The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment
Open accessAbstract
Summary: Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants. This PheWAS implementation allows users to translate ICD-9 codes to PheWAS case and control groups, perform analyses using these and/or other phenotypes with covariate adjustments and plot the results. We demonstrate the methods by replicating a PheWAS on rs3135388 (near HLA-DRB, associated with multiple sclerosis) and performing a novel PheWAS using an individual’s maximum white blood cell count (WBC) as a continuous measure. Our results for rs3135388 replicate known associations with more significant results than the original study on the same dataset. Our PheWAS of WBC found expected results, including associations with infections, myeloproliferative diseases and associated conditions, such as anemia. These results demonstrate the performance of the improved classification scheme and the flexibility of PheWAS encapsulated in this package. Availability and implementation: This R package is freely available under the Gnu Public License (GPL-3) from http://phewascatalog.org. It is implemented in native R and is platform independent. Contact: phewas@vanderbilt.edu Supplementary information: Supplementary Data are available at Bioinformatics online.
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
A new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations
Denny, J. C., Ritchie, M. D., Basford, M. A., Pulley, J. M., Bastarache, L., Brown-Gentry, K., Wang, D., Masys, D. R., Roden, D. M., & Crawford, D. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq126 · Cited by 1,219
Self-citationDenny, J. C., Bastarache, L., Ritchie, M. D., Carroll, R. J., Zink, R., Mosley, J. D., Field, J. R., Pulley, J. M., Ramirez, A. H., Bowton, E., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2749 · Cited by 1,013
Self-citationInternational MS Genetics Consortium, De Jager, P. L., Jia, X., Wang, J., de Bakker, P. I. W., Ottoboni, L., Aggarwal, N. T., Piccio, L., Raychaudhuri, S., Tran, D., et al. (2009) · Nature Genetics · doi:10.1038/ng.401 · Cited by 800
Denny, J. C., Crawford, D. C., Ritchie, M. D., Bielinski, S. J., Basford, M. A., Bradford, Y., Chai, H. S., Bastarache, L., Zuvich, R., Peissig, P., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.008 · Cited by 246
Self-citationPendergrass, S. A., Brown-Gentry, K., Dudek, S., Frase, A., Torstenson, E. S., Goodloe, R., Ambite, J. L., Avery, C. L., Buyske, S., Bůžková, P., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003087 · Cited by 178
Pendergrass, S. A., DUDEK, S. M., Crawford, D. C., & Ritchie, M. D. (2012) · BioData Mining · doi:10.1186/1756-0381-5-5 · Cited by 49
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Vujkovic, M., Keaton, J. M., Lynch, J. A., Miller, D. R., Zhou, J., Tcheandjieu, C., Huffman, J. E., Assimes, T. L., Lorenz, K., Zhu, X., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0637-y · Cited by 741
Chen, M.-H., Raffield, L. M., Mousas, A., Sakaue, S., Huffman, J. E., Moscati, A., Trivedi, B., Jiang, T., Akbari, P., Vuckovic, D., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.045 · Cited by 661
Stroke genetics informs drug discovery and risk prediction across ancestries
Mishra, A., Malik, R., Hachiya, T., Jürgenson, T., Namba, S., Posner, D. C., Kamanu, F. K., Koido, M., Le Grand, Q., Shi, M., et al. (2022) · Nature · doi:10.1038/s41586-022-05165-3 · Cited by 600
Self-citationTrans-ethnic association study of blood pressure determinants in over 750,000 individuals
Understanding Society Scientific Group, Giri, A., International Consortium for Blood Pressure, Blood Pressure-International Consortium of Exome Chip Studies, Program, M. V., Hellwege, J. N., Keaton, J. M., Park, J., Qiu, C., Warren, H. R., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0303-9 · Cited by 459
Self-citationPrivé, F., Aschard, H., Carmi, S., Folkersen, L., Hoggart, C., O’Reilly, P. F., & Vilhjálmsson, B. J. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.008 · Cited by 375
Metadata
- Authors
- Carroll, R. J., Bastarache, L., & Denny, J. C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-04-14
- Volume
- 30
- Issue
- 16
- Pages
- 2375-2376
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2102215872
- Cited by
- 450
- References
- 8
- FWCI
- 6.14
- Type
- journal article
- Language
- en
- Open access
- green
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- Carroll, R. J., Bastarache, L., & Denny, J. C. (2014). R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu197
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