Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442 · see citing works

A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works

The International HapMap Project

†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057 · see citing works

A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains

Baum, L. E., Petrie, T., Soules, G., & Weiss, N. (1970) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177697196 · Cited by 4,299 · see citing works

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

Howie, B. N., Donnelly, P., & Marchini, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000529 · Cited by 3,928 · see citing works

A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data

Stephens, M., & Donnelly, P. (2003) · The American Journal of Human Genetics · doi:10.1086/379378 · Cited by 3,492 · see citing works

Integrating common and rare genetic variation in diverse human populations

The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026 · see citing works

A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants

Scott, L. J., Mohlke, K. L., Bonnycastle, L. L., Willer, C. J., Li, Y., Duren, W. L., Erdos, M. R., Stringham, H. M., Chines, P. S., Jackson, A. U., et al. (2007) · Science · doi:10.1126/science.1142382 · Cited by 2,753 · see citing works

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 · see citing works

Design of the Women’s Health Initiative Clinical Trial and Observational Study

The Women’s Health Initiative Study Group (1998) · Controlled Clinical Trials · doi:10.1016/s0197-2456(97)00078-0 · Cited by 2,580 · see citing works

A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase

Scheet, P. A., & Stephens, M. (2006) · The American Journal of Human Genetics · doi:10.1086/502802 · Cited by 1,949 · see citing works

A linear complexity phasing method for thousands of genomes

Delaneau, O., Marchini, J., & Zagury, J.-F. (2012) · Nature Methods · doi:10.1038/nmeth.1785 · Cited by 1,850 · see citing works

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

Li, Y., Willer, C. J., Ding, J., Scheet, P., & Abecasis, G. R. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20533 · Cited by 1,843 · see citing works

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

Browning, B. L., & Browning, S. R. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.01.005 · Cited by 1,640 · see citing works

Genotype imputation for genome-wide association studies

Marchini, J., & Howie, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2796 · Cited by 1,597 · see citing works

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

Nair, R. P., Duffin, K. C., Helms, C. A., Ding, J., Stuart, P. E., Goldgar, D. E., Gudjonsson, J. E., Li, Y., Tejasvi, T., Feng, B., et al. (2009) · Nature Genetics · doi:10.1038/ng.311 · Cited by 1,414 · see citing works

Genotype Imputation

Li, Y., Willer, C., Sanna, S., & Abecasis, G. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164242 · Cited by 990 · see citing works

Use of population isolates for mapping complex traits

Peltonen, L., Palotie, A. V., & Lange, K. L. (2000) · Nature Reviews Genetics · doi:10.1038/35042049 · Cited by 455 · see citing works

Detection of sharing by descent, long-range phasing and haplotype imputation

Kong, A., Masson, G., Frigge, M. L., Gylfason, A., Zusmanovich, P., Thorleifsson, G., Olason, P. I., Ingason, A., Steinberg, S., Rafnar, T., et al. (2008) · Nature Genetics · doi:10.1038/ng.216 · Cited by 447 · cited 2× · see citing works

Family-Based Association Tests for Genomewide Association Scans

Chen, W., & Abecasis, G. R. (2007) · The American Journal of Human Genetics · doi:10.1086/521580 · Cited by 398 · see citing works

A Comparison of Phasing Algorithms for Trios and Unrelated Individuals

Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro, H. M., Abecasis, G. R., et al. (2006) · The American Journal of Human Genetics · doi:10.1086/500808 · Cited by 341 · see citing works

New models of collaboration in genome-wide association studies: the Genetic Association Information Network

Manolio, T. A., Rodriguez, L. L., Brooks, L., Guttmacher, A. E., Harris, E. L., Collins, F. S., Abecasis, G. R., Ballinger, D. G., Frazer, K. A., Daly, M. J., et al. (2007) · Nature Genetics · doi:10.1038/ng2127 · Cited by 316 · see citing works

Handling Marker-Marker Linkage Disequilibrium: Pedigree Analysis with Clustered Markers

Abecasis, G. R., & Wigginton, J. E. (2005) · The American Journal of Human Genetics · doi:10.1086/497345 · Cited by 264 · see citing works

