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

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

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

Open this paper in CoChat — free account

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

Integrity signals

Registry

Crossref · 10.1093/bioinformatics/btm108

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397
Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous
Schaid, D. J., Rowland, C. M., Tines, D. E., Jacobson, R. M., & Poland, G. A. (2002) · The American Journal of Human Genetics · doi:10.1086/338688 · Cited by 1,777
A Note on Exact Tests of Hardy-Weinberg Equilibrium
Wigginton, J. E., Cutler, D. J., & Abecasis, G. R. (2005) · The American Journal of Human Genetics · doi:10.1086/429864 · Cited by 1,492
Genome-wide association: a promising start to a long race
Evans, D. M., & Cardon, L. R. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.05.001 · Cited by 33

Show all 4 references

Sorted by citations

Items 901–1,000 of 1,001

A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern
Küttel, L., Letko, A., Häfliger, I. M., Signer‐Hasler, H., Joller, S., Hirsbrunner, G., Mészáros, G., Sölkner, J., Flury, C., Leeb, T., et al. (2019) · Animal Genetics · doi:10.1111/age.12821 · Cited by 23
Genetic parameters of muscle fatty acid profile in a purebred Large White heavy pig population
Zappaterra, M., Catillo, G., Belmonte, A., Fiego, D. P. L., Zambonelli, P., Steri, R., Buttazzoni, L., & Davoli, R. (2020) · Meat Science · doi:10.1016/j.meatsci.2020.108057 · Cited by 23
Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm
Yan, H., Zhou, P., Peng, Y., Bekele, W. A., Ren, C., Tinker, N. A., & Peng, Y. (2020) · Theoretical and Applied Genetics · doi:10.1007/s00122-020-03674-1 · Cited by 23
Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer
Rosier, F., Brisebarre, A., Dupuis, C., Baaklini, S., Puthier, D., Brun, C., Pradel, L. C., Rihet, P., & Payen, D. M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115852 · Cited by 24
“marker” based method implemented in the R package GenABEL [67] to assess the call rate for the SNPs.”
MethodInfluential
Fur colour in the Arctic fox: genetic architecture and consequences for fitness
Tietgen, L., Hagen, I. J., Kleven, O., Bernardi, C. D., Kvalnes, T., Norén, K., Hasselgren, M., Wallén, J., Angerbjörn, A., Landa, A. M., et al. (2021) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2021.1452 · Cited by 26
Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China
Sun, X., Jiang, J., Wang, G., Zhou, P., Li, J., Chen, C., Liu, L., Li, N., Xia, Y., & Ren, H. (2022) · Animal Bioscience · doi:10.5713/ab.21.0577 · Cited by 23
Genomic Analysis of Gastrointestinal Parasite Resistance in Akkaraman Sheep
Arzık, Y., Kızılaslan, M., White, S. N., Piel, L. M. W., & Çınar, M. U. (2022) · Genes · doi:10.3390/genes13122177 · Cited by 23
Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans
Seoighe, C., & Gehring, C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011657 · Cited by 23
The Heritability of Mammographic Breast Density and Circulating Sex-Hormone Levels: Two Independent Breast Cancer Risk Factors
Varghese, J. S., Smith, P. L., Folkerd, E. J., Brown, J. D., Leyland, J., Audley, T., Warren, R. M. L., Dowsett, M., Easton, D. F., & Thompson, D. J. (2012) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-12-0789 · Cited by 23
Brain-derived neurotrophic factor serum levels in genetically isolated populations: gender-specific association with anxiety disorder subtypes but not with anxiety levels or Val66Met polymorphism
Carlino, D., Francavilla, R., Baj, G., Kulak, K., d’Adamo, P., Ulivi, S., Cappellani, S., Gasparini, P., & Tongiorgi, E. (2015) · PeerJ · doi:10.7717/peerj.1252 · Cited by 23
Two Loci on Chromosome 5 Are Associated with Serum IgE Levels in Labrador Retrievers
Owczarek‐Lipska, M., Lauber, B. A., Molitor, V., Meury, S., Kierczak, M., Tengvall, K., Webster, M. T., Jagannathan, V., Schlotter, Y. M., Willemse, T., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039176 · Cited by 23
“We used GenABEL [41] to perform genome-wide association analyses (GWAS).”
Method
Genome-Wide Association Study of Insect Bite Hypersensitivity in Swedish-Born Icelandic Horses
Shrestha, M., Eriksson, S., Schurink, A., Andersson, L. S., Sundquist, M., Frey, R., Broström, H., Bergström, T. F., Ducro, B. J., & Lindgren, G. (2015) · Journal of Heredity · doi:10.1093/jhered/esv033 · Cited by 23
Evidence for genetic regulation of the human parieto‐occipital 10‐Hz rhythmic activity
