The DOI matches its Crossref record; 59 of the 60 references it cites were found in a registry or an index.
A second generation human haplotype map of over 3.1 million SNPs
Open accessAbstract
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The fine-scale pattern of LD in humans confirms that the human genome is comprised of haplotype blocks within which most or all SNPs are in high LD21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [21]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The second generation HapMap published recently characterized 3.1 million SNPs in the same group of individuals21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [21]
The cited source says what the claim attributes to it.
In the citing paper
“that the number of inferred ancestral recombination events per genomic window agrees with a previously published population recombination map (17) (fig. S20B; Spearman’s rho = 0.46; P < 2.2 × 10−16), as expected.”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [17]
The cited source says what the claim attributes to it.
In the citing paper
“As expected, the tag SNP allele frequencies in our samples mirrored previously described distributions in major geographic groups (Lamason et al. 2005;Yuasa et al. 2006;Frazer et al. 2007;Miller et al. 2007;Norton et al. 2007;Soejima and Koda 2007) (table 1).”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Frazer et al. 2007
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Haplotype blocks vary somewhat among human populations — they tend to be somewhat shorter in African populations15,20,21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [21]
Experimental — accuracy not yet measured
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Previous studies using several population samples from different continents have shown that, unlike SLC45A2, derived alleles at SLC24A5, TYRP1, and KITLG are present at low frequencies in some sub-Saharan populations (table 1, see also Yuasa et al. 2006;Frazer et al. 2007;Norton et al. 2007;Soejima and Koda 2007;Coop et al. 2009;Pickrell et al. 2009).”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Frazer et al. 2007
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.1111/j.1558-5646.1984.tb05657.x · Cited by 18,909
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248
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
Self-citationThe 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
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
Self-citationGlobal variation in copy number in the human genome
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., et al. (2006) · Nature · doi:10.1038/nature05329 · Cited by 4,377
PANTHER: A Library of Protein Families and Subfamilies Indexed by FunctionPreprint
Thomas, P. D., Campbell, M. J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., & Narechania, A. (2003) · Genome Research · doi:10.1101/gr.772403 · Cited by 2,979
A Map of Recent Positive Selection in the Human Genome
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,925
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
Research works printed but not linked: 1
- Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007) · DOI · Paper page
Cited by
Sorted by citations
Items 501–600 of 1,030
McEvoy, B. P., & Visscher, P. M. (2009) · Economics & Human Biology · doi:10.1016/j.ehb.2009.09.005 · Cited by 175
FLAGS, frequently mutated genes in public exomes
Shyr, C., Tarailo‐Graovac, M., Gottlieb, M., Lee, J. J. Y., van Karnebeek, C., & Wasserman, W. W. (2014) · BMC Medical Genomics · doi:10.1186/s12920-014-0064-y · Cited by 174
Current genetic methodologies in the identification of disaster victims and in forensic analysis