In silico method for inferring genotypes in pedigrees

Burdick, J. T., Chen, W., Abecasis, G. R., & Cheung, V. G. (2006) · Nature Genetics · doi:10.1038/ng1863 · Cited by 145 · see citing works

Isolates and their potential use in complex gene mapping efforts

Varilo, T., & Peltonen, L. (2004) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2004.04.008 · Cited by 121 · see citing works

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works

The UK Biobank resource with deep phenotyping and genomic data

Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., Motyer, A., Vukcevic, D., Delaneau, O., O’Connell, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0579-z · Cited by 8,876 · see citing works

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004383 · Cited by 4,261 · see citing works

Next-generation genotype imputation service and methods

Das, S., Forer, L., Schönherr, S., Sidore, C., Locke, A. E., Kwong, A., Vrieze, S. I., Chew, E. Y., Levy, S., McGue, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3656 · Cited by 4,190 · see citing works

10 Years of GWAS Discovery: Biology, Function, and Translation

Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.06.005 · Cited by 3,719 · see citing works

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

Alzheimer Disease Genetics Consortium (ADGC), Kunkle, B. W., The European Alzheimer’s Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, P. A. E. R. F. A. D. C. (., Grenier-Boley, B., Sims, R., Bis, J. C., Damotte, V., Naj, A. C., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0358-2 · Cited by 2,946 · see citing works

A reference panel of 64,976 haplotypes for genotype imputation

the Haplotype Reference Consortium (2016) · Nature Genetics · doi:10.1038/ng.3643 · Cited by 2,836 · see citing works

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

the CARDIoGRAMplusC4D Consortium (2015) · Nature Genetics · doi:10.1038/ng.3396 · Cited by 2,447 · see citing works

Identification of common genetic risk variants for autism spectrum disorder

Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium, Grove, J., BUPGEN, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, 23andMe Research Team, Ripke, S., Als, T. D., Mattheisen, M., Walters, R. K., Won, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0344-8 · Cited by 2,421 · see citing works

A One-Penny Imputed Genome from Next-Generation Reference Panels

Browning, B. L., Zhou, Y., & Browning, S. R. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.07.015 · Cited by 2,081 · see citing works

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

23andMe Research Team, Liu, M., Psychiatry, H. A.-I., Jiang, Y., Wedow, R., Li, Y., Brazel, D. M., Chen, F., Datta, G., Davila-Velderrain, J., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0307-5 · Cited by 1,896 · see citing works

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson’s disease

International Parkinson's Disease Genomics Consortium (IPDGC), Nalls, M. A., Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI), 23andMe, GenePD, NeuroGenetics Research Consortium (NGRC), Hussman Institute of Human Genomics (HIHG), Investigator, T. A. J. D., (CHARGE), C. F. H. A. A. R. I. G. E., North American Brain Expression Consortium (NABEC), et al. (2014) · Nature Genetics · doi:10.1038/ng.3043 · Cited by 1,895 · see citing works

A gene-based association method for mapping traits using reference transcriptome data

Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., Eyler, A. E., Denny, J. C., Nicolae, D. L., Cox, N. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3367 · Cited by 1,762 · see citing works

Large-scale association analyses identify host factors influencing human gut microbiome composition

Kurilshikov, A., Medina-Gomez, C., Bacigalupe, R., Radjabzadeh, D., Wang, J., Demirkan, A., Le Roy, C. I., Raygoza Garay, J. A., Finnicum, C. T., Liu, X., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00763-1 · Cited by 1,786 · see citing works

Reference-based phasing using the Haplotype Reference Consortium panel

Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,894 · see citing works

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

GERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552 · see citing works

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

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 · see citing works

Association analysis identifies 65 new breast cancer risk loci

Michailidou, K., Lindström, S., Dennis, J., Beesley, J., Hui, S., Kar, S., Lemaçon, A., Soucy, P., Glubb, D. M., Rostamianfar, A., et al. (2017) · Nature · doi:10.1038/nature24284 · Cited by 1,380 · see citing works

