Cited by 1,836Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestock

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GenABEL: an R library for genome-wide association analysis

Aulchenko, Yurii S., Ripke, Stephan, Isaacs, Aaron, van Duijn, Cornelia M.·2007·Bioinformatics

DOI 10.1093/bioinformatics/btm108

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Abstract

Here we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis. We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers. Availability: http://cran.r-project.org Contact: i.aoultchenko@erasmusmc.nl

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Self-citation
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Method
Bioinformatics for agriculture in the Next-Generation sequencing era
Esposito, A., Colantuono, C., Ruggieri, V., & Chiusano, M. L. (2016) · Chemical and Biological Technologies in Agriculture · doi:10.1186/s40538-016-0054-8 · Cited by 58
Genetic potential for disease resistance in critically endangered amphibians decimated by chytridiomycosis
Kosch, T. A., Silva, C. N. S., Brannelly, L. A., Roberts, A. A., Lau, Q., Marantelli, G., Berger, L., & Skerratt, L. F. (2018) · Animal Conservation · doi:10.1111/acv.12459 · Cited by 54
Genome Diversity and Signatures of Selection for Production and Performance Traits in Dromedary Camels
Bahbahani, H. M., Musa, H. H., Wragg, D., Shuiep, E. S., Almathen, F. S., & Hanotte, O. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00893 · Cited by 55
ATHENA: the analysis tool for heritable and environmental network associations
Holzinger, E. R., Dudek, S. M., Frase, A. T., Pendergrass, S. A., & Ritchie, M. D. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt572 · Cited by 54
Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
Höglund, J., Rafati, N., Rask‐Andersen, M., Enroth, S., Karlsson, T., Ek, W. E., & Johansson, Å. (2019) · Scientific Reports · doi:10.1038/s41598-019-53111-7 · Cited by 55
Genomic selection using a subset of SNPs identified by genome-wide association analysis for disease resistance traits in aquaculture species
Luo, Z., Yu, Y., Xiang, J., & Li, F. (2021) · Aquaculture · doi:10.1016/j.aquaculture.2021.736620 · Cited by 54
Associations between Single Nucleotide Polymorphisms in Iron-Related Genes and Iron Status in Multiethnic Populations
McLaren, C. E., McLachlan, S., Garner, C. P., Vulpe, C. D., Gordeuk, V. R., Eckfeldt, J. H., Adams, P. C., Acton, R. T., Murray, J. A., Leiendecker‐Foster, C., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038339 · Cited by 56
“Quality control tests were completed using the GenABEL library [24] of the R statistical package (http://www.”
Method
Genome-Wide Association Analyses for Fatty Acid Composition in Porcine Muscle and Abdominal Fat Tissues
Yang, B. J., Zhang, W., Zhang, Z., Yin, F., Xie, X., Ai, H., Ma, J., Xiao, S., Huang, L., & Ren, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065554 · Cited by 57
“The associations between SNPs and phenotypic values were evaluated using a mixed model based score test [35].”
Method
A Mutation in the FAM83G Gene in Dogs with Hereditary Footpad Hyperkeratosis (HFH)
Drögemüller, M., Jagannathan, V., Becker, D., Drögemüller, C., Schelling, C., Plassais, J., Kaerle, C., de Citres, C. D., Thomas, A., Müller, E. J., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004370 · Cited by 54
Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly
Wragg, D., Marti-Marimon, M., Basso, B., Bidanel, J. P., Labarthe, E., Bouchez, O., Conte, Y. L., & Alain Vignal, A. (2016) · Scientific Reports · doi:10.1038/srep27168 · Cited by 54
A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens
Guo, Y., Gu, X., Sheng, Z., Wang, Y., Luo, C., Liu, R., Qu, H., Shu, D., Wen, J., Crooijmans, R. P. M. A., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006071 · Cited by 58
Norepinephrine Transporter Gene Variants and Remission From Depression With Venlafaxine Treatment in Older Adults
Marshe, V. S., Maciukiewicz, M., Rej, S., Tiwari, A. K., Sibille, E. L., Blumberger, D. M., Karp, J. F., Lenze, E. J., Reynolds, C. F., Kennedy, J. L., et al. (2017) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2016.16050617 · Cited by 54
Adjusted Sequence Kernel Association Test for Rare Variants Controlling for Cryptic and Family Relatedness
Oualkacha, K., Dastani, Z., Li, R., Cingolani, P. E., Spector, T. D., Hammond, C. J., Richards, J. B., Ciampi, A., & Greenwood, C. M. T. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21725 · Cited by 58
“Estimated kinship matrices have been used in several LMMs [Aulchenko et al., 2007a; Hayes et al., 2009; Kang et al., 2010, 2008; Yu et al., 2006].”
MethodInfluential
Quantitative High-Throughput Screening for Chemical Toxicity in a Population-Based In Vitro Model
Lock, E. F., Abdo, N. M., Huang, R., Xia, M., Kosyk, O., O'Shea, S. H., Zhou, Y., Sedykh, A., Tropsha, A., Austin, C. P., et al. (2012) · Toxicological Sciences · doi:10.1093/toxsci/kfs023 · Cited by 53
“To measure genotype-toxicity relationships, genome-wide association studies (GWAS) were performed in R using the GenABEL package (Aulchenko et al., 2007).”
Method
Pharmacogenetic Discovery in CALGB (Alliance) 90401 and Mechanistic Validation of a VAC14 Polymorphism that Increases Risk of Docetaxel-Induced Neuropathy
Hertz, D. L., Owzar, K., Lessans, S., Wing, C., Jiang, C., Kelly, W. K., Patel, J. N., Halabi, S., Furukawa, Y., Wheeler, H. E., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2823 · Cited by 53
Genome-wide regression models considering general and specific combining ability predict hybrid performance in oilseed rape with similar accuracy regardless of trait architecture
Werner, C. R., Qian, L., Voss‐Fels, K. P., Abbadi, A., Leckband, G., Frisch, M., & Snowdon, R. J. (2017) · Theoretical and Applied Genetics · doi:10.1007/s00122-017-3002-5 · Cited by 53
“Analyses were performed in “GenABEL” (Aulchenko et al.”
Method
Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
Maroilley, T., Lemonnier, G., Lecardonnel, J., Esquerré, D., Ramayo‐Caldas, Y., Mercat, M.-J., Rogel-Gaillard, C., & Estellé, J. (2017) · BMC Genomics · doi:10.1186/s12864-017-4354-6 · Cited by 54
Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population
Aykanat, T., Johnston, S. E., Orell, P., Niemelä, E., Erkinaro, J., & Primmer, C. R. (2015) · Molecular Ecology · doi:10.1111/mec.13383 · Cited by 50