Salmela, E., Renvall, H., Kujala, J., Hakosalo, O., Illman, M., Vihla, M., Leinonen, E., Salmelin, R. H., & Kere, J. (2016) · European Journal of Neuroscience · doi:10.1111/ejn.13300 · Cited by 23
Genomewide analysis of bull sperm quality and fertility traits
Puglisi, R., Gaspa, G., Balduzzi, D., Severgnini, A., Vanni, R., Macciotta, N., & Galli, A. (2016) · Reproduction in Domestic Animals · doi:10.1111/rda.12747 · Cited by 23
“6 in the population (Aulchenko et al. 2007), implemented in the GenABLE R package (polygenic and 94”
Method
Genome-wide association and pathway-based analysis using latent variables related to milk protein composition and cheesemaking traits in dairy cattle
Dadousis, C., Pegolo, S., Rosa, G. J. M., Bittante, G., & Cecchinato, A. (2017) · Journal of Dairy Science · doi:10.3168/jds.2017-13219 · Cited by 23
“A single marker regression was fitted for GWAS using the GenABEL package in R (Aulchenko et al., 2007) and the GRAMMAR-GC (Genome-Wide Association using Mixed Model and Regression-Genomic Control) approach, with the default function gamma (Amin et al., 2007; Svishcheva et al., 2012).”
Method
Genome-wide association study in ethnic Russians suggests an association of the MHC class III genomic region with the risk of primary varicose veins
Shadrina, A. S., Tsepilov, Y. A., Sokolova, E. А., Smetanina, M. A., Voronina, E. N., Pakhomov, E., Sevost’ianova, K. S., Shevela, A. I., Ilyukhin, Е. А., Seliverstov, E. I., et al. (2018) · Gene · doi:10.1016/j.gene.2018.03.039 · Cited by 22
Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
Yuan, Y., Peng, D., Gu, X., Gong, Y., Sheng, Z., & Hu, X. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00229 · Cited by 23
Potentially functional genetic variants in the complement‐related immunity gene‐set are associated with non‐small cell lung cancer survival
Qian, D., Liu, H., Wang, X., Ge, J., Luo, S., Patz, E. F., Moorman, P. G., Su, L., Shen, S., Christiani, D. C., et al. (2018) · International Journal of Cancer · doi:10.1002/ijc.31896 · Cited by 23
“In the single-locus analysis, multivariate Cox hazards regression analysis was used to evaluate associations between each of the SNPs and OS (in an additive model) with adjustment for age, sex, smoking status, histology, tumor stage, chemotherapy, radiotherapy, surgery and the first four principal components of the po…”
Method
Association genetics of acetophenone defence against spruce budworm in mature white spruce
Lamara, M., Parent, G. J., Giguère, I., Beaulieu, J., Bousquet, J., & MacKay, J. J. (2018) · BMC Plant Biology · doi:10.1186/s12870-018-1434-y · Cited by 23
A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats
Luigi‐Sierra, M. G., Landi, V., Guan, D., Bermejo, J. V. D., Castelló, A., Cabrera, B., Mármol‐Sánchez, E., Álvarez, J. F., Carpio, M. M. G., Martínez, A. M., et al. (2020) · Journal of Dairy Science · doi:10.3168/jds.2020-18461 · Cited by 23
Potentially functional variants of HBEGF and ITPR3 in GnRH signaling pathway genes predict survival of non-small cell lung cancer patients
Wu, Y., Liu, Z., Tang, D., Liu, H., Luo, S., Stinchcombe, T. E., Glass, C., Su, L., Lin, L., Christiani, D. C., et al. (2021) · Translational research · doi:10.1016/j.trsl.2020.12.009 · Cited by 23
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Sun, J., Zhao, M., Jia, P., Lily, W., Wu, Y., Carissa, I., Zhou, Y., Bowton, E., Roden, D. M., Denny, J. C., et al. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004202 · Cited by 24
“The association between each SNP, assuming an additive genetic model, and overall survival was examined using Cox proportional hazards models, adjusted for age, sex and one principal component, using the GenABLE package of R [123].”
Method
Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment
Trampush, J. W., Lencz, T., Knowles, E., Davies, G., Guha, S., Pe'er, I., Liewald, D. C., Starr, J. M., Djurovic, S., Melle, I., et al. (2015) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32319 · Cited by 24
“( Yang et al., 2014) Regression coefficients and standard error estimates were generated within each study and then carried forward for meta-analysis using Metasoft(Han and Eskin, 2011) and the R MetABEL package(Aulchenko et al., 2007) for plotting of results.”
FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium
kConFab Investigators, Agarwal, D., Australian Ovarian Cancer Study Group, The GENICA Network, TNBCC, Pineda, S., Michailidou, K., Herránz, J., Pita, G., Moreno, L. T., et al. (2014) · British Journal of Cancer · doi:10.1038/bjc.2013.769 · Cited by 29