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Lee, P. H., Anttila, V., Won, H., Feng, Y.-C. A., Rosenthal, J., Zhu, Z., Tucker-Drob, E. M., Nivard, M. G., Grotzinger, A. D., Posthuma, D., et al. (2019) · Cell · doi:10.1016/j.cell.2019.11.020 · Cited by 1,381 · see citing works

Improved whole-chromosome phasing for disease and population genetic studies

Delaneau, O., Zagury, J., & Marchini, J. (2012) · Nature Methods · doi:10.1038/nmeth.2307 · Cited by 1,309 · see citing works

Genotype Imputation with Millions of Reference Samples

Browning, B. L., & Browning, S. R. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.020 · Cited by 1,149 · see citing works

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

ARUK Consortium, Sims, R., GERAD/PERADES, C., van der Lee, S. J., Naj, A. C., Bellenguez, C., Badarinarayan, N., Jakobsdottir, J., Kunkle, B. W., Boland, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3916 · Cited by 1,126 · see citing works

A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci

Chang, D., Nalls, M. A., Hallgrímsdóttir, I. B., Hunkapiller, J., van der Brug, M., Cai, F., International Parkinson's Disease Genomics Consortium, 23andMe Research Team, Kerchner, G. A., Ayalon, G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3955 · Cited by 1,112 · see citing works

Gene expression elucidates functional impact of polygenic risk for schizophrenia

Fromer, M., Roussos, P., Sieberts, S. K., Johnson, J. S., Kavanagh, D. H., Perumal, T. M., Ruderfer, D. M., Oh, E. C., Topol, A., Shah, H. R., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4399 · Cited by 1,091 · see citing works

A new approach for efficient genotype imputation using information from relatives

Sargolzaei, M., Chesnais, J. P., & Schenkel, F. S. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-478 · Cited by 1,043 · see citing works

Rare-Variant Association Analysis: Study Designs and Statistical Tests

Lee, S., Abecasis, G. R., Boehnke, M., & Lin, X. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.06.009 · Cited by 1,042 · see citing works

Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity

Collaborative Association Study of Psoriasis (CASP), Tsoi, L. C., Genetic Analysis of Psoriasis Consortium, Psoriasis Association Genetics Extension, Wellcome Trust Case Control Consortium 2, Spain, S. L., Knight, J., Ellinghaus, E., Stuart, P. E., Capon, F., et al. (2012) · Nature Genetics · doi:10.1038/ng.2467 · Cited by 1,024 · see citing works

Exome sequencing and analysis of 454,787 UK Biobank participants

Backman, J., Li, A. H., Marcketta, A., Sun, D., Mbatchou, J. S., Kessler, M. D., Benner, C., Liu, D., Locke, A. E., Balasubramanian, S., et al. (2021) · Nature · doi:10.1038/s41586-021-04103-z · Cited by 915 · see citing works

Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk

Chornokur, G., Lin, H., Tyrer, J. P., Lawrenson, K., Dennis, J., Amankwah, E. K., Qu, X., Tsai, Y.-Y., Jim, H., Chen, Z., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128106 · Cited by 907 · see citing works

Fast two-stage phasing of large-scale sequence data

Browning, B. L., Tian, X., Zhou, Y., & Browning, S. R. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.08.005 · Cited by 905 · see citing works

Common genetic variants influence human subcortical brain structures

Initiative, T. A. D. N., Hibar, D. P., The CHARGE Consortium, EPIGEN, IMAGEN, SYS, Stein, J. L., Renteria, M. E., Arias-Vasquez, A., Desrivières, S., et al. (2015) · Nature · doi:10.1038/nature14101 · Cited by 858 · see citing works

Cohort Profile: LifeLines, a three-generation cohort study and biobank.