“8.0 (Aulchenko et al. 2007) implemented in R v 3.1.0 (R Core Development Team 2012).”
Influential
Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle
Smith, J. L., Wilson, M. L., Nilson, S. M., Rowan, T. N., Oldeschulte, D. L., Schnabel, R. D., Decker, J. E., & Seabury, C. M. (2019) · BMC Genomics · doi:10.1186/s12864-019-6231-y · Cited by 53
A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations
Li, L., Xiao, S., Tu, J. ‐., Zhang, Z., Zheng, H., Huang, L., Huang, Z., Yan, M., Liu, X., & Guo, Y. (2021) · Animal Genetics · doi:10.1111/age.13112 · Cited by 52
A combined genome-wide association and molecular study of age-related hearing loss in H. sapiens
Liu, W., Johansson, Å., Rask‐Andersen, H., & Rask‐Andersen, M. (2021) · BMC Medicine · doi:10.1186/s12916-021-02169-0 · Cited by 54
“Mean thresholds were rank transformed using the “rntransform” function, which is included in the GenABEL package [158], in R [159] while adjusting for age and age-squared.”
Method
Recent genomic heritage in Scotland
Amador, C., Huffman, J. E., Trochet, H., Campbell, A., Porteous, D. J., Scotland, G., Wilson, J. F., Hastie, N. D., Vitart, V., Hayward, C., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1605-2 · Cited by 50
Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data
Salmela, E., Lappalainen, T., Liu, J., Sistonen, P., Andersen, P. M., Schreiber, S., Savontaus, M., Czene, K., Lahermo, P., Hall, P. N., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016747 · Cited by 55
“4–2 [32].”
Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs
Xiong, X., Liu, X., Zhou, L., Yang, J., Yang, B. J., Ma, H., Xie, X., Huang, Y., Fang, S., Xiao, S., et al. (2015) · Mammalian Genome · doi:10.1007/s00335-015-9558-y · Cited by 53
“7 (Aulchenko et al. 2007).”
FAM-MDR: A Flexible Family-Based Multifactor Dimensionality Reduction Technique to Detect Epistasis Using Related Individuals
Cattaert, T., Urrea, V., Naj, A. C., Lobel, L. D., Wit, V. D., Fu, M., John, J. M., Shen, H., Calle, M. L., Ritchie, M. D., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010304 · Cited by 52
“After removing Mendelian errors as found by FBAT (downloadable from URL http://www.biostat.harvard.edu/ ,fbat/default.html), we used the check.marker function of R package GenABEL on these 725 non-diabetics with GAUC measurement available.”
MethodInfluential
Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?
Chen, J., Tsuda, Y., Stocks, M., Källman, T., Xu, N., Kärkkäinen, K., Huotari, T., Semerikov, V. L., VENDRAMIN, G. G., & Lascoux, M. (2014) · Genetics · doi:10.1534/genetics.114.163063 · Cited by 52
Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands
Schurink, A., Wolc, A., Ducro, B. J., Frankena, K., Garrick, D. J., Dekkers, J. C. M., & van Arendonk, J. A. M. (2012) · Genetics Selection Evolution · doi:10.1186/1297-9686-44-31 · Cited by 53
“Breed-specific genomic kinship among animals was therefore computed using the ibs function of the R package GenABEL [18] as:”
Method
A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive
Bergfelder-Drüing, S., Große‐Brinkhaus, C., Lind, B., Erbe, M., Schellander, K., Simianer, H., & Tholen, E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0117468 · Cited by 52
“In order to correct for this problem, model 2 was extended by principal components (PC) estimated from the genomic kinship (EIGENSTRAT) [13,15] which were included as fixed covariables.”
BackgroundMethodInfluential
Genome-wide association and Mendelian randomization study of NT-proBNP in patients with acute coronary syndrome
Johansson, Å., Eriksson, N., Lindholm, D. P., Varenhorst, C., James, S. K., Syvänen, A., Axelsson, T., Siegbahn, A., Barratt, B. J., Becker, R. C., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw012 · Cited by 53
NRSN1 associated grey matter volume of the visual word form area reveals dyslexia before school
Skeide, M. A., Kraft, I., Müller, B., Schaadt, G., Neef, N. E., Bräuer, J., Wilcke, A., Kirsten, H., Boltze, J., & Friederici, A. D. (2016) · Brain · doi:10.1093/brain/aww153 · Cited by 55
Genomewide association analysis of growth traits in Charolais beef cattle1
Jahuey‐Martínez, F. J., Parra‐Bracamonte, G. M., Sifuentes‐Rincón, A. M., Martínez-González, J. C., Gondro, C., García-Pérez, C. A., & López-Bustamante, L. A. (2016) · Journal of Animal Science · doi:10.2527/jas.2016-0359 · Cited by 52
“All described analyses and estimations were performed using GenABEL package (Aulchenko et al., 2007).”
Method
Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker–trait associations
Londoño, S. P., Kavka, M., Samans, B., Snowdon, R. J., Wieckhorst, S., & Uptmoor, R. (2017) · Annals of Botany · doi:10.1093/aob/mcx157 · Cited by 52
Inferences of genetic architecture of bill morphology in house sparrow using a high‐density SNP array point to a polygenic basis
Lundregan, S. L., Hagen, I. J., Gohli, J., Niskanen, A. K., Kemppainen, P., Ringsby, T. H., Kvalnes, T., Pärn, H., Rønning, B., Holand, H., et al. (2018) · Molecular Ecology · doi:10.1111/mec.14811 · Cited by 54
Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis
Boulton, K., Nolan, M. J., Wu, Z., Psifidi, A., Riggio, V., Harman, K., Bishop, S. C., Kaiser, P., Abrahamsen, M. S., Hawken, R., et al. (2018) · Genetics Selection Evolution · doi:10.1186/s12711-018-0433-7 · Cited by 52
“GenABEL [31] was used to construct a genetic relationship matrix (GRM) based on the SNP genotypes and used in a univariate linear mixed model for each trait (using ASReml (1) y = Xb+ ǫ,”
Method
Accuracy of within- and among-family genomic prediction for Fusarium head blight and Septoria tritici blotch in winter wheat
Herter, C. P., Ebmeyer, E., Kollers, S., Korzun, V. N., Würschum, T., & Miedaner, T. (2018) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3264-6 · Cited by 51
Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p
Chen, C., Liu, C., Xiong, X., Fang, S., Yang, H., Zhang, Z., Ren, J., Guo, Y., & Huang, L. (2018) · Genetics Selection Evolution · doi:10.1186/s12711-018-0442-6 · Cited by 52
“The single-marker GWAS was performed using the GenABEL package [17, 19].”
MethodInfluential
Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird
Lindner, M., Laine, V. N., Verhagen, I., Viitaniemi, H. M., Visser, M. E., van Oers, K., & Husby, A. (2021) · Molecular Ecology · doi:10.1111/mec.15803 · Cited by 52

Authors: Aulchenko, Y. S., Ripke, S., Isaacs, A., & van Duijn, C. M.
Affiliations: Erasmus MC (NL)
1 Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands and 2Statistical Genetics Group, Max-Planck-Institute of Psychiatry, Kraepelinstr. 10, D-80804 Munich, Germany
Corresponding author: Aulchenko, Yurii S.
ORCID: Aulchenko, Yurii S.
Ripke, Stephan
Isaacs, Aaron
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2007-03-23
Volume: 23
Issue: 10
Pages: 1294-1296
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btm108
OpenAlex: W2161245845
Cited by: 1,836
References: 4
Citations by year: 2026: 22 · 2025: 39 · 2024: 91 · 2023: 72 · 2022: 65 · 2021: 129 · 2020: 113 · 2019: 161 · 2018: 178 · 2017: 153 · 2016: 139 · 2015: 143 · 2014: 140 · 2013: 116 · 2012: 89
FWCI: 19.99
Type: journal article
Language: en
Open access: closed
Locations: Bioinformatics (publishedVersion)
PubMed (publishedVersion)
EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
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 › Genetics › Genetic and phenotypic traits in livestock
Keywords: genome-wide association study, R library, single nucleotide polymorphisms, association testing, binary traits, quantitative traits, statistical software
MeSH terms: Computer Simulation, Haplotypes, Humans, Software, Gene Library, Genome, Human, Information Storage and Retrieval, Genome, Computational Biology, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide

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GenABEL: an R library for genome-wide association analysis

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