scholarly journals The impact of genome-wide association studies on biomedical research publications

2017 ◽  
Author(s):  
Travis J. Struck ◽  
Brian K. Mannakee ◽  
Ryan N. Gutenkunst

AbstractThe past decade has seen major investment in genome-wide association studies (GWAS), with the goal of identifying and motivating research on novel genes involved in complex human disease. To assess whether this goal is being met, we quantified the effect of GWAS on the overall distribution of biomedical research publications and on the subsequent publication history of genes newly associated with complex disease. We found that the historical skew of publications toward genes involved in Mendelian disease has not changed since the advent of GWAS. Genes newly implicated by GWAS in complex disease do experience additional publications compared to control genes, and they are more likely to become exceptionally studied. But the magnitude of both effects has declined dramatically over the past decade. Our results suggest that reforms to encourage follow-up studies may be needed for GWAS to most successfully guide biomedical research toward the molecular mechanisms underlying complex human disease.Author summaryOver the past decade, thousands of genome-wide association studies (GWAS) have been performed to link genetic variation with complex human disease. A major goal of such studies is to identify novel disease genes, so they can be further studied. We tested whether this goal is being met, by studying patterns of scientific research publications on human genes. We found that publications are still concentrated on genes involved in simple Mendelian disease, even after the advent of GWAS. Compared to other genes, disease genes discovered by GWAS do experience additional publications, but that effect has declined dramatically since GWAS were first performed. Our results suggest that the ability of GWAS to stimulate research into novel disease genes is declining. To realize the full potential of GWAS to reveal the molecular mechanisms driving human disease, this decline and the reasons for it must be understood, so that it can be reversed.

2015 ◽  
Author(s):  
Inti Inal Pedroso ◽  
Michael R Barnes ◽  
Anbarasu Lourdusamy ◽  
Ammar Al-Chalabi ◽  
Gerome Breen

Genome-wide association studies (GWAS) have proven a valuable tool to explore the genetic basis of many traits. However, many GWAS lack statistical power and the commonly used single-point analysis method needs to be complemented to enhance power and interpretation. Multivariate region or gene-wide association are an alternative, allowing for identification of disease genes in a manner more robust to allelic heterogeneity. Gene-based association also facilitates systems biology analyses by generating a single p-value per gene. We have designed and implemented FORGE, a software suite which implements a range of methods for the combination of p-values for the individual genetic variants within a gene or genomic region. The software can be used with summary statistics (marker ids and p-values) and accepts as input the result file formats of commonly used genetic association software. When applied to a study of Crohn's disease susceptibility, it identified all genes found by single SNP analysis and additional genes identified by large independent meta-analysis. FORGE p-values on gene-set analyses highlighted association with the Jak-STAT and cytokine signalling pathways, both previously associated with CD. We highlight the software's main features, its future development directions and provide a comparison with alternative available software tools. FORGE can be freely accessed at https://github.com/inti/FORGE.


2009 ◽  
Vol 195 (2) ◽  
pp. 97-99 ◽  

SummaryOver the past 2 years genome-wide association studies have made major contributions to understanding the genetic architecture of many common human diseases. This editorial outlines the development of such studies in psychiatry and highlights the opportunities for advancing understanding of the biological underpinnings and nosological structure of psychiatric disorders.


2012 ◽  
Vol 91 (7) ◽  
pp. 637-641 ◽  
Author(s):  
J.R. Shaffer ◽  
E. Feingold ◽  
M.L. Marazita

The genomic era of biomedical research has given rise to the genome-wide association study (GWAS) approach, which attempts to discover novel genes affecting an outcome by testing a large number ( i.e., hundreds of thousands to millions) of genetic variants for association. This article discusses the issues surrounding the GWAS approach with emphasis on the prospects and challenges relevant to the oral health research community.


Author(s):  
Braden T Tierney ◽  
Yixuan He ◽  
George M Church ◽  
Eran Segal ◽  
Aleksandar D Kostic ◽  
...  

AbstractOver the past decade, studies of the human genome and microbiome have deepened our understanding of the connections between human genes, environments, microbes, and disease. For example, the sheer number of indicators of the microbiome and human genetic common variants associated with disease has been immense, but clinical utility has been elusive. Here, we compared the predictive capabilities of the human microbiome versus human genomic common variants across 13 common diseases. We concluded that microbiomic indicators outperform human genetics in predicting host phenotype (overall Microbiome-Association-Study [MAS] area under the curve [AUC] = 0.79 [SE = 0.03], overall Genome-Wide-Association-Study [GWAS] AUC = 0.67 [SE = 0.02]). Our results, while preliminary and focused on a subset of the totality of disease, demonstrate the relative predictive ability of the microbiome, indicating that it may outperform human genetics in discriminating human disease cases and controls. They additionally motivate the need for population-level microbiome sequencing resources, akin to the UK Biobank, to further improve and reproduce metagenomic models of disease.


Author(s):  
Thomas W Mühleisen ◽  
Sven Cichon

Genome-wide association studies (GWAS) have evolved over the past ten years into a very successful tool for investigating the genetic architecture of multifactorial human traits and disorders. One major advantage of GWAS is that they do not require any a priori knowledge about the biological mechanisms underlying the traits and disorders under study. This chapter describes the scientific and technological developments that made GWAS possible and the underlying basic concept of these studies. The chapter considers what has been learned from GWAS in psychiatric research so far, what are the limitations, and looks forward to the future of GWAS.


2018 ◽  
Vol 15 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Selcan Demir ◽  
Hafize Emine Sönmez ◽  
Seza Özen

Background: In the last decade, we have come to better understand and manage the vasculitides. The classification of vasculitides has been revised. Genome- wide association studies and linkage analyses have been undertaken in hope of better understanding the pathogenesis of vasculitides. Comprehensive genetic studies have highlighted new pathways that may guide us in more targeted therapies. Description of the monogenic forms of vasculitis, such as deficiency of adenosine deaminase type 2 (DADA2), Haploinsufficiency of A20 (HA20), have introduced a new perspective to vasculopathies, and introduced alternative treatments for these diseases. Conclusion: In this review, the important discoveries in pathogenesis and consensus treatment recommendations from the past decade will be summarized.


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