Scholtens, S., Smidt, N., Swertz, M. A., Bakker, S. J., Dotinga, A., Vonk, J. M., van Dijk, F., van Zon, S. K., Wijmenga, C., Wolffenbuttel, B. H., et al. (2015) · International Journal of Epidemiology · doi:10.1093/ije/dyu229 · Cited by 847 · see citing works

Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle

Daetwyler, H. D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brøndum, R. F., Liao, X., Djari, A., Rodriguez, S. C., Grohs, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.3034 · Cited by 838 · see citing works

Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations

Peterson, R. E., Kuchenbaecker, K., Walters, R. K., Chen, C.-Y., Popejoy, A. B., Periyasamy, S., Lam, M., Iyegbe, C., Strawbridge, R. J., Brick, L., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.051 · Cited by 797 · see citing works

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

Study, T. L. C., Yang, J., Bakshi, A., Zhu, Z., Hemani, G., Vinkhuyzen, A. A. E., Lee, S. H., Robinson, M. R., Perry, J. R. B., Nolte, I. M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3390 · Cited by 745 · see citing works

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

Scott, R. A., Scott, L. J., Mägi, R., Marullo, L., Gaulton, K. J., Kaakinen, M., Pervjakova, N., Pers, T. H., Johnson, A. D., Eicher, J. D., et al. (2017) · Diabetes · doi:10.2337/db16-1253 · Cited by 736 · see citing works

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine

Gormley, P., Anttila, V., Winsvold, B. S., Palta, P., Esko, T., Pers, T. H., Farh, K.-H., Cuenca-León, E., Muona, M., Furlotte, N. A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3598 · Cited by 681 · see citing works

Comparative genetic architectures of schizophrenia in East Asian and European populations

Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lam, M., Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and the Netherlands (GREAT-CN), Chen, C.-Y., Li, Z., Martin, A. R., Bryois, J., Ma, X., Gaspar, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0512-x · Cited by 655 · see citing works

minimac2: faster genotype imputation

Fuchsberger, C., Abecasis, G. R., & Hinds, D. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu704 · Cited by 622 · see citing works

Genome-wide genetic data on ~500,000 UK Biobank participantsPreprint

Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., Motyer, A., Vukcevic, D., Delaneau, O., O’Connell, J., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/166298 · Cited by 606 · see citing works

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

Klarin, D. M., Program, T. V. M. V., Damrauer, S. M., Cho, K., Sun, Y. V., Teslovich, T. M., Honerlaw, J. P., GAGNON, D. R., DuVall, S. L., Li, J., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0222-9 · Cited by 594 · see citing works

Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

BOCS, Michailidou, K., kConFab Investigators, AOCS Group, NBCS, GENICA Network, Beesley, J., Lindström, S., Canisius, S., Dennis, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3242 · Cited by 593 · see citing works

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

Evangelou, E., & Ioannidis, J. P. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3472 · Cited by 596 · see citing works

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

O'Connell, J., Gurdasani, D., Delaneau, O., Pirastu, N., Ulivi, S., Cocca, M., Traglia, M., Huang, J., Huffman, J. E., Rudan, I., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004234 · Cited by 593 · see citing works

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Qin, Y., Havulinna, A. S., Liu, Y., Jousilahti, P., Ritchie, S. C., Tokolyi, A., Sanders, J. G., Valsta, L., Brożyńska, M., Zhu, Q., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00991-z · Cited by 586 · see citing works

Meta-analysis of genome-wide association studies of anxiety disorders

Otowa, T., Hek, K., Lee, M., Byrne, E. M., Mirza, S. S., Nivard, M. G., Bigdeli, T. B., Aggen, S. H., Adkins, D. E., Wolen, A. R., et al. (2016) · Molecular Psychiatry · doi:10.1038/mp.2015.197 · Cited by 558 · see citing works

A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations

Bønnelykke, K., Abou‐Sleiman, P. M., Nielsen, K. R., Kreiner‐Møller, E., Mercader, J. M., Belgrave, D. C. M., den Dekker, H. T., Husby, A., Sevelsted, A., Tellez, G. F., et al. (2013) · Nature Genetics · doi:10.1038/ng.2830 · Cited by 569 · see citing works

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.10.004 · Cited by 544 · see citing works

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z. A., Pacis, A., Dumaine, A., Grenier, J.-C., Freiman, A., Sams, A. J., Hebert, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.025 · Cited by 512 · see citing works

Menopause accelerates biological aging

Levine, M. E., Lu, A. T.-H., Chen, B. H., Hernandez, D. G., Singleton, A., Ferrucci, L., Bandinelli, S., Salfati, E., Manson, J. E., Quach, A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604558113 · Cited by 507 · see citing works