Ziętkiewicz, E., Witt, M. M., Daca‐Roszak, P., Żebracka‐Gala, J., Goniewicz, M., Jarząb, B., & Witt, M. (2011) · Journal of Applied Genetics · doi:10.1007/s13353-011-0068-7 · Cited by 174
Hofer, T., Ray, N., Wegmann, D., & Excoffier, L. (2008) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2008.00489.x · Cited by 173
Singapore Genome Variation Project: A haplotype map of three Southeast Asian populationsPreprint
Teo, Y., Sim, X., Ong, R. T., Tan, A. K. S., Chen, J., Tantoso, E., Small, K. S., Ku, C., Lee, E. J. D., Seielstad, M. T., et al. (2009) · Genome Research · doi:10.1101/gr.095000.109 · Cited by 173
Genovese, G., Tonna, S. J., Knob, A. U., Appel, G. B., Katz, A., Bernhardy, A. J., Needham, A. W., Lazarus, R. M., & Pollak, M. R. (2010) · Kidney International · doi:10.1038/ki.2010.251 · Cited by 172
Little, J., Higgins, J. P. T., Ioannidis, J. P. A., Moher, D., Gagnon, F., von Elm, E. B., Khoury, M. J., Cohen, B., Smith, G. D., Grimshaw, J., et al. (2009) · Annals of Internal Medicine · doi:10.7326/0003-4819-150-3-200902030-00011 · Cited by 172
H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in AfricaPreprint
Mulder, N., Adebiyi, E. F., Alami, R., Benkahla, A., Brandful, J., Doumbia, S., Everett, D., Fadlelmola, F. M., Gaboun, F., Gaseitsiwe, S., et al. (2015) · Genome Research · doi:10.1101/gr.196295.115 · Cited by 172
Han, B., Kang, H. M., & Eskin, E. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000456 · Cited by 171
Auton, A., Bryc, K., Boyko, A. R., Lohmueller, K. E., Novembre, J., Reynolds, A., Indap, A. R., Wright, M. H., Degenhardt, J. D., Gutenkunst, R. N., et al. (2009) · Genome Research · doi:10.1101/gr.088898.108 · Cited by 171
Functional Copy-Number Alterations in Cancer
Taylor, B. S., Barretina, J., Socci, N. D., DeCarolis, P., Ladanyi, M., Meyerson, M., Singer, S., & Sander, C. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003179 · Cited by 170
Prando, C., Samarina, A., Bustamante, J. C., Boisson‐Dupuis, S., Cobat, A., Pïcard, C., Alsum, Z., Aljumaah, S., Al-Hajjar, S. H., Frayha, H. H., et al. (2013) · Medicine · doi:10.1097/md.0b013e31828a01f9 · Cited by 170
Risk for myasthenia gravis maps to a 151 Pro→Ala change in TNIP1 and to human leukocyte antigen‐B*08
Gregersen, P. K., Kosoy, R., Lee, A. T., Lamb, J. A., Sussman, J. D., McKee, D., Simpfendorfer, K. R., Pirskanen, R., Piehl, F., Pan‐Hammarström, Q., et al. (2012) · Annals of Neurology · doi:10.1002/ana.23691 · Cited by 170
Metspalu, M., Romero, I. G., Yunusbayev, B., Chaubey, G., Mallick, C. B., Hudjashov, G., Nelis, M., Mägi, R., Metspalu, E., Remm, M., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.010 · Cited by 170
Personalized Medicine: Marking a New Epoch in Cancer Patient Management
Diamandis, M., White, N. M. A., & Yousef, G. M. (2010) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-10-0264 · Cited by 170
HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes
Dilthey, A., Moutsianas, L., Leslie, S., & McVean, G. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr061 · Cited by 170
Admixture as the basis for genetic mapping
Buerkle, C. A., & Lexer, C. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.07.008 · Cited by 169
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
Bruno, A. E., Li, L., Kalabus, J. L., Pan, Y., Yu, A., & Hu, Z. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-44 · Cited by 168
Verweij, K. J. H., Zietsch, B. P., Medland, S. E., Gordon, S. D., Benyamin, B., Nyholt, D. R., McEvoy, B. P., Sullivan, P. F., Heath, A. C., Madden, P. A. F., et al. (2010) · Biological Psychology · doi:10.1016/j.biopsycho.2010.07.018 · Cited by 168
A Genome-Wide Association Study Reveals Variants in ARL15 that Influence Adiponectin Levels
Richards, J. B., Waterworth, D. M., O’Rahilly, S., Hivert, M., Loos, R. J. F., Perry, J. R. B., Tanaka, T., Timpson, N. J., Semple, R. K., Soranzo, N., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000768 · Cited by 168
Inouye, M., Ripatti, S., Kettunen, J., Lyytikäinen, L., Oksala, N., Laurila, P., Kangas, A. J., Soininen, P., Savolainen, M. J., Viikari, J. S. A., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002907 · Cited by 168
Resistance to malaria through structural variation of red blood cell invasion receptors
Leffler, E. M., Band, G., Busby, G., Kivinen, K., Le, S. Q., Clarke, G. M., Bojang, K., Conway, D. J., Jallow, M., Sisay-Joof, F., et al. (2017) · Science · doi:10.1126/science.aam6393 · Cited by 169
Linsel‐Nitschke, P., Götz, A., Erdmann, J., Brænne, I., Braund, P. S., Hengstenberg, C., Stark, K. J., Fischer, M., Schreiber, S., Mokhtari, N. E. E., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002986 · Cited by 168
Shulman, J. M., Imboywa, S., Giagtzoglou, N., Powers, M. P., Hu, Y., Devenport, D., Chipendo, P., Chibnik, L. B., Diamond, A., Perrimon, N., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddt478 · Cited by 167
High resolution melting analysis of almond SNPs derived from ESTs
Wu, S., Wirthensohn, M. G., Hunt, P. W., Gibson, J. P., & Sedgley, M. (2008) · Theoretical and Applied Genetics · doi:10.1007/s00122-008-0870-8 · Cited by 167
Prediction of individual genetic risk of complex disease
Wray, N. R., Goddard, M. E., & Visscher, P. M. (2008) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2008.07.006 · Cited by 167
The challenges, advantages and future of phenome‐wide association studies
Hebbring, S. J. (2013) · Immunology · doi:10.1111/imm.12195 · Cited by 166
High-resolution haplotype block structure in the cattle genome
Villa-Angulo, R., Matukumalli, L. K., Gill, C. A., Choi, J.-W., Tassell, C. P. V., & Grefenstette, J. J. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-19 · Cited by 166
Current status of genome-wide association studies in cancer
Chung, C. C., & Chanock, S. J. (2011) · Human Genetics · doi:10.1007/s00439-011-1030-9 · Cited by 166
Gibbons, J. G., Branco, A. T., Yu, S., & Lemos, B. (2014) · Nature Communications · doi:10.1038/ncomms5850 · Cited by 165
Haasl, R. J., & Payseur, B. A. (2015) · Molecular Ecology · doi:10.1111/mec.13339 · Cited by 165
A comprehensive evaluation of SNP genotype imputation
Nothnagel, M., Ellinghaus, D., Schreiber, S., Krawczak, M., & Franke, A. (2008) · Human Genetics · doi:10.1007/s00439-008-0606-5 · Cited by 164
Genetic variation in the autophagy gene ULK1 and risk of Crohnʼs disease
Henckaerts, L., Cleynen, I., Brinar, M., John, J. M., Steen, K. V., Rutgeerts, P. J., & Vermeire, S. (2010) · Inflammatory Bowel Diseases · doi:10.1002/ibd.21486 · Cited by 164
Herráez, D. L., Bauchet, M., Tang, K., Theunert, C., Pugach, I., Li, J., Nandineni, M. R., Gross, A., Scholz, M. R., & Stoneking, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007888 · Cited by 163
Genetic studies of alcohol dependence in the context of the addiction cycle
Reilly, M. T., Noronha, A., Goldman, D. A., & Koob, G. F. (2017) · Neuropharmacology · doi:10.1016/j.neuropharm.2017.01.017 · Cited by 163
Genomics in Personalized Nutrition: Can You “Eat for Your Genes”?
Mullins, V. A., Bresette, W., Johnstone, L. M., Hallmark, B., & Chilton, F. H. (2020) · Nutrients · doi:10.3390/nu12103118 · Cited by 163
The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population
Jakkula, E., Rehnström, K., Varilo, T., Pietiläinen, O. P. H., Paunio, T., Pedersen, N. L., DeFaire, U., Järvelin, M., Saharinen, J., Freimer, N. B., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.11.005 · Cited by 162
Is Mate Choice in Humans MHC-Dependent?
Chaix, R., Cao, C., & Donnelly, P. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000184 · Cited by 162
Heath, S. C., Gut, I. G., Brennan, P., McKay, J., Bencko, V., Fabiánová, E., Foretová, L., Georges, M., Janout, V., Kabesch, M., et al. (2008) · European Journal of Human Genetics · doi:10.1038/ejhg.2008.210 · Cited by 161
Mammary Tumor Development in Dogs Is Associated with BRCA1 and BRCA2
Rivera, P., Melin, M., Biagi, T., Fall, T., Häggström, J. U., Lindblad‐Toh, K., & von Euler, H. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-1725 · Cited by 161
Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H
Harari, A., Ooms, M., Mulder, L. C. F., & Simon, V. R. (2008) · Journal of Virology · doi:10.1128/jvi.01665-08 · Cited by 160
Recovering signals of ghost archaic introgression in African populations
Durvasula, A., & Sankararaman, S. (2020) · Science Advances · doi:10.1126/sciadv.aax5097 · Cited by 160
CYP2C19*2 and CYP2C9*3 alleles are associated with stent thrombosis: a case-control study
Harmsze, A. M., van Werkum, J. W., ten Berg, J. M., Zwart, B., Bouman, H. J., Breet, N. J., Hof, A. W. J. V. ’., Ruven, H. J. T., Hackeng, C. M., Klungel, O. H., et al. (2010) · European Heart Journal · doi:10.1093/eurheartj/ehq321 · Cited by 159
Kemp, J. P., Medina‐Gómez, C., Estrada, K., Pourcain, B. S., Heppe, D. H. M., Warrington, N. M., Oei, L., Ring, S. M., Kruithof, C. J., Timpson, N. J., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004423 · Cited by 159
Childhood obesity: are genetic differences involved?
Bouchard, C. (2009) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.2009.27113c · Cited by 159
The Characterization of Twenty Sequenced Human Genomes
Pelak, K., Shianna, K. V., Ge, D., Maia, J. M., Zhu, M., Smith, J. P., Cirulli, E. T., Fellay, J., Dickson, S. P., Gumbs, C. E., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001111 · Cited by 159
Genome-wide association study identifies multiple loci associated with bladder cancer risk
Figueroa, J. D., Ye, Y., Siddiq, A., García‐Closas, M., Chatterjee, N., Prokunina‐Olsson, L., Cortessis, V. K., Kooperberg, C. L., Cussenot, O., Benhamou, S., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt519 · Cited by 159
Ataxia and hypogonadism caused by the loss of ubiquitin ligase activity of the U box protein CHIP
Shi, C.-H., Schisler, J. C., Rubel, C. E., Tan, S., Song, B., McDonough, H., Xu, L., Portbury, A. L., Mao, C., True, C. A., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt497 · Cited by 158
Furney, S. J., Simmons, A., Breen, G., Pedroso, I., Lunnon, K., Proitsi, P., Hodges, A., Powell, J., Wahlund, L.-O., Kloszewska, I., et al. (2011) · Molecular Psychiatry · doi:10.1038/mp.2010.123 · Cited by 157
Yu, Y., Zhang, X., Yuan, J., Li, F., Chen, X., Zhao, Y., Huang, L., Zheng, H., & Xiang, J. (2015) · Scientific Reports · doi:10.1038/srep15612 · Cited by 157
The timing of pigmentation lightening in Europeans
Beleza, S., Santos, A. M., McEvoy, B., Alves, I., Martinho, C., Cameron, E., Shriver, M. D., Parra, E. J., & Rocha, J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss207 · Cited by 156
Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea
Deulvot, C., Charrel, H., Marty, A., Jacquin, F., Donnadieu, C., Lejeune-Hénaut, I., Burstin, J., & Aubert, G. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-468 · Cited by 156
Cai, X., Bazerque, J. A., & Giannakis, G. B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003068 · Cited by 158