“These were converted to allele doses using the impute2mach function in the GenABEL library in R (Aulchenko et al, 2007) and analysed under a per-allele model.”
Method
A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits
Zhu, J., Chen, C., Yang, B. J., Guo, Y., Ai, H., Ren, J., Peng, Z., Tu, Z., Yang, X., Meng, Q., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1240-y · Cited by 22
“The associations between phenotypes and genome-wide SNP genotype data were analyzed with the single-marker association model in the GenABEL package [12] based on a mixed linear model implemented with the mmscore function of GenABEL in R package.”
Method
Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3
EMBRACE, Hamdi, Y., Collaborators, G. S., HEBON, KConFab Investigators, Soucy, P., Kuchenbaecker, K. B., Pastinen, T., Droit, A., Lemaçon, A., et al. (2016) · Breast Cancer Research and Treatment · doi:10.1007/s10549-016-4018-2 · Cited by 22
Genome-wide association study for an efficient selection of Fusarium head blight resistance in winter triticale
Galiano-Carneiro, A. L., Boeven, P. H. G., Maurer, H. P., Würschum, T., & Miedaner, T. (2018) · Euphytica · doi:10.1007/s10681-018-2327-8 · Cited by 21
Potentially functional genetic variants in the TNF/TNFR signaling pathway genes predict survival of patients with non‐small cell lung cancer in the PLCO cancer screening trial
Guo, Y., Feng, Y., Liu, H., Luo, S., Clarke, J., Moorman, P. G., Su, L., Shen, S., Christiani, D. C., & Wei, Q. (2019) · Molecular Carcinogenesis · doi:10.1002/mc.23017 · Cited by 22
Genome-wide association study for backfat thickness at 100 kg and loin muscle thickness in domestic pigs based on genotyping by sequencing
Chen, D., Wu, P., Yang, Q., Wang, K., Zhou, J., Yang, X., Jiang, A., Shen, L., Xiao, W., Jiang, Y., et al. (2019) · Physiological Genomics · doi:10.1152/physiolgenomics.00008.2019 · Cited by 22
Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects
Liu, X., Zhou, L., Xie, X., Wu, Z., Xiong, X., Zhang, Z., Yang, J., Xiao, S., Zhou, M., Ma, J., et al. (2019) · Genetics Selection Evolution · doi:10.1186/s12711-019-0488-0 · Cited by 22
Genetic Factors Associated With Nodulation and Nitrogen Derived From Atmosphere in a Middle American Common Bean Panel
Oladzad, A., González, A., Macchiavelli, R., de Jensen, C. E., Beaver, J. S., Porch, T. G., & McClean, P. E. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.576078 · Cited by 22
Discovering of Genomic Variations Associated to Growth Traits by GWAS in Braunvieh Cattle
Zepeda-Batista, J. L., Núñez-Domínguez, R., Ramírez‐Valverde, R., Jahuey‐Martínez, F. J., Herrera-Ojeda, J. B., & Parra‐Bracamonte, G. M. (2021) · Genes · doi:10.3390/genes12111666 · Cited by 22
“All described analyses and estimations were performed using the GenABEL package [21].”
MethodInfluential
Potentially functional variants of MAP3K14 in the NF-κB signaling pathway genes predict survival of HBV-related hepatocellular carcinoma patients
Huang, Q., Liu, Y., Qiu, M., Lin, Q., Wei, X., Zhou, Z., Liang, X., Li, R., Chen, W., Zhou, X., et al. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.990160 · Cited by 22
“Multivariate cox proportional hazards regression analysis was used to assess associations between SNPs of key genes in the NF-kB signaling pathway and HBV-related HCC OS (in an additive genetic model) in the discovery and validation datasets, with adjustment for age, sex, smoking status, drinking status, AFP level, ci…”
Method
Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula
Al‐Abri, M., Alfoudari, A., Mohammad, Z., Almathen, F. S., Al‐Marzooqi, W., Al-Hajri, S., Al-Amri, M., & Bahbahani, H. M. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1296610 · Cited by 22
Heritabilities of Ocular Biometrical Traits in Two Croatian Isolates with Extended Pedigrees
Vitart, V., Benčić, G., Hayward, C., Herman, J. Š., Huffman, J. E., Campbell, S. E., Bućan, K., Zgaga, L., Kolčić, I., Polašek, O., et al. (2010) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.09-3720 · Cited by 22
“This model is the base model of choice for quantitative trait heritability estimation when phenotypic values can be correlated in pairs of individuals of multiple relationships.25 Models were implemented by using the polygenic function of GenABEL.26 The pair-wise kinship coefficients, elements of the kinship matrix fi…”
MethodInfluential
Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations
Shirali, M., Pong‐Wong, R., Navarro, P., Knott, S., Hayward, C., Vitart, V., Rudan, I., Campbell, H., Hastie, N. D., Wright, A. F., et al. (2015) · Heredity · doi:10.1038/hdy.2015.107 · Cited by 22
Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd
Al‐Abri, M., von Borstel, U. K., Strecker, V., & Brooks, S. A. (2017) · Journal of Heredity · doi:10.1093/jhered/esx025 · Cited by 21
Association of Raynaud’s phenomenon with a polymorphism in the NOS1 gene
Munir, S., Freidin, M. B., Brain, S. D., & Williams, F. M. K. (2018) · PLoS ONE · doi:10.1371/journal.pone.0196279 · Cited by 22
Alteration of HDL Protein Composition with Hemodialysis Initiation
Wang, K., Zelnick, L. R., Hoofnagle, A. N., Vaisar, T., Henderson, C. M., Imrey, P. B., Robinson‐Cohen, C., de Boer, I. H., Shiu, Y.-T. E., Himmelfarb, J., et al. (2018) · Clinical Journal of the American Society of Nephrology · doi:10.2215/cjn.11321017 · Cited by 22
Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians
Sjöstrand, A. E., Sjödin, P., Hegay, T., Nikolaeva, A., Farhad, S., Blum, M. G. B., Heyer, É., & Jakobsson, M. (2020) · European Journal of Human Genetics · doi:10.1038/s41431-020-00736-2 · Cited by 22
Neurobiological origins of individual differences in mathematical ability
Skeide, M. A., Wehrmann, K., Emami, Z., Kirsten, H., Hartmann, A. M., & Rujescu, D. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000871 · Cited by 22
cgmisc: enhanced genome-wide association analyses and visualization
Kierczak, M., Jabłońska, J., Forsberg, S. K. G., Bianchi, M., Tengvall, K., Pettersson, M. E., Scholz, V., Meadows, J. R. S., Jern, P., Carlborg, Ö., et al. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv426 · Cited by 21
Adjusting for Familial Relatedness in the Analysis of GWAS Data
Thomson, R. J., & McWhirter, R. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6613-4_10 · Cited by 21
Whole-genome sequencing association analysis reveals the genetic architecture of meat quality traits in Chinese Qingyu pigs
Wu, P., Wang, K., Zhou, J., Chen, D., Yang, X., Jiang, A., Shen, L., Zhang, S., Xiao, W., Jiang, Y., et al. (2020) · Genome · doi:10.1139/gen-2019-0227 · Cited by 21
“…studies have reported that ignoring 315 population stratification can result in the inflation of false positives and 316 reduce the statistical power(Aulchenko et al., 2007; Matthieu, Christophe, Page 14 of 42 https://mc06.manuscriptcentral.com/genome-pubs Genome Draft 317 Mickael, & Thomas, 2011).”
Background
NAC Candidate Gene Marker for bgm-1 and Interaction With QTL for Resistance to Bean Golden Yellow Mosaic Virus in Common Bean
Soler‐Garzón, A., Oladzad, A., Beaver, J. S., Beebe, S., Lee, R., Lobaton, J. D., Macea, E., McClean, P. E., Raatz, B., Rosas, J. C., et al. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.628443 · Cited by 21
Age-dependent genetic architectures of chicken body weight explored by multidimensional GWAS and molQTL analyses
Zhong, C., Li, X., Guan, D., Zhang, B., Wang, X., Qu, L., Zhou, H., Fang, L., Sun, C., & Yang, N. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.09.003 · Cited by 22
Genome-Wide Association Analysis of Avian Resistance to Campylobacter jejuni Colonization Identifies Risk Locus Spanning the CDH13 Gene
Connell, S., Meade, K. G., Allan, B. J., Lloyd, A. T., Downing, T., O’Farrelly, C., & Bradley, D. G. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.006031 · Cited by 21
“Average IBS was calculated from all SNP genotypes in the R package GenABEL [38].”
MethodInfluential
Genome-wide Association Study of Chicken Plumage Pigmentation
Park, M. N., Choi, J. A., Lee, K., Lee, H. J., Choi, B., Kim, H., Kim, T.-H., Cho, S., & Lee, T. (2013) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.2013.13413 · Cited by 21
Caries and Innate Immunity: DEFB1 Gene Polymorphisms and Caries Susceptibility in Genetic Isolates from North-Eastern Italy
Navarra, C. O., Robino, A., Pirastu, N., Bevilacqua, L., Gasparini, P., Lenarda, R. D., & Crovella, S. (2016) · Caries Research · doi:10.1159/000450965 · Cited by 21
“Furthermore, MixABEL was used for the association of the imputed SNPs [Aulchenko et al., 2007].”
Method
Defeating the Warrior: genetic architecture of triticale resistance against a novel aggressive yellow rust race
Losert, D., Maurer, H. P., Leiser, W. L., & Würschum, T. (2016) · Theoretical and Applied Genetics · doi:10.1007/s00122-016-2843-7 · Cited by 18
“Genome-wide association mapping was performed with the R package GenABEL (Aulchenko et al. 2007), using a mixed linear model that integrates a kinship matrix to correct for population stratification (Yu et al.”
MethodInfluential
