VEGAS2: Software for More Flexible Gene-Based Testing
Open accessAbstract
Gene-based tests such as ve rsatile g ene-based a ssociation s tudy (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 HapMap2 has now been superseded by the 1,000 Genomes reference set, and whereas early GWASs frequently ignored the X chromosome, it is now commonly included.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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A genome-wide gene-based test using VEGAS2 identified 18 genes that reached the conservative gene-based threshold of P<2.23 × 10−6.
“A genome-wide gene-based test using VEGAS2 (ref. 28) identified 18 genes that reached our conservative gene-based threshold of P<2.23 × 10−6 (Supplementary Data 10)”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [28]
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- Authors
- Mishra, A., & Macgregor, S.
- Affiliations
- QIMR Berghofer Medical Research Institute (AU)
- Corresponding author
- Macgregor, Stuart
- Venue
- Twin Research and Human Genetics
- Publisher
- Cambridge University Press (CUP)
- Published
- 2014-12-18
- Volume
- 18
- Issue
- 1
- Pages
- 86-91
- ISSN
- 1832-4274 (ISSN-L)
- 1839-2628
- OpenAlex
- W1984636340
- Cited by
- 257
- References
- 19
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 13 · 2023: 18 · 2022: 17 · 2021: 35 · 2020: 36 · 2019: 24 · 2018: 39 · 2017: 33 · 2016: 25 · 2015: 2
- FWCI
- 13.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Twin Research and Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Melanoma Research Alliance
- QIMR Berghofer Medical Research Institute
- National Institutes of Health (HHSN268200782096C)
- University of Texas MD Anderson Cancer Center (P30-CA-016672)
- National Cancer Institute (R01CA133996, R01CA100264, R01CA133966, P30CA016672, P50CA093459)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- gene-based association testing, X chromosome, genome-wide association study, web application
- MeSH terms
- Computer Simulation, Female, Humans, Male, Models, Genetic, Online Systems, Sex Characteristics, Software, Twins, User-Computer Interface, Genome, Human, Twin Studies as Topic, Internet, Polymorphism, Single Nucleotide, Chromosomes, Human, X, Genome-Wide Association Study, Genetic Association Studies, HapMap Project
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