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldner, F., Stelzer, Y., Shivalila, C., Abraham, B. J., Latourelle, J. C., Barrasa, M. I., Goldmann, J. E., Myers, R. H., Young, R. A., & Jaenisch, R. (2016) · Nature · doi:10.1038/nature17939 · Cited by 496 · see citing works

Genome-wide associations for birth weight and correlations with adult disease

Horikoshi, M., Beaumont, R. N., Day, F. R., Warrington, N. M., Kooijman, M. N., Fernandez-Tajes, J. J., Feenstra, B., van Zuydam, N. R., Gaulton, K. J., Grarup, N., et al. (2016) · Nature · doi:10.1038/nature19806 · Cited by 495 · see citing works

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

Voight, B. F., Kang, H. M., Ding, J., Palmer, C. D., Sidore, C., Chines, P. S., Burtt, N. P., Fuchsberger, C., Li, Y., Erdmann, J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002793 · Cited by 464 · see citing works

Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer’s disease related cognitive functioning

Levine, M. E., Lu, A. T., Bennett, D. A., & Horvath, S. (2015) · Aging · doi:10.18632/aging.100864 · Cited by 455 · see citing works

Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer

Wang, Y., McKay, J., Rafnar, Þ., Wang, Z., Timofeeva, M. N., Broderick, P., Zong, X., Laplana, M., Wei, Y., Han, Y., et al. (2014) · Nature Genetics · doi:10.1038/ng.3002 · Cited by 453 · see citing works

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

McVicker, G., van de Geijn, B., Degner, J. F., Cain, C. E., Banovich, N. E., Raj, A., Lewellen, N., Myrthil, M., Gilad, Y., & Pritchard, J. K. (2013) · Science · doi:10.1126/science.1242429 · Cited by 443 · see citing works

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H. H., Johnson, W. E., et al. (2013) · Genome Medicine · doi:10.1186/gm432 · Cited by 443 · see citing works

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders

Lo, M., Hinds, D. A., Tung, J. Y., Franz, C. E., Fan, C.-C., Wang, Y., Smeland, O. B., Schork, A. J., Holland, D., Kauppi, K., et al. (2016) · Nature Genetics · doi:10.1038/ng.3736 · Cited by 452 · see citing works

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes

Mahajan, A., Wessel, J., Willems, S. M., Zhao, W., Robertson, N. R., Chu, A. Y., Gan, W., Kitajima, H., Taliun, D., Rayner, N. W., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0084-1 · Cited by 442 · see citing works

Variants in the ATP-Binding Cassette Transporter (ABCA7), Apolipoprotein E ϵ4, and the Risk of Late-Onset Alzheimer Disease in African Americans

Reitz, C., Jun, G., Naj, A., Rajbhandary, R., Vardarajan, B. N., Wang, L.-S., Valladares, O., Lin, C.-F., Larson, E. B., Graff-Radford, N. R., et al. (2013) · JAMA · doi:10.1001/jama.2013.2973 · Cited by 431 · see citing works

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

ABCTB Investigators, Milne, R. L., EMBRACE, Collaborators, G. S., HEBON, kConFab/AOCS Investigators, Collaborators, N., Kuchenbaecker, K. B., Michailidou, K., Beesley, J., et al. (2017) · Nature Genetics · doi:10.1038/ng.3785 · Cited by 412 · see citing works

Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

The PRACTICAL Consortium, Day, F. R., kConFab Investigators, AOCS Investigators, Scotland, G., EPIC-InterAct Consortium, Study, L. C., Ruth, K. S., Thompson, D. J., Lunetta, K. L., et al. (2015) · Nature Genetics · doi:10.1038/ng.3412 · Cited by 402 · see citing works

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

Gaulton, K. J., Ferreira, T. C., Lee, Y., Raimondo, A., Mägi, R., Reschen, M. E., Mahajan, A., Locke, A. E., Rayner, N. W., Robertson, N., et al. (2015) · Nature Genetics · doi:10.1038/ng.3437 · Cited by 390 · see citing works

Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study

Hou, L., Heilbronner, U., Degenhardt, F., Adli, M., Akiyama, K., Akula, N., Ardau, R., Arias, B., Backlund, L., Banzato, C. E. M., et al. (2016) · The Lancet · doi:10.1016/s0140-6736(16)00143-4 · Cited by 388 · see citing works

Prioritizing diversity in human genomics research

Hindorff, L. A., Bonham, V. L., Brody, L. C., Ginoza, M. E. C., Hutter, C. M., Manolio, T. A., & Green, E. D. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.89 · Cited by 386 · see citing works

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

Tsoi, L. C., Stuart, P. E., Tian, C., Gudjonsson, J. E., Das, S., Zawistowski, M., Ellinghaus, E., Barker, J. N., Chandran, V., Dand, N., et al. (2017) · Nature Communications · doi:10.1038/ncomms15382 · Cited by 384 · see citing works

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

Sidore, C., Busonero, F., Maschio, A., Porcu, E., Naitza, S., Żołędziewska, M., Mulas, A., Pistis, G., Steri, M., Danjou, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3368 · Cited by 376 · see citing works

Identification of 55,000 Replicated DNA Methylation QTL

McRae, A. F., Marioni, R. E., Shah, S. H., Yang, J., Powell, J. E., Harris, S. E., Gibson, J., Henders, A. K., Bowdler, L. M., Painter, J. N., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-35871-w · Cited by 355 · see citing works

The European Genome-phenome Archive of human data consented for biomedical research

Lappalainen, I., Almeida, J. P., Kumanduri, V., Senf, A., Spalding, D., Ur-Rehman, S., Saunders, G. I., Kandasamy, J., Cáccamo, M., Leinonen, R., et al. (2015) · Nature Genetics · doi:10.1038/ng.3312 · Cited by 359 · see citing works

Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error

Tedja, M. S., Wojciechowski, R., Hysi, P. G., Eriksson, N., Furlotte, N. A., Verhoeven, V. J. M., Iglesias, A. I., Meester‐Smoor, M. A., Tompson, S. W. J., Fan, Q., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0127-7 · Cited by 352 · see citing works

An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation

Hannon, E., Dempster, E., Viana, J., Burrage, J., Smith, A. R., Macdonald, R., St Clair, D., Mustard, C., Breen, G., Therman, S., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-1041-x · Cited by 349 · see citing works

Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis

Cho, M. H., McDonald, M., Zhou, X., Mattheisen, M., Castaldi, P. J., Hersh, C. P., DeMeo, D. L., Sylvia, J. S., Ziniti, J. P., Laird, N. M., et al. (2014) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(14)70002-5 · Cited by 348 · see citing works

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Huang, J., Howie, B., McCarthy, S., Memari, Y., Walter, K., Min, J. L., Danecek, P., Malerba, G., Trabetti, E., Zheng, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms9111 · Cited by 346 · see citing works

Methylation quantitative trait loci in the developing brain and their enrichment in schizophrenia-associated genomic regions

Hannon, E., Spiers, H., Viana, J., Pidsley, R., Burrage, J., Murphy, T. M., Troakes, C., Turecki, G., O'Donovan, M., Schalkwyk, L., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4182 · Cited by 297 · see citing works

Fast and accurate long-range phasing in a UK Biobank cohort

Loh, P.-R., Palamara, P. F., & Price, A. L. (2016) · Nature Genetics · doi:10.1038/ng.3571 · Cited by 342 · see citing works

Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

Carrot‐Zhang, J., Chambwe, N., Damrauer, J. S., Knijnenburg, T., Robertson, A. G., Yau, C. S. F., Zhou, W., Berger, A. C., Huang, K., Newberg, J. Y., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.012 · Cited by 328 · see citing works

Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses

Als, T. D., Kurki, M., Grove, J., Voloudakis, G., Therrien, K., Tasanko, E. M., Nielsen, T. T., Naamanka, J., Veerapen, K., Levey, D. F., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02352-1 · Cited by 321 · see citing works

GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person

Hu, Y., Shmygelska, A., Tran, D., Eriksson, N., Tung, J. Y., & Hinds, D. A. (2016) · Nature Communications · doi:10.1038/ncomms10448 · Cited by 321 · see citing works