Candidate gene based association mapping in Fusarium culmorum for field quantitative pathogenicity and mycotoxin production in wheat
Castiblanco, V., Marulanda, J., Würschum, T., & Miedaner, T. (2017) · BMC Genetics · doi:10.1186/s12863-017-0511-9 · Cited by 21
“A mixed linear model incorporating the BLUES obtained from the phenotypic analysis (Additional file 3), SNP’s information (Additional file 4), the three main principal coordinates as fixed effect and a kinship matrix for the random genotypic isolate effect was used to identify marker-trait associations [53].”
Method
Genome-scale identification of microRNA-related SNPs associated with risk of head and neck squamous cell carcinoma
Wilkins, O. M., Titus, A., Gui, J., Eliot, M., Butler, R. A., Sturgis, E. M., Li, G., Kelsey, K. T., & Christensen, B. C. (2017) · Carcinogenesis · doi:10.1093/carcin/bgx056 · Cited by 21
“Genomic inflation factor λ was calculated using the R package GenABEL (31).”
Method
Genome‐wide association analyses reveal polygenic genomic architecture underlying divergent shell morphology in Spanish Littorina saxatilis ecotypes
Kess, T., & Boulding, E. G. (2019) · Ecology and Evolution · doi:10.1002/ece3.5378 · Cited by 24
“We used the ibs function in GenABEL to calculate a genomic kinship matrix (K) containing pairwise identity-by-state (IBS) values estimated using all of the 2405 putatively neutral SNPs that were successfully genotyped for that pair of individuals (Aulchenko et al., 2007a).”
Method
A novel genomic region on chromosome 11 associated with fearfulness in dogs
Sarviaho, R., Hakosalo, O., Tiira, K., Sulkama, S., Niskanen, J. E., Hytönen, M. K., Sillanpää, M. J., & Lohi, H. (2020) · Translational Psychiatry · doi:10.1038/s41398-020-0849-z · Cited by 21
Development and Application of Genomic Control Methods for Genome-Wide Association Studies Using Non-Additive Models
Tsepilov, Y. A., Ried, J. S., Strauch, K., Grallert, H., van Duijn, C. M., Axenovich, T. I., & Aulchenko, Y. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081431 · Cited by 21
Self-citation
Robustness of the linear mixed effects model to error distribution assumptions and the consequences for genome-wide association studies
Warrington, N. M., Tilling, K. M., Howe, L. D., Paternoster, L., Pennell, C. E., Wu, Y. Y., & Briollais, L. (2014) · Statistical Applications in Genetics and Molecular Biology · doi:10.1515/sagmb-2013-0066 · Cited by 22
Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs
Quan, J., Ding, R., Wang, X., Yang, M. J., Yang, Y., Zheng, E., Gu, T., Cai, G., Wu, Z., Liu, D., et al. (2017) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.17.0356 · Cited by 21
“Generalized mixed linear model and population stratification assay Association analyses based on the generalized MLM were conducted using GenABEL in R software [15].”
Method
Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures
Satpathy, S., Clark, N. M., Chen, Y., Hosseini, N., Chang, Y.-H., Hsiao, Y., Lei, J. T., Petralia, F., Chen, J., Geffen, Y., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.07.011 · Cited by 23
A whole genome SNP genotyping by DNA microarray and candidate gene association study for kidney stone disease
Rungroj, N., Nettuwakul, C., Sudtachat, N., Praditsap, O., Sawasdee, N., Sritippayawan, S., Chuawattana, D., & Yenchitsomanus, P. (2014) · BMC Medical Genetics · doi:10.1186/1471-2350-15-50 · Cited by 20
“05) between 101 patients and 105 normal control subjects were examined by GenABEL package with no adjustment for binary traits; the test is equivalent to the Armitage test [24].”
Method
Detection and analysis of genome‐wide copy number variation in the pig genome using an 80 K SNP Beadchip
Wang, Y., Zhang, T., & Wang, C. (2019) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12435 · Cited by 20
Novel genetic variants in HDAC2 and PPARGC1A of the CREB‐binding protein pathway predict survival of non‐small‐cell lung cancer
Tang, D., Zhao, Y. C., Qian, D., Liu, H., Luo, S., Patz, E. F., Moorman, P. G., Su, L., Shen, S., Christiani, D. C., et al. (2019) · Molecular Carcinogenesis · doi:10.1002/mc.23132 · Cited by 20
Identification of SNPs Associated with Somatic Cell Score in Candidate Genes in Italian Holstein Friesian Bulls
Moretti, R., Soglia, D., Chessa, S., Sartore, S., Finocchiaro, R., Rasero, R., & Sacchi, P. (2021) · Animals · doi:10.3390/ani11020366 · Cited by 20
Splenic clearance of rigid erythrocytes as an inherited mechanism for splenomegaly and natural resistance to malaria
