The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Quality Control Procedures for Genome‐Wide Association Studies
Open accessAbstract
Genome‐wide association studies (GWAS) are being conducted at an unprecedented rate in population‐based cohorts and have increased our understanding of the pathophysiology of complex disease. Regardless of context, the practical utility of this information will ultimately depend upon the quality of the original data. Quality control (QC) procedures for GWAS are computationally intensive, operationally challenging, and constantly evolving. Here we enumerate some of the challenges in QC of GWAS data and describe the approaches that the electronic MEdical Records and Genomics (eMERGE) network is using for quality assurance in GWAS data, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of GWAS data, including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We propose best practices and discuss areas of ongoing and future research. Curr. Protoc. Hum. Genet. 68:1.19.1‐1.19.18 © 2011 by John Wiley & Sons, Inc.
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Cites
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
Principal components analysis corrects for stratification in genome-wide association studies
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The International HapMap Project
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Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
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Self-citationGenomic Control for Association Studies
Devlin, B., & Roeder, K. (1999) · Biometrics · doi:10.1111/j.0006-341x.1999.00997.x · Cited by 3,162 · cited 1×
“Genomic control (Devlin and Roeder, 1999; Reich and Goldstein, 2001) aims to control for population stratification by first estimating an inflation factor ( λ ), then adjusting all of the test statistics downward by this factor (Fig.”
BackgroundSLCO1B1 Variants and Statin-Induced Myopathy — A Genomewide Study
(2008) · New England Journal of Medicine · doi:10.1056/nejmoa0801936 · Cited by 2,043 · cited 1×
“More recently, GWAS are being conducted in cohorts that are clinic-based (Link et al., 2008; Daly et al., 2009; Thompson et al., 2009; Barber et al., 2010).”
BackgroundGenes mirror geography within Europe
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Common variants at 30 loci contribute to polygenic dyslipidemia
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Cited by
Fritsche, L. G., Igl, W., Bailey, J. N. C., Grassmann, F., Sengupta, S., Bragg-Gresham, J. L., Burdon, K. P., Hebbring, S. J., Wen, C., Gorski, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3448 · Cited by 1,544
Self-citationMethods of integrating data to uncover genotype-phenotype interactions
Ritchie, M. D., Holzinger, E. R., Li, R., Pendergrass, S. A., & Kim, D. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3868 · Cited by 1,085
Self-citationHayes, M. G., Urbanek, M., Ehrmann, D. A., Armstrong, L. L., Lee, J. Y., Sisk, R., Karaderi, T., Barber, T. M., McCarthy, M. I., Franks, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms8502 · Cited by 478
Self-citationContrasting the Genetic Architecture of 30 Complex Traits from Summary Association Data
Shi, H., Kichaev, G., & Pasaniuc, B. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.05.013 · Cited by 387
How to Include Chromosome X in Your Genome‐Wide Association Study
König, I. R., Loley, C., Erdmann, J., & Ziegler, A. (2014) · Genetic Epidemiology · doi:10.1002/gepi.21782 · Cited by 113
Metadata
- Authors
- Turner, S., Armstrong, L. L., Bradford, Y., Carlson, C. S., Crawford, D. C., Crenshaw, A. T., de Andrade, M., Doheny, K. F., Haines, J. L., Hayes, G., Jarvik, G., Jiang, L., Kullo, I. J., Li, R., Ling, H., Manolio, T. A., Matsumoto, M., McCarty, C. A., McDavid, A. N., Mirel, D. B., Paschall, J. E., Pugh, E. W., Rasmussen, L. V., Wilke, R. A., Zuvich, R. L., & Ritchie, M. D.
- Venue
- Current Protocols in Human Genetics
- Publisher
- Wiley
- Published
- 2011-01
- Volume
- 68
- Issue
- 1
- Pages
- Unit1.19-Unit1.19
- ISSN
- 1934-8258 (ISSN-L)
- 1934-8266
- OpenAlex
- W1878939331
- Cited by
- 356
- References
- 15
- FWCI
- 9.68
- Type
- journal article
- Language
- en
- Open access
- green
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- Turner, S., Armstrong, L. L., Bradford, Y., Carlson, C. S., Crawford, D. C., Crenshaw, A. T., de Andrade, M., Doheny, K. F., Haines, J. L., Hayes, G., Jarvik, G., Jiang, L., Kullo, I. J., Li, R., Ling, H., Manolio, T. A., Matsumoto, M., McCarty, C. A., McDavid, A. N., . . . Ritchie, M. D. (2011). Quality Control Procedures for Genome‐Wide Association Studies. Current Protocols in Human Genetics. https://doi.org/10.1002/0471142905.hg0119s68
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
