GenABEL: an R library for genome-wide association analysis

Generating samples under a Wright–Fisher neutral model of genetic variation

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Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous

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A Note on Exact Tests of Hardy-Weinberg Equilibrium

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Genome-wide association: a promising start to a long race

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GCTA: a tool for genome-wide complex trait analysis

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Genome-wide efficient mixed-model analysis for association studies

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ranger : A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

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Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

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adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data

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Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

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New insights into the genetic etiology of Alzheimer’s disease and related dementias

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New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

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Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies

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Efficient Bayesian mixed-model analysis increases association power in large cohorts

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Data quality control in genetic case-control association studies

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The Rotterdam Study: objectives and design update

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Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

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rMVP: A Memory-Efficient, Visualization-Enhanced, and Parallel-Accelerated Tool for Genome-Wide Association Study

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GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction

Wang, J., & Zhang, Z. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.08.005 · Cited by 1,240 · see citing works

Modulation of Genetic Associations with Serum Urate Levels by Body-Mass-Index in Humans

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Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries

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Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits

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Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts

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A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis

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New loci associated with kidney function and chronic kidney disease

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Mapping cis- and trans-regulatory effects across multiple tissues in twins

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Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies

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Identification of a urate transporter, ABCG2, with a common functional polymorphism causing gout

Woodward, O. M., Köttgen, A., Coresh, J., Boerwinkle, E., Guggino, W. B., & Köttgen, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901249106 · Cited by 684 · see citing works

Genome-wide association study identifies five new breast cancer susceptibility loci

The Breast Cancer Susceptibility Collaboration (UK), Turnbull, C., Ahmed, S., Morrison, J., Pernet, D., Renwick, A., Maranian, M., Seal, S., Ghoussaini, M., Hines, S., et al. (2010) · Nature Genetics · doi:10.1038/ng.586 · Cited by 687 · see citing works

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S. H., Czajkowski, J., Esko, T., Fall, T., Kilpeläinen, T. O., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005378 · Cited by 664 · see citing works

Meta-analysis methods for genome-wide association studies and beyond

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Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function

Hancock, D. B., Eijgelsheim, M., Wilk, J. B., Gharib, S. A., Loehr, L. R., Marciante, K. D., Franceschini, N., van Durme, Y. M. T. A., Chen, T.-H., Barr, R. G., et al. (2009) · Nature Genetics · doi:10.1038/ng.500 · Cited by 633 · see citing works

Fast and efficient QTL mapper for thousands of molecular phenotypes

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Genome-wide association study identifies multiple loci influencing human serum metabolite levels

Kettunen, J., Tukiainen, T., Sarin, A.-P., Ortega-Alonso, A., Tikkanen, E., Lyytikäinen, L.-P., Kangas, A. J., Soininen, P., Würtz, P., Silander, K., et al. (2012) · Nature Genetics · doi:10.1038/ng.1073 · Cited by 553 · see citing works

CAG Repeat Not Polyglutamine Length Determines Timing of Huntington’s Disease Onset

Lee, J., Correia, K., Loupe, J. M., Kim, K., Barker, D., Hong, E. P., Chao, M. J., Long, J. D., Lucente, D. E., Vonsattel, J. P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.036 · Cited by 531 · see citing works

Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array

Eeles, R. A., Bioresource, T. A. P. C., Collaborators, T. U. P. (. T. F. C. A. T. S., Olama, A. A. A., Benlloch, S., Saunders, E. J., Leongamornlert, D. A., Tymrakiewicz, M., Ghoussaini, M., Luccarini, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2560 · Cited by 542 · see citing works

A supergene determines highly divergent male reproductive morphs in the ruff

Küpper, C., Stocks, M., Risse, J. E., dos Remedios, N., Farrell, L. L., McRae, S. B., Morgan, T. C., Karlionova, N., Pinchuk, P., Verkuil, Y. I., et al. (2015) · Nature Genetics · doi:10.1038/ng.3443 · Cited by 524 · see citing works

A resource-efficient tool for mixed model association analysis of large-scale data

Jiang, L., Zheng, Z., Qi, T., Kemper, K. E., Wray, N. R., Visscher, P. M., & Yang, J. (2019) · Nature Genetics · doi:10.1038/s41588-019-0530-8 · Cited by 513 · see citing works

SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

Barbato, M., Orozco‐terWengel, P., Tapio, M., & Bruford, M. W. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00109 · Cited by 512 · see citing works

Meta-Analysis of Genome-Wide Association Studies in >80 000 Subjects Identifies Multiple Loci for C-Reactive Protein Levels

Dehghan, A., Dupuis, J., Barbalić, M., Bis, J. C., Eiríksdóttir, G., Lu, C., Pellikka, N., Wallaschofski, H., Kettunen, J., Henneman, P., et al. (2011) · Circulation · doi:10.1161/circulationaha.110.948570 · Cited by 512 · see citing works

Genetics meets proteomics: perspectives for large population-based studies

Suhre, K., McCarthy, M. I., & Schwenk, J. M. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-0268-2 · Cited by 478 · see citing works