Henry, B., Volle, G., Akpovi, H., Gineau, L., Roussel, C., Ndour, P. A., Tossou, F., Suárez, F., PALSTRA, F. P., Fricot, A., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.104167 · Cited by 20
Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science
Pathak, R. K., & Kim, J. (2022) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.1008728 · Cited by 22
KAT2Bpolymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex
Johnson, E. O., Hancock, D. B., Levy, J. L., Gaddis, N., Page, G. P., Glasheen, C., Saccone, N. L., Bierut, L. J., & Kral, A. H. (2015) · Addiction Biology · doi:10.1111/adb.12286 · Cited by 18
“Discovery genome-wide association study analyses GWAS analyses were conducted in each ancestry group to test the imputed SNP and indel genotype dosages for association with drug abuse using logistic regression models in ProbABEL (Aulchenko et al. 2007).”
The Buffalo Genome and the Application of Genomics in Animal Management and Improvement
Iamartino, D., Williams, J. L., Sonstegard, T. S., Reecy, J. M., Tassell, C. P. V., Nicolazzi, E. L., Biffani, S., Biscarini, F., Schroeder, S., Oliveira, D. A. A., et al. (2013) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) · doi:10.13140/rg.2.2.30951.85924 · Cited by 20
An Empirical Comparison of Joint and Stratified Frameworks for Studying G × E Interactions: Systolic Blood Pressure and Smoking in the CHARGE Gene‐Lifestyle Interactions Working Group
Sung, Y. J., Winkler, T. W., Manning, A. K., Aschard, H., Gudnason, V. G., Harris, T. B., Smith, A. V., Boerwinkle, E., Brown, M. R., Morrison, A. C., et al. (2016) · Genetic Epidemiology · doi:10.1002/gepi.21978 · Cited by 19
“The remaining two studies used the linear mixed effect model approach with a random polygenic component (for which the covariance matrix depends on the kinship matrix) with GenABEL [Aulchenko et al., 2007] or R (supplementary Table S1).”
Method
NLRC5 polymorphism is associated with susceptibility to chronic periodontitis
Zupin, L., Navarra, C. O., Robino, A., Bevilacqua, L., Lenarda, R. D., Gasparini, P., & Crovella, S. (2017) · Immunobiology · doi:10.1016/j.imbio.2017.01.001 · Cited by 20
Analysis of single nucleotide polymorphisms variation associated with important economic and computed tomography measured traits in Texel sheep
Garza-Hernandez, D., Mucha, S., Banos, G., Kaseja, K., Moore, K., Lambe, N. R., Yates, J., & Bünger, L. (2017) · animal · doi:10.1017/s1751731117002488 · Cited by 20
“177 Quality control (QC) was performed with the GenABEL R package by considering 178 genotypes of all rams (Aulchenko et al., 2007).”
Method
Genome‐wide association studies for milk production traits in Valle del Belice sheep using repeated measures
Sutera, A. M., Riggio, V., Mastrangelo, S., Gerlando, R. D., Sardina, M. T., Pong‐Wong, R., Tolone, M., & Portolano, B. (2019) · Animal Genetics · doi:10.1111/age.12789 · Cited by 20
Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study
Qu, L., Shen, M., Guo, J., Wang, X., Dou, T., Hu, Y., Li, Y., Ma, M., Wang, K., & Liu, H. (2019) · Archives animal breeding/Archiv für Tierzucht · doi:10.5194/aab-62-113-2019 · Cited by 20
“The GenABEL package (Aulchenko et al., 2007) in the R project was used to calculate the genomic inflation factor resulting from the estimate of false positive signals.”
Method
Family-based genome wide association analysis for salmon lice (Lepeophtheirus salmonis) resistance in North American Atlantic salmon using a 50 K SNP array
Holborn, M. K., Rochus, C. M., Ang, K. P., Elliott, J. A. K., Leadbeater, S., Powell, F., & Boulding, E. G. (2019) · Aquaculture · doi:10.1016/j.aquaculture.2019.734215 · Cited by 20
Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors
Hassouni, K. E., Sielaff, M., Curella, V., Neerukonda, M., Leiser, W. L., Würschum, T., Schuppan, D., Tenzer, S., & Longin, C. F. H. (2021) · Theoretical and Applied Genetics · doi:10.1007/s00122-021-03906-y · Cited by 20
Determinants of retinal microvascular features and their relationships in two European populations
Kirin, M., Nagy, R., MacGillivray, T., Polašek, O., Hayward, C., Rudan, I., Campbell, H., Wild, S. H., Wright, A. F., Wilson, J. F., et al. (2017) · Journal of Hypertension · doi:10.1097/hjh.0000000000001408 · Cited by 20
Canine NAPEPLD-associated models of human myelin disorders
Minor, K. M., Letko, A., Becker, D., Drögemüller, M., Mandigers, P. J. J., Bellekom, S., Leegwater, P. A. J., Stassen, Q. E. M., Putschbach, K., Fischer, A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-23938-7 · Cited by 20
Correction: Common Genetic Variants and Modification of Penetrance of BRCA2-Associated Breast Cancer
