scholarly journals Genome-Wide Association Studies of Refractive Error and Myopia, Lessons Learned, and Implications for the Future

2014 ◽  
Vol 55 (5) ◽  
pp. 3344 ◽  
Author(s):  
Pirro G. Hysi ◽  
Robert Wojciechowski ◽  
Jugnoo S. Rahi ◽  
Chris J. Hammond
Keyword(s):  
Refractive Error ◽  
Association Studies ◽  
Lessons Learned ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
The Future

scholarly journals Host genetics and microbiome associations from the lens of genome wide association studies

2018 ◽  
Author(s):  
Omer Weissbrod ◽  
Daphna Rothschild ◽  
Elad Barkan ◽  
Eran Segal
Keyword(s):  
Gut Microbiome ◽  
Complex Traits ◽  
Association Studies ◽  
Meta Analysis ◽  
Lessons Learned ◽  
Host Genome ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
History Of

Recent studies indicate that the gut microbiome is partially heritable, motivating the need to investigate microbiome-host genome associations via microbial genome-wide association studies (mGWAS). Existing mGWAS demonstrate that microbiome-host genotypes associations are typically weak and are spread across multiple variants, similar to associations often observed in genome-wide association studies (GWAS) of complex traits. Here we reconsider mGWAS by viewing them through the lens of GWAS, and demonstrate that there are striking similarities between the challenges and pitfalls faced by the two study designs. We further advocate the mGWAS community to adopt three key lessons learned over the history of GWAS: (a) Adopting uniform data and reporting formats to facilitate replication and meta-analysis efforts; (b) enforcing stringent statistical criteria to reduce the number of false positive findings; and (c) considering the microbiome and the host genome as distinct entities, rather than studying different taxa and single nucleotide polymorphism (SNPs) separately. Finally, we anticipate that mGWAS sample sizes will have to increase by orders of magnitude to reproducibly associate the host genome with the gut microbiome.

How to discover a metabolic pathway? An update on gene identification in aliphatic glucosinolate biosynthesis, regulation and transport

2014 ◽  
Vol 395 (5) ◽  
pp. 529-543 ◽  
Author(s):  
Lea Møller Jensen ◽  
Barbara Ann Halkier ◽  
Meike Burow
Keyword(s):  
Association Studies ◽  
Phylogenetic Analyses ◽  
Lessons Learned ◽  
Genome Wide Association ◽  
Gene Identification ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Aliphatic Glucosinolates ◽  
Biosynthesis Regulation

Abstract Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all biosynthetic genes, as well as the first sets of regulators and transporters, have been identified. An array of approaches, i.e. classical mapping, quantitative trait loci (QTL) mapping, eQTL mapping, co-expression, genome wide association studies (GWAS), mutant screens and phylogenetic analyses, has been exploited to increase the number of identified genes. Here we summarize the lessons learned from the different approaches used over the years with the aim to help designing and combining new approaches in the future.

scholarly journals Pharmacogenomic genome-wide association studies: lessons learned thus far

2009 ◽  
Vol 10 (2) ◽  
pp. 161-163 ◽  
Author(s):  
James J Crowley ◽  
Patrick F Sullivan ◽  
Howard L McLeod
Keyword(s):  
Association Studies ◽  
Lessons Learned ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Nine Loci for Ocular Axial Length Identified through Genome-wide Association Studies, Including Shared Loci with Refractive Error

2013 ◽  
Vol 93 (2) ◽  
pp. 264-277 ◽  
Author(s):  
Ching-Yu Cheng ◽  
Maria Schache ◽  
M. Kamran Ikram ◽  
Terri L. Young ◽  
Jeremy A. Guggenheim ◽  
...  
Keyword(s):  
Refractive Error ◽  
Axial Length ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals On Genome-Wide Association Studies and Their Meta-Analyses: Lessons Learned From Osteoporosis Studies

2013 ◽  
Vol 98 (7) ◽  
pp. E1278-E1282 ◽  
Author(s):  
Yong-Jun Liu ◽  
Lei Zhang ◽  
Yufang Pei ◽  
Christopher J. Papasian ◽  
Hong-Wen Deng
Keyword(s):  
Association Studies ◽  
Lessons Learned ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Meta Analyses
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