Genome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture

Stuart, P. E., Nair, R. P., Tsoi, L. C., Tejasvi, T., Das, S., Kang, H. M., Ellinghaus, E., Chandran, V., Callis-Duffin, K. P., Ike, R. W., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.10.019 · Cited by 321 · see citing works

Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation

Hoffmann, T. J., Ehret, G., Nandakumar, P., Ranatunga, D. K., Schaefer, C. A., Kwok, P., Iribarren, C., Chakravarti, A., & RISCH, N. J. (2016) · Nature Genetics · doi:10.1038/ng.3715 · Cited by 320 · see citing works

RICOPILI: Rapid Imputation for COnsortias PIpeLIne

Lam, M., Awasthi, S., Watson, H. J., Goldstein, J., Panagiotaropoulou, G., Trubetskoy, V., Karlsson, R., Frei, O., Fan, C.-C., De Witte, W., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz633 · Cited by 315 · see citing works

Apparent latent structure within the UK Biobank sample has implications for epidemiological analysis

Haworth, S., Mitchell, R., Corbin, L., Wade, K. H., Dudding, T., Budu-Aggrey, A., Carslake, D., Hemani, G., Paternoster, L., Smith, G. D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08219-1 · Cited by 314 · see citing works

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Moss, D. J. H., Pardiñas, A. F., Langbehn, D., Lo, K., Leavitt, B. R., Roos, R., Durr, A., Mead, S., Coleman, A., Santos, R. D., et al. (2017) · The Lancet Neurology · doi:10.1016/s1474-4422(17)30161-8 · Cited by 312 · see citing works

Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways

Huang, B., Chen, Z., Geng, L., Wang, J., Liang, H., Cao, Y., Chen, H., Huang, W., Su, M., Wang, H., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.027 · Cited by 312 · see citing works

Population genetics of the coral Acropora millepora : Toward genomic prediction of bleaching

Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N. E., Shepherd, J., Sarre, L. A., Peng, J., Liao, Y., Pickrell, J. K., Andolfatto, P., et al. (2020) · Science · doi:10.1126/science.aba4674 · Cited by 287 · see citing works

A large electronic-health-record-based genome-wide study of serum lipids

Hoffmann, T. J., Theusch, E., Haldar, T., Ranatunga, D. K., Jorgenson, E., Medina, M. W., Kvale, M. N., Kwok, P., Schaefer, C. A., Krauss, R. M., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0064-5 · Cited by 286 · see citing works

The clinical and genetic features of COPD-asthma overlap syndrome

Hardin, M. E., Cho, M., McDonald, M., Beaty, T. H., Ramsdell, J., Bhatt, S. P., van Beek, E. J. R., Make, B. J., Crapo, J. D., Silverman, E. K., et al. (2014) · European Respiratory Journal · doi:10.1183/09031936.00216013 · Cited by 294 · see citing works

Identification of nine new susceptibility loci for endometrial cancer

O’Mara, T. A., Glubb, D. M., Amant, F. C., Annibali, D., Ashton, K. A., Attia, J., Auer, P. L., Beckmann, M. W., Black, A., Bolla, M. K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05427-7 · Cited by 285 · see citing works

Genome-wide association study of peripheral artery disease in the Million Veteran Program

Program, V. M. V., Klarin, D. M., Lynch, J. A., Aragam, K. G., Chaffin, M. D., Assimes, T. L., Huang, J., Lee, K. M., Shao, Q., Huffman, J. E., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0492-5 · Cited by 286 · see citing works

Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts

Rashkin, S. R., Graff, R. E., Kachuri, L., Thai, K. K., Alexeeff, S., Blatchins, M. A., Cavazos, T. B., Corley, D. A., Emami, N. C., Hoffman, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18246-6 · Cited by 278 · see citing works

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Franzén, O., Ermel, R., Cohain, A., Akers, N. K., Di Narzo, A., Talukdar, H. A., Foroughi-Asl, H., Giambartolomei, C., Fullard, J. F., Sukhavasi, K., et al. (2016) · Science · doi:10.1126/science.aad6970 · Cited by 288 · see citing works