Gaudet, M. M., Kirchhoff, T., Green, T. J., Vijai, J., Korn, J. M., Guiducci, C., Segrè, A. V., McGee, K., McGuffog, L., Kartsonaki, C., et al. (2010) · PLoS Genetics · doi:10.1371/annotation/b28cf02d-7196-4a16-8b36-6562a0b84f75 · Cited by 20
Heritability of ocular component dimensions in mice phenotyped using depth-enhanced swept source optical coherence tomography
Wang, L., Považay, B., Chen, Y. P., Höfer, B., Drexler, W., & Guggenheim, J. A. (2011) · Experimental Eye Research · doi:10.1016/j.exer.2011.06.008 · Cited by 19
Identification of QTL on Chromosome 18 Associated with Non-Coagulating Milk in Swedish Red Cows
Duchemin, S. I., Glantz, M., de Koning, D., Paulsson, M. A., & Fikse, W. F. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00057 · Cited by 19
“Quality controls of the data were performed using the R-package GenAbel (Aulchenko et al., 2007), and consisted of a minimum of 95% of non-missing SNP per called genotypes (call rate) andminor allele frequency (MAF) of a minimum of 1% for a called SNP.”
Method
Genome‐wide association study for plasma very low‐density lipoprotein concentration in chicken
Zhang, H., Shen, L., Li, Y., Xu, Z., Zhang, X., Yu, J., Cao, Z., & Luan, P. (2019) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12397 · Cited by 19
Genomic Analysis of Spontaneous Abortion in Holstein Heifers and Primiparous Cows
Oliver, K. F., Wahl, A., Dick, M., Toenges, J., Kiser, J. N., Galliou, J. M., Moraes, J. G. N., Burns, G. W., Dalton, J. C., Spencer, T. E., et al. (2019) · Genes · doi:10.3390/genes10120954 · Cited by 19
“The permuted P-value was calculated using GenABEL in R with 10,000 phenotype-based permutations for each gene-set [32].”
Method
Identification of seed protein and oil related QTL in 944 RILs from a diallel of early-maturing European soybean
Zhu, X., Leiser, W. L., Hahn, V., & Würschum, T. (2020) · The Crop Journal · doi:10.1016/j.cj.2020.06.006 · Cited by 19
CCDC66 frameshift variant associated with a new form of early-onset progressive retinal atrophy in Portuguese Water Dogs
Murgiano, L., Becker, D., Spector, C., Carlin, K., Santana, E., Niggel, J. K., Jagannathan, V., Leeb, T., Pearce-Kelling, S., Aguirre, G., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-77980-5 · Cited by 16
Single-Nucleotide Polymorphism Variations Associated With Specific Genes Putatively Identified Enhanced Genetic Predisposition for 305-Day Milk Yield in the Girolando Crossbreed
da Cruz, A. S., Silva, D. C., Minasi, L. B., Teixeira, L. K. D. F., Rodrigues, F. M., da Silva, C. C., do Carmo, A. S., da Silva, M. V. G. B., Utsunomiya, Y. T., Garcia, J. F., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.573344 · Cited by 19
Multi‐year field trials provide a massive repository of trait data on a highly diverse population of tomato and uncover novel determinants of tomato productivity
Zemach, I., Alseekh, S., Tadmor‐Levi, R., Fisher, J., Torgeman, S., Trigerman, S., Nauen, J., Hayut, S. F., Mann, V., Rochsar, E., et al. (2023) · The Plant Journal · doi:10.1111/tpj.16268 · Cited by 19
The Genetic Architecture of Recombination Rates is Polygenic and Differs Between the Sexes in Wild House Sparrows ( Passer domesticus )
McAuley, J. B., Servin, B., Burnett, H. A., Brekke, C., Peters, L., Hagen, I. J., Niskanen, A. K., Ringsby, T. H., Husby, A., Jensen, H., et al. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae179 · Cited by 19
Integrated multiomics approach identifies calcium and integrin-binding protein-2 as a novel gene for pulse wave velocity
Mangino, M., Cecelja, M., Menni, C., Tsai, P.-C., Yuan, W., Small, K. S., Bell, J. T., Mitchell, G. F., Chowienczyk, P., & Spector, T. D. (2015) · Journal of Hypertension · doi:10.1097/hjh.0000000000000732 · Cited by 19
“As per the discovery, the validation analysis was performed using GenABEL [19] to correct for family structure and zygosity on the residuals of the methylation probes adjusted for age and sex, and know sources of batch effect (methylation chip, sample position on methylation chip and blood cell count).”
MethodInfluential
Detecting Low Frequent Loss-of-Function Alleles in Genome Wide Association Studies with Red Hair Color as Example
Liu, F., Struchalin, M. V., van Duijn, K., Albert Hofman, D., Uitterlinden, A. G., van Duijn, C. M., Aulchenko, Y. S., & Kayser, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028145 · Cited by 22
“GWA analysis The GWA analysis was conducted using GenABEL [35] and followed closely the methods previously described [34].”
InfluentialSelf-citation
SNPpy - Database Management for SNP Data from Genome Wide Association Studies