Genomewide Rapid Association Using Mixed Model and Regression: A Fast and Simple Method For Genomewide Pedigree-Based Quantitative Trait Loci Association Analysis

Aulchenko, Y., de Koning, D., & Haley, C. (2007) · Genetics · doi:10.1534/genetics.107.075614 · Cited by 460 · see citing works

Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes

The GoDARTS and UKPDS Diabetes Pharmacogenetics Study Group (2010) · Nature Genetics · doi:10.1038/ng.735 · Cited by 448 · see citing works

FTO genotype is associated with phenotypic variability of body mass index

Yang, J., Loos, R., Powell, J. E., Medland, S., Speliotes, E. K., Chasman, D., Rose, L., Thorleifsson, G., Steinthorsdottir, V., Mägi, R., et al. (2012) · Nature · doi:10.1038/nature11401 · Cited by 457 · see citing works

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

Randall, J. C., Winkler, T. W., Kutalik, Z., Berndt, S. I., Jackson, A. U., Monda, K. L., Kilpeläinen, T. O., Esko, T., Mägi, R., Li, S., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003500 · Cited by 409 · see citing works

Genetic Variants Influencing Circulating Lipid Levels and Risk of Coronary Artery Disease

Waterworth, D. M., Ricketts, S. L., Song, K., Chen, L., Zhao, J. H., Ripatti, S., Aulchenko, Y. S., Zhang, W., Yuan, X., Lim, N., et al. (2010) · Arteriosclerosis, Thrombosis, and Vascular Biology · doi:10.1161/atvbaha.109.201020 · Cited by 405 · see citing works

Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis

Chen, D., Neumann, K., Friedel, S., Kilian, B., Chen, M., Altmann, T., & Klukas, C. (2014) · The Plant Cell · doi:10.1105/tpc.114.129601 · Cited by 404 · see citing works

Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements

Grundberg, E., Meduri, E., Sandling, J. K., Hedman, Å. K., Keildson, S., Buil, A., Busche, S., Yuan, W., Nisbet, J., Sekowska, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.004 · Cited by 370 · see citing works

Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function

Artigas, M. S., Loth, D. W., Wain, L. V., Gharib, S. A., Obeidat, M., Tang, W., Zhai, G., Zhao, J. H., Smith, A. V., Huffman, J. E., et al. (2011) · Nature Genetics · doi:10.1038/ng.941 · Cited by 400 · see citing works

ProbABEL package for genome-wide association analysis of imputed data

Aulchenko, Y. S., Struchalin, M. V., & van Duijn, C. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-134 · Cited by 396 · see citing works

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

Riedelsheimer, C., Lisec, J., Czedik‐Eysenberg, A., Ronan Sulpice, A., Flis, A., Grieder, C., Altmann, T., Stitt, M., Willmitzer, L., & Melchinger, A. E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120813109 · Cited by 375 · see citing works

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr

Privé, F., Aschard, H., Ziyatdinov, A., & Blum, M. G. B. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty185 · Cited by 371 · see citing works

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

Couch, F. J., Wang, X., McGuffog, L., Lee, A., Olswold, C., Kuchenbaecker, K. B., Soucy, P., Fredericksen, Z., Barrowdale, D., Dennis, J., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003212 · Cited by 375 · see citing works

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease

Bryois, J., Skene, N., Hansen, T. F., Kogelman, L. J. A., Watson, H. J., Liu, Z., Adan, R. A. H., Alfredsson, L. S., Ando, T., Andreassen, O. A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0610-9 · Cited by 375 · see citing works

Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers

Lauc, G., Huffman, J. E., Pučić‐Baković, M., Zgaga, L., Adamczyk, B., Mužinić, A., Novokmet, M., Polašek, O., Gornik, O., Krištić, J., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003225 · Cited by 360 · see citing works

Quantitative variability of 342 plasma proteins in a human twin population

Liu, Y., Buil, A., Collins, B. C., Gillet, L. C., Blum, L. C., Cheng, L., Vitek, O., Mouritsen, J., Lachance, G., Spector, T. D., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145728 · Cited by 328 · see citing works

Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci

Zhernakova, A., Stahl, E. A., Trynka, G., Raychaudhuri, S., Festen, E. A. M., Franke, L., Westra, H.-J., Fehrmann, R. S. N., Kurreeman, F. A. S., Thomson, B. P., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002004 · Cited by 355 · see citing works

A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor–negative breast cancer in the general population

EMBRACE, Antoniou, A. C., Collaborators, G. S., HEBON, kConFab, SWE-BRCA, SQUAD, M., GENICA, Wang, X., Fredericksen, Z. S., et al. (2010) · Nature Genetics · doi:10.1038/ng.669 · Cited by 333 · see citing works

Evaluation of Polygenic Risk Scores for Breast and Ovarian Cancer Risk Prediction in BRCA1 and BRCA2 Mutation Carriers

Kuchenbaecker, K. B., McGuffog, L., Barrowdale, D., Lee, A., Soucy, P., Healey, S., Dennis, J., Lush, M., Robson, M., Spurdle, A., et al. (2017) · Journal of the National Cancer Institute · doi:10.1093/jnci/djw302 · Cited by 294 · see citing works

Cardiac Troponin T and Troponin I in the General Population

Welsh, P. I., Preiss, D., Hayward, C., Shah, A. S. V., McAllister, D., Briggs, A. H., Boachie, C., McConnachie, A., Padmanabhan, S., Welsh, C. E., et al. (2019) · Circulation · doi:10.1161/circulationaha.118.038529 · Cited by 329 · see citing works

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans

Liu, F., van der Lijn, F., Schurmann, C., Zhu, G., Chakravarty, M. M., Hysi, P. G., Wollstein, A., Lao, O., de Bruijne, M., Ikram, M. A., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002932 · Cited by 326 · see citing works

Application of high-dimensional feature selection: evaluation for genomic prediction in man

Bermingham, M. L., Pong‐Wong, R., Spiliopoulou, A., Hayward, C., Rudan, I., Campbell, H., Wright, A. F., Wilson, J. F., Agakov, F. V., Navarro, P., et al. (2015) · Scientific Reports · doi:10.1038/srep10312 · Cited by 320 · see citing works

The Genetic Architecture of the Human Immune System: A Bioresource for Autoimmunity and Disease Pathogenesis

Roederer, M., Quaye, L., Mangino, M., Beddall, M. H., Mahnke, Y., Chattopadhyay, P., Tosi, I., Napolitano, L., Terranova Barberio, M., Menni, C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.02.046 · Cited by 296 · see citing works

Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes

Small, K. S., Grundberg, E., Soranzo, N., Ahmadi, K. R., Spector, T. D., Shin, S., Deloukas, P., Hedman, Å. K., Lindgren, C. M., McCarthy, M. I., et al. (2011) · Nature Genetics · doi:10.1038/ng.833 · Cited by 319 · see citing works

Contribution of genetics to visceral adiposity and its relation to cardiovascular and metabolic disease

Karlsson, T., Rask‐Andersen, M., Pan, G., Höglund, J., Wadelius, C., Ek, W. E., & Johansson, Å. (2019) · Nature Medicine · doi:10.1038/s41591-019-0563-7 · Cited by 318 · see citing works

A genome-wide association study of anorexia nervosa

Perica, V. B., Franklin, C. S., Floyd, J. A. B., Thornton, L. M., Huckins, L. M., Southam, L., Rayner, N. W., Tachmazidou, I., Klump, K. L., Treasure, J. L., et al. (2014) · Molecular Psychiatry · doi:10.1038/mp.2013.187 · Cited by 314 · see citing works

New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism

The Meta-Analyses of Glucose- and Insulin-related traits Consortium (MAGIC), Horikoshi, M., Early Growth Genetics (EGG) Consortium, Yaghootkar, H., Mook-Kanamori, D. O., Sovio, U., Taal, H. R., Hennig, B. J., Bradfield, J. P., St Pourcain, B., et al. (2013) · Nature Genetics · doi:10.1038/ng.2477 · Cited by 309 · see citing works

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

Scheben, A., Batley, J., & Edwards, D. (2016) · Plant Biotechnology Journal · doi:10.1111/pbi.12645 · Cited by 306 · see citing works

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

Patin, É., Hasan, M., Bergstedt, J., Rouilly, V., Libri, V., Urrutia, A., Alanio, C., Šćepanović, P., Hammer, C., Jönsson, F., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0049-7 · Cited by 301 · see citing works

Identification of heart rate–associated loci and their effects on cardiac conduction and rhythm disorders

den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J. J. M., Peal, D. S., Evans, D. M., Nolte, I. M., Segrè, A. V., Hólm, H., Handsaker, R. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2610 · Cited by 296 · see citing works

Gender-specific pathway differences in the human serum metabolome

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Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study

Kote‐Jarai, Z., The UK ProtecT Study Collaborators, T. A. P. C. B., Olama, A. A. A., Giles, G. G., Severi, G., Schleutker, J., Weischer, M., Campa, D., Ríboli, E., Key, T. J., et al. (2011) · Nature Genetics · doi:10.1038/ng.882 · Cited by 289 · see citing works

The Rotterdam Study: 2012 objectives and design update

Albert Hofman, D., van Duijn, C. M., Franco, O. H., Ikram, M. A., Janssen, H. L. A., Klaver, C. C. W., Kuipers, E. J., Nijsten, T. E. C., Stricker, B. H. C., Tiemeier, H. W., et al. (2011) · European Journal of Epidemiology · doi:10.1007/s10654-011-9610-5 · Cited by 289 · see citing works

Exome array analysis identifies new loci and low-frequency variants influencing insulin processing and secretion

Huyghe, J. R., Jackson, A., Fogarty, M. P., Buchkovich, M. L., Stančáková, A., Stringham, H. M., Sim, X., Yang, L., Fuchsberger, C., Cederberg, H., et al. (2012) · Nature Genetics · doi:10.1038/ng.2507 · Cited by 275 · see citing works

NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium

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Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

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Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

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CUBN Is a Gene Locus for Albuminuria

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genome-wide association studies in R

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