A direct test of the diathesis-stress model for depression

Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Colodro-Conde, L., Couvy-Duchesne, B., Zhu, G., Coventry, W. L., Byrne, E. M., Gordon, S., Wright, M. J., Montgomery, G. W., Madden, P. A. F., et al. (2018) · Molecular Psychiatry · doi:10.1038/mp.2017.130 · Cited by 285 · see citing works

Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution

Mägi, R., Horikoshi, M., Sofer, T., Mahajan, A., Kitajima, H., Franceschini, N., McCarthy, M. I., & Morris, A. P. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx280 · Cited by 283 · see citing works

Rapid genotype imputation from sequence without reference panels

Davies, R. W., Jonathan Flint, C., Myers, S. R., & Mott, R. (2016) · Nature Genetics · doi:10.1038/ng.3594 · Cited by 274 · see citing works

Genome-wide association study of eosinophilic granulomatosis with polyangiitis reveals genomic loci stratified by ANCA status

Lyons, P., Peters, J. E., Alberici, F., Liley, J., Coulson, R., Astle, W. J., Baldini, C., Bonatti, F., Cid, M. C., Elding, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12515-9 · Cited by 285 · see citing works

Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma

Bailey, J. N. C., Loomis, S. J., Kang, J. H., Allingham, R. R., Gharahkhani, P., Khor, C. C., Burdon, K. P., Aschard, H., Chasman, D. I., Igo, R. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3482 · Cited by 273 · see citing works

Genetically Predicted Body Mass Index and Breast Cancer Risk: Mendelian Randomization Analyses of Data from 145,000 Women of European Descent

Guo, Y. P., Andersen, S. W., Shu, X., Michailidou, K., Bolla, M. K., Wang, Q., García‐Closas, M., Milne, R. L., Schmidt, M. K., Chang-Claude, J. C., et al. (2016) · PLoS Medicine · doi:10.1371/journal.pmed.1002105 · Cited by 272 · see citing works

The <i>MS4A</i> gene cluster is a key modulator of soluble TREM2 and Alzheimer’s disease risk

Deming, Y., Filipello, F., Cignarella, F., Cantoni, C., Hsu, S., Mikesell, R., Li, Z., Del-Aguila, J. L., Dube, U., Farias, F. G., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aau2291 · Cited by 271 · see citing works

Contribution of genetic variation to transgenerational inheritance of DNA methylation

McRae, A. F., Powell, J. E., Henders, A. K., Bowdler, L. M., Hemani, G., Shah, S. H., Painter, J. N., Martin, N. G., Visscher, P. M., & Montgomery, G. W. (2014) · Genome biology · doi:10.1186/gb-2014-15-5-r73 · Cited by 270 · see citing works

Germ line variants predispose to both JAK2 V617F clonal hematopoiesis and myeloproliferative neoplasms

Hinds, D. A., Barnholt, K. E., Mesa, R. A., Kiefer, A. K., Do, C. B., Eriksson, N., Mountain, J. L., Francke, U., Tung, J. Y., Nguyen, H. (., et al. (2016) · Blood · doi:10.1182/blood-2015-06-652941 · Cited by 267 · see citing works

EagleImp : fast and accurate genome-wide phasing and imputation in a single tool

Wienbrandt, L., & Ellinghaus, D. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac637 · Cited by 13 · see citing works

Genotype imputation methods for next generation datasets

Rubinacci, S. (2020) · Oxford University Research Archive (ORA) (University of Oxford) · doi:10.5287/ora-e2mwgvg6r

Marchini J: A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009

Howie, B. N., Donnelly, P., & Marchini, J. (2013)

A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels

Faux, P., & Druet, T. (2017) · Genetics Selection Evolution · doi:10.1186/s12711-017-0321-6 · Cited by 5 · see citing works

Comparing performance of modern genotype imputation methods in different ethnicities

Roshyara, N. R., Horn, K., Kirsten, H., Ahnert, P., & Scholz, M. R. (2016) · Scientific Reports · doi:10.1038/srep34386 · Cited by 44 · see citing works