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GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies

2019 Nucleic Acids Research  
The GWAS Central resource provides a toolkit for integrative access and visualization of a uniquely extensive collection of genome-wide association study data, while ensuring safe open access to prevent  ...  Harmonization of the phenotype descriptions used across several GWAS-related resources has extended the phenotype search capabilities to enable cross-database study discovery using a range of ontologies  ...  ACKNOWLEDGEMENTS The authors thank all researchers that have deposited data with GWAS Central, and expert users that have provided feedback about the website functionality.  ... 
doi:10.1093/nar/gkz895 pmid:31612961 pmcid:PMC7145571 fatcat:o262o7q3mzdu7oi457djrezzym

GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies

Tim Beck, Robert K Hastings, Sirisha Gollapudi, Robert C Free, Anthony J Brookes
2013 European Journal of Human Genetics  
ACKNOWLEDGEMENTS We thank all GWAS data generators and submitters, several previous GWAS Central data curators, Charalambos Chrysostomou and James Eales for providing technical assistance, and Gudmundur  ...  Thorisson for help with processing the dbSNP data.  ...  INTRODUCTION The genome-wide association study (GWAS) era has improved our understanding of disease aetiology by identifying genetic variants associated with complex human traits and disease phenotypes  ... 
doi:10.1038/ejhg.2013.274 pmid:24301061 pmcid:PMC4060122 fatcat:4htpblrgw5esxdqyncppitbz2a

From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries

Binglan Li, Marylyn D. Ritchie
2021 Frontiers in Genetics  
The majority of GWAS discoveries are located in non-coding regions of the human genome and have unknown functions.  ...  the transcriptome-wide association study (TWAS).  ...  ACKNOWLEDGMENTS We thank Yoseph Barash, Milton Pividori, and William Bone from the University of Pennsylvania for scientific discussions and feedback.  ... 
doi:10.3389/fgene.2021.713230 pmid:34659337 pmcid:PMC8515949 fatcat:nobwblls4bd5xllozd4y7w652e

Using GWAS to identify novel therapeutic targets for osteoporosis

Olivia L. Sabik, Charles R. Farber
2017 Translational Research: The Journal of Laboratory and Clinical Medicine  
Genetic discovery has been shown to be effective in the unbiased identification of novel drug targets and genome-wide association studies (GWASs) have begun to provide insight into genetic basis of osteoporosis  ...  In this review, we summarize the current state of the field and discuss strategies for causal gene discovery and the evidence that the novel genes underlying GWAS loci are likely to be a new source of  ...  C.R.F is funded by grants R01-AR057759, R01-AR64790 and R01-AR068345 from the National Institute of Arthritis and Musculoskeletal and Skin Diseases.  ... 
doi:10.1016/j.trsl.2016.10.009 pmid:27837649 pmcid:PMC5357198 fatcat:cegxrsq4bbb7dhofai3gcuexpu

The Psychiatric GWAS Consortium: Big Science Comes to Psychiatry

Patrick F. Sullivan
2010 Neuron  
Funding for this project was from the US National Institutes of Health who had no role in manuscript preparation.  ...  For the PGC, raw individual-level and deidentified phenotype and genotype data from each study were uploaded to a highperformance computing cluster and processed through a robust and comprehensive quality  ...  As the individual studies used different genotyping platforms, the cleaned data were imputed against a widely used panel of data from European subjects (HapMap3) so that all studies had a common set of  ... 
doi:10.1016/j.neuron.2010.10.003 pmid:20955924 pmcid:PMC2991765 fatcat:a4t4sviahvcl5hxbkzizu27epu

Identifying loci with breeding potential across temperate and tropical adaptation via Eigen GWAS and Env GWAS

Jing Li, Guo‐Bo Chen, Awais Rasheed, Delin Li, Kai Sonder, Cristian Zavala Espinosa, Jiankang Wang, Denise E. Costich, Patrick S. Schnable, Sarah J. Hearne, Huihui Li
2019 Molecular Ecology  
Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics  ...  Combining large-scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic  ...  Conceptually similar to genome-wide association studies (GWAS), the analysis procedure of EigenGWAS is similar to the conventional regression analysis for GWAS but the phenotype is substituted by an eigenvector  ... 
doi:10.1111/mec.15169 pmid:31287919 pmcid:PMC6851670 fatcat:4rzkj4yopnek5kjnisnzhffkzm

Reviews of Science for Science Librarians: Genome-Wide Association Studies (GWAS)

Sarah H. Jeong, Seong-Tae Kim
2011 Science & technology libraries (New York, N.Y.)  
Since the completion of the Human Genome Project and the International HapMap Project, Genome-Wide Association Studies (GWAS) have been undertaken to uncover associations between genetic variants and human  ...  GWAS research is a step forward in biomedical research, and this article provides an overview of the history, study design and significant achievements in this field.  ...  Department of Energy that identified and sequenced 2 the human genome and provided the initial foundation for Genome-Wide Association Studies (GWAS) .  ... 
doi:10.1080/0194262x.2011.595315 fatcat:b6j462h7gbdjjheftl76xdnokq

After GWAS: mice to the rescue?

Joerg Ermann, Laurie H Glimcher
2012 Current Opinion in Immunology  
The genetics of human autoimmune diseases remain incompletely understood, despite significant progress from genome-wide association studies (GWAS).  ...  Despite of these complexities, mice are essential discovery tools in the post GWAS era.  ...  Acknowledgments We would like to thank Julia Charles, Tony Aliprantis, and William Ridgway for their critical reading of the manuscript and comments.  ... 
doi:10.1016/j.coi.2012.09.005 pmid:23031443 pmcid:PMC3631559 fatcat:ozzzdbzbjvco3p2bcchoykog4u

Microbial Genome-Wide Association Studies: Lessons from Human GWAS [article]

Robert Power, Julian Parkhill, Tulio de Oliveira
2016 bioRxiv   pre-print
The reduced costs of sequencing have led to the availability of whole genome sequences for a large number of microorganisms, enabling the application of microbial genome wide association studies (GWAS)  ...  In this review, we outline the methodologies of GWAS, the state of the field of microbial GWAS today, and how lessons from GWAS can direct the future of the field.  ...  He received his PhD in statistical genetics from the Institute of Psychiatry, King's College London.  ... 
doi:10.1101/093211 fatcat:ohsd5fsdmjb67ijyucb5fax2fi

A GWAS platform built on iPlant cyber-infrastructure [article]

Liya Wang, Doreen Ware, Carol Lushbough, Nirav Merchant, Lincoln Stein
2014 bioRxiv   pre-print
We demonstrated a flexible Genome-Wide Association Study (GWAS) platform built upon the iPlant Collaborative Cyber-infrastructure.  ...  The platform supports big data management, sharing, and large scale study of both genotype and phenotype data on clusters.  ...  The authors would like to thank the two anonymous reviewers for their helpful comments. L. W. would like to thank Drs. Joshua Stein and Stephen Goff for critical reading of the paper, Drs.  ... 
doi:10.1101/002881 fatcat:k74kn67mgvfevadbchashlp3ea

Ovarian Physiology and GWAS: Biobanks, Biology, and Beyond

Triin Laisk-Podar, Cecilia M. Lindgren, Maire Peters, Juha S. Tapanainen, Cornelis B. Lambalk, Andres Salumets, Reedik Mägi
2016 Trends in endocrinology and metabolism  
Ovarian function is central to female fertility, and several genome-wide association studies (GWAS) have been carried out to elucidate the genetic background of traits and disorders that reflect and affect  ...  While GWAS have been successful in reporting numerous genetic associations and highlighting involved pathways relevant to reproductive aging, for ovarian disorders, such as premature ovarian insufficiency  ...  Ovarian function is central to female fertility, and several genome-wide association studies (GWAS) have been carried out to elucidate the genetic background of traits and disorders that reflect and affect  ... 
doi:10.1016/j.tem.2016.04.011 pmid:27221566 pmcid:PMC7610559 fatcat:67efgerf4nho3kl7klllvh4scq

Translating Lung Function Genome-Wide Association Study (GWAS) Findings [chapter]

A.K. Kheirallah, S. Miller, I.P. Hall, I. Sayers
2016 Advances in Genetics  
Chronic respiratory diseases are a major cause of worldwide mortality and morbidity.  ...  Acknowledgements The authors' laboratory is funded by grants from Medical Research Council (G10000861) and Asthma UK (AUK-PG-2013-188).  ...  Genome-wide association (GWA) studies The advent of genome-wide association (GWA) studies is attributable to advances in genotyping technology (Syvanen, 2005) , the Human Genome Project (Venter et al  ... 
doi:10.1016/bs.adgen.2015.12.002 pmid:26915270 fatcat:3gp6zmfr3vbtjlsvtr7bo2lrsy

Building an open Genome Wide Association Study (GWAS) platform

Liya Wang, Doreen Ware, Nirav Merchant, Carol Lushbough
2013 2013 IEEE International Conference on Cluster Computing (CLUSTER)  
ACKNOWLEDGEMENT This work is supported by the National Science Foundation Plant Cyber-infrastructure Program (#DBI-0735191) and USDA-ARS.  ...  Here, GBS represents the analysis pipeline for the Genotyping-By Sequencing protocol [10] . This pipeline takes short reads from sequencing machine and outputs variants for GWAS.  ...  In this case, trait data are extracted from a previous study with accession names [12] .  ... 
doi:10.1109/cluster.2013.6702696 dblp:conf/cluster/WangWML13 fatcat:7lrctvrkz5erlbjar77onmetfe

GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data [article]

Dongjun Chung, Can Yang, Cong Li, Joel Gelernter, Hongyu Zhao
2014 arXiv   pre-print
Genome-wide association studies (GWAS) suggests that a complex disease is typically affected by many genetic variants with small or moderate effects.  ...  We also applied GPA to the bladder cancer GWAS data with the ENCODE DNase-seq data from 125 cell lines and showed that GPA can detect cell lines that are more biologically relevant to the phenotype of  ...  Introduction Hundreds of genome-wide association studies (GWAS) have been conducted to study the genetic bases of complex human traits/diseases.  ... 
arXiv:1401.4764v1 fatcat:4lndcecynfej7f5zw5oks52bxu

Transcriptomics insights into interpreting AMD-GWAS discoveries for biological and clinical applications

Rinki Ratnapriya
2022 Journal of Translational Genetics and Genomics  
Genome-wide association studies (GWAS) have been successful in identifying genetic risk factors for a large number of complex diseases, including age-related macular degeneration (AMD), which is a highly  ...  The purpose of this review is to provide an overview of how transcriptome studies can help in identifying the genes, pathways and therapeutic targets underlying GWAS discoveries in AMD.  ...  At the same time, human genome sequencing and development in methods to genotype genome-wide variants in humans led to the transition to GWAS for genetic studies in AMD.  ... 
doi:10.20517/jtgg.2021.54 fatcat:6scu32motzazfjxnzocu5rdsyq
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