Mitha, F., Herodotou, H., Borisov, N., Chen, J., Yoder, J., & Owzar, K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024982 · Cited by 19
“For example, PLINK [1] and GenABEL [2] verify that for each SNP the same number of patients have been called and that the SNPs are bi-allelic.”
Method
Genetic Variation in Candidate Genes Like the HMGA2 Gene in the Extremely Tall
Hendriks, E., Brown, M. R., Boot, A. M., Oostra, B. A., Drop, S. L. S., & Parks, J. S. (2011) · Hormone Research in Paediatrics · doi:10.1159/000330764 · Cited by 19
Unravelling the basis of variability in cobalamin levels in the general population
Andrew, T., Gill, R., Gillham‐Nasenya, I., & Ahmadi, K. R. (2013) · British Journal Of Nutrition · doi:10.1017/s0007114513000974 · Cited by 19
“Tests of the genetic association between Cbl levels and each SNP were conducted using GenABEL implemented within the statistical package R((17)).”
Method
Effect of genetic and environmental factors on protein biomarkers for common non-communicable disease and use of personally normalized plasma protein profiles (PNPPP)
Enroth, S., Enroth, S. B., Johansson, Å., & Gyllensten, U. B. (2015) · Biomarkers · doi:10.3109/1354750x.2015.1093546 · Cited by 19
“, 2014) using the GenABEL or ProbABEL (Aulchenko et al., 2007) software suites, which have been developed to enable statistical analyses of genetic data of related individuals.”
MethodInfluential
Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium ® HD SNP BeadChip
Miller, J. M., Festa‐Bianchet, M., & Coltman, D. W. (2018) · PeerJ · doi:10.7717/peerj.4364 · Cited by 19
“, 2016) an extension of the GenABLE package (Aulchenko et al., 2007; Karssen, Van Duijn & Aulchenko, 2016).”
BackgroundMethodInfluential
Polymorphisms of genes involved in inflammation and blood vessel development influence the risk of varicose veins
Shadrina, A. S., Tsepilov, Y. A., Smetanina, M. A., Voronina, E. N., Seliverstov, E. I., Ilyukhin, Е. А., Кириенко, А. И., Zolotukhin, I. A., & Филипенко, М. Л. (2018) · Clinical Genetics · doi:10.1111/cge.13362 · Cited by 19
“org; glm function).(6) Adherence of genotype distribution to Hardy-Weinberg equi-”
Method
Epigenome-Wide Analyses Identify Two Novel Associations With Recurrent Stroke in the Vitamin Intervention for Stroke Prevention Clinical Trial
Armstrong, N. D., Chen, W., Brewer, M. S., Williams, S. R., Sale, M. M., Worrall, B. B., & Keene, K. L. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00358 · Cited by 19
“Manhattan plots were generated using qqman (Turner, 2018) and lambda values were estimated using GenABEL (Aulchenko et al., 2007).”
Method
Identification and validation of a novel candidate gene regulating net meat weight in Simmental beef cattle based on imputed next‐generation sequencing
Bordbar, F., Jensen, J., Du, ‬., Abied, A., Guo, W., Xu, L., Gao, H., Zhang, L., & Li, J. (2020) · Cell Proliferation · doi:10.1111/cpr.12870 · Cited by 18
Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing
Moraleda, C. P., Robledo, D., Gutiérrez, A. P., Del‐Pozo, J., Yañez, J. M., & Houston, R. D. (2021) · BMC Genomics · doi:10.1186/s12864-021-07443-2 · Cited by 19
A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
Wu, P., Wang, K., Zhou, J., Chen, D., Jiang, A., Jiang, Y., Zhu, L., Qiu, X., Li, X., & Tang, G. (2021) · Communications Biology · doi:10.1038/s42003-021-02416-3 · Cited by 20
Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer ( Cervus elaphus )
Peters, L., Huisman, J., Kruuk, L. E. B., Pemberton, J. M., & Johnston, S. E. (2021) · Molecular Ecology · doi:10.1111/mec.16314 · Cited by 18
“4.2 (Aulchenko et al., 2007).”
Influential
Genomic study of the response of chicken to highly pathogenic avian influenza virus
Sironi, L., Williams, J. L., Stella, A., Minozzi, G., Moreno, A. M., Ramelli, P., Han, J., Weigend, S., Junxing, W., Lombardi, G., et al. (2011) · BMC Proceedings · doi:10.1186/1753-6561-5-s4-s25 · Cited by 19
Genetic variation in the estrogen metabolic pathway and mammographic density as an intermediate phenotype of breast cancer
Li, J., Eriksson, L., Humphreys, K., Czene, K., Liu, J., Tamimi, R. M., Lindström, S., Hunter, D. J., Vachon, C. M., Couch, F. J., et al. (2010) · Breast Cancer Research · doi:10.1186/bcr2488 · Cited by 19
“For the analysis of imputed data, the ProbABEL package from the ABEL set of programs was used [29].”
Method

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

GenABEL: an R library for genome-wide association analysis

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks