VEGAS2: Software for More Flexible Gene-Based Testing.
paper
Cited
Public
Unavailable
- Authors
- Mishra, Aniket; Macgregor, Stuart
- Year
- 2015
- Journal
- Twin research and human genetics : the official journal of the International Society for Twin Studies
- PMID
- 25518859
- DOI
- 10.1017/thg.2014.79
Gene-based tests such as versatile gene-based association study (VEGAS) are commonly used following per-single nucleotide polymorphism (SNP) GWAS (genome-wide association studies) analysis. Two limitations of VEGAS were that the HapMap2 reference set was used to model the correlation between SNPs and only autosomal genes were considered. HapMap2 has now been superseded by the 1,000 Genomes reference set, and whereas early GWASs frequently ignored the X chromosome, it is now commonly included. Here we have developed VEGAS2, an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. VEGAS2 allows greater flexibility when defining gene boundaries. VEGAS2 offers both a user-friendly, web-based front end and a command line Linux version. The online version of VEGAS2 can be accessed through https://vegas2.qimrberghofer.edu.au/. The command line version can be downloaded from https://vegas2.qimrberghofer.edu.au/zVEGAS2offline.tgz. The command line version is developed in Perl, R and shell scripting languages; source code is available for further development.
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| Genome-wide associations for birth weight and correlations with adult disease. | Horikoshi M et al. | — | 2016 | → |
| Genome-wide association study of pathological gambling. | Lang M et al. | — | 2016 | → |
| Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density. | Mullin BH et al. | — | 2016 | → |
| Meta-Analysis of Genome-Wide Association Studies and Network Analysis-Based Integration with Gene Expression Data Identify New Suggestive Loci and Unravel a Wnt-Centric Network Associated with Dupuytren's Disease. | Becker K et al. | — | 2016 | → |
| Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin. | Galesloot TE et al. | — | 2016 | → |
| Pathway and network-based strategies to translate genetic discoveries into effective therapies. | Greene CS et al. | — | 2016 | → |
| Preliminary evidence for association of genetic variants in pri-miR-34b/c and abnormal miR-34c expression with attention deficit and hyperactivity disorder. | Garcia-Martínez I et al. | — | 2016 | → |
| Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. | Delahaye-Duriez A et al. | — | 2016 | → |
| Telomere structure and maintenance gene variants and risk of five cancer types. | Karami S et al. | — | 2016 | → |
| The Association between Gene-Environment Interactions and Diseases Involving the Human GST Superfamily with SNP Variants. | Hollman AL et al. | — | 2016 | → |
| Genome-wide association study of schizophrenia in Ashkenazi Jews. | Goes FS et al. | — | 2015 | → |
| Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder. | Genetics of Personality Consortium et al. | — | 2015 | → |