Genome Wide ◽  
Follow Up Studies

Over the last 15 years, genome-wide association studies (GWAS) have greatly advanced our understanding of the genetic landscape of complex phenotypes. Nevertheless, causal interpretations of GWAS data are challenging but crucial to understand underlying mechanisms and pathologies. In this review, we explore to what extend the research community follows up on GWAS data. We have traced the scientific activities responding to the two largest GWAS conducted on age-related macular degeneration (AMD) so far. Altogether 703 articles were manually categorized according to their study type. This demonstrates that follow-up studies mainly involve “Review articles” (33%) or “Genetic association studies” (33%), while 19% of publications report on findings from experimental work. It is striking to note that only three of 16 AMD-associated loci described de novo in 2016 were examined in the four-year follow-up period after publication. A comparative analysis of five studies on gene expression regulation in AMD-associated loci revealed consistent gene candidates for 15 of these loci. Our random survey highlights the fact that functional follow-up studies on GWAS results are still in its early stages hampering a significant refinement of the vast association data and thus a more accurate insight into mechanisms and pathways.

Efficient estimation of disease odds ratios for follow-up genetic association studies

2017 ◽  
Vol 28 (7) ◽  
pp. 1927-1941
Author(s):  
Jiyuan Hu ◽  
Wei Zhang ◽  
Xinmin Li ◽  
Dongdong Pan ◽  
Qizhai Li
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Efficient Estimation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Odds Ratios ◽  
Genome Wide ◽  
Follow Up Studies

In the past decade, genome-wide association studies have identified thousands of susceptible variants associated with complex human diseases and traits. Conducting follow-up genetic association studies has become a standard approach to validate the findings of genome-wide association studies. One problem of high interest in genetic association studies is to accurately estimate the strength of the association, which is often quantified by odds ratios in case-control studies. However, estimating the association directly by follow-up studies is inefficient since this approach ignores information from the genome-wide association studies. In this article, an estimator called GFcom, which integrates information from genome-wide association studies and follow-up studies, is proposed. The estimator includes both the point estimate and corresponding confidence interval. GFcom is more efficient than competing estimators regarding MSE and the length of confidence intervals. The superiority of GFcom is particularly evident when the genome-wide association study suffers from severe selection bias. Comprehensive simulation studies and applications to three real follow-up studies demonstrate the performance of the proposed estimator. An R package, “GFcom”, implementing our method is publicly available at https://github.com/JiyuanHu/GFcom .

scholarly journals Genetic Basis of Age-related Macular Degeneration

2011 ◽  
Vol 04 (02) ◽  
pp. 119
Author(s):  
Mohammad Othman ◽  
Kari Branham ◽  
John R Heckenlively ◽  
◽  
◽  
...  
Keyword(s):  
Macular Degeneration ◽  
Complex Disease ◽  
Vision Loss ◽  
Association Studies ◽  
Developed Countries ◽  
Age Related Macular Degeneration ◽  
Genome Wide Association Studies ◽  
Factors Affecting ◽  
Age Related ◽  
Genome Wide

Age-related macular degeneration (AMD) is the main cause of vision loss and impairment in the aging population in developed countries. It is clinically and genetically a complex disease with both environmental and genetic factors affecting the outcome of the disease. Other than the wet type of AMD, there is no treatment for the other forms of AMD. It is estimated that the number of AMD patients will double in the next decade, which will have a significant financial impact on the health system and will compete for health dollars. Understanding the role of genetics in the development of AMD is paramount to help with diagnosis and future treatment. Over the past few years, we have studied the genetics of AMD and reported modest to significant association between AMD and several genes including CFH, ARMS2, TLR4 and ApoE. Our recent genome-wide association studies confirmed these AMD susceptibility loci in addition to other genes in the complement system (C2, C3, CFB and CFI). Recent studies identified new loci near TIMP3 and HDL influencing susceptibility to AMD.

Abstract 33: A Meta-analysis Of Three Genome-wide Association Studies Identifies A Novel Susceptibility Locus For Kawasaki Disease.

Circulation ◽  
2015 ◽  
Vol 131 (suppl_2) ◽  
Author(s):  
Todd A Johnson ◽  
Jer-Yuarn Wu ◽  
Dankyu Yoon ◽  
Akira Hata ◽  
Michiaki Kubo ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
Association Studies ◽  
Meta Analysis ◽  
East Asian ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Asian Populations ◽  
Genome Wide ◽  
Follow Up Studies

Background: Although genome-wide association studies (GWAS) have conclusively identified several susceptibility genes / loci for Kawasaki disease (KD), a large part of the genetic etiology of this disease have not been unraveled and, above all, its marked predilection for East Asian populations have not been explained. Objective: To identify genetic variants commonly associated with KD in the East Asian populations, we conducted a meta-analysis of three GWASes from Japan, Korea and Taiwan. Methods: In the GWAS analyses, we genotyped 6322 subjects (1236 cases and 5086 controls) using either Illumina 550K or Affymetrix SNP 6.0 platforms and then imputed untyped genotypes using Impute2 or minimac software with 1000 Genomes Project’s East Asian population (JPT, CHB and CHS) reference haplotype data. We then performed a meta-analysis using a weighted-average method with inverse-variance weights and selected representative SNPs in 49 top associated loci, which were then genotyped in 4798 independent subjects (2151 cases and 2747 controls). Finally, we combined the data for the three GWASes and follow up studies in a meta-analysis. Results: SNPs within previously identified susceptibility loci showed significant association in the meta-analysis of the GWASes (ITPKC: rs28493229, P = 3.07 x 10-9; CASP3: rs2720377, P = 2.66 x 10-9; BLK: rs2736340, P = 1.23 x 10-16; CD40: rs1883832, P = 1.76 x 10-8; HLA class2: rs189914842, P = 4.57 x 10-11). In a meta-analysis of the three GWASes and follow-up studies, we observed a genome-wide significant level of association at a SNP in a chromosomal region different from the six known loci (P = 6.49 x 10-9). Conclusion: The meta-analysis of three GWAses and follow-up studies successfully identified a new SNP significantly associated with KD. Further investigation of the region where the SNP is located toward specification of the susceptibility gene, the responsible variant, as well as its effect on gene function is warranted. Acknowledgement: T.A.J., J.Y.W. and D.Y. equally contributed to this work and J.K.L., Y.T.C., and Y.O. are co-directing this project.

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