Accelerated genetic drift on chromosome X during the human dispersal out of Africa
Keinan, A., Mullikin, J. C., Patterson, N. J., & Reich, D. (2008) · Nature Genetics · doi:10.1038/ng.303 · Cited by 156
Refined genetic maps reveal sexual dimorphism in human meiotic recombination at multiple scales
Bhérer, C., Campbell, C. L., & Auton, A. (2017) · Nature Communications · doi:10.1038/ncomms14994 · Cited by 156
Grillet, N., Schwander, M., Hildebrand, M. S., Sczaniecka, A., Kolatkar, A. R., Velasco, J., Webster, J., Kahrizi, K., Najmabadi, H., Kimberling, W. J., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.07.017 · Cited by 155
Pharmacogenetics and pharmacogenomics of anticancer agents
Huang, R. S., & Ratain, M. J. (2009) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.20002 · Cited by 155
Hoffmann, T. J., Zhan, Y., Kvale, M. N., Hesselson, S., Gollub, J., Iribarren, C., Lu, Y., Mei, G., Purdy, M. M., Quesenberry, C. P., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.08.007 · Cited by 155
Multiple Loci within the Major Histocompatibility Complex Confer Risk of Psoriasis
Feng, B., Sun, L.-D., Soltani‐Arabshahi, R., Bowcock, A. M., Nair, R. P., Stuart, P. E., Elder, J. T., Schrodi, S. J., Begovich, A. B., Abecasis, G. R., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000606 · Cited by 154
Ancient human parallel lineages within North America contributed to a coastal expansion
Scheib, C. L., Li, H., Desai, T., Link, V., Kendall, C., Dewar, G., Griffith, P. W., Mörseburg, A., Johnson, J. R., Potter, A., et al. (2018) · Science · doi:10.1126/science.aar6851 · Cited by 125
Pouyet, F., Aeschbacher, S., Thiéry, A., & Excoffier, L. (2018) · eLife · doi:10.7554/elife.36317 · Cited by 153
Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation
Duran, C., Appleby, N., Edwards, D., & Batley, J. (2009) · Current Bioinformatics · doi:10.2174/157489309787158198 · Cited by 153
Low-frequency and common genetic variation in ischemic stroke
Malik, R., Traylor, M., Pulit, S. L., Bevan, S., Hopewell, J. C., Holliday, E. G., Zhao, W., Abrantes, P., Amouyel, P., Attia, J., et al. (2016) · Neurology · doi:10.1212/wnl.0000000000002528 · Cited by 153
Transferability of Type 2 Diabetes Implicated Loci in Multi-Ethnic Cohorts from Southeast Asia
Sim, X., Ong, R. T.-H., Suo, C., Tay, W.-T., Liu, J., Ng, D. P.-K., Boehnke, M., Chia, K.-S., Wong, T.-Y., Seielstad, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001363 · Cited by 152
“Population structure ascertainment was carried out using principal components analysis (PCA) [59] with 4 panels from International Hapmap [60] and the Singapore Genome Variation Project [61] (http://www.nus-cme. org.sg/SGVP/) which includes 96 Chinese, 89 Malays and 83 Asian Indians from Singapore.”
MethodNeafsey, D. E., Schaffner, S. F., Volkman, S. K., Park, D. J., Montgomery, P. G., Milner, D. A., Lukens, A. K., Rosen, D. M., Daniels, R. F., Houde, N., et al. (2008) · Genome biology · doi:10.1186/gb-2008-9-12-r171 · Cited by 152
Moyer, R. A., Wang, D., Papp, A. C., Smith, R. M., Duque, L., Mash, D. C., & Sadée, W. (2010) · Neuropsychopharmacology · doi:10.1038/npp.2010.208 · Cited by 151
Naitza, S., Porcu, E., Steri, M., Taub, D. D., Mulas, A., Xiao, X., Strait, J., Dei, M., Lai, S., Busonero, F., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002480 · Cited by 151
Zhu, X., & Stephens, M. (2017) · The Annals of Applied Statistics · doi:10.1214/17-aoas1046 · Cited by 151
Liang, L., Morar, N., Dixon, A. L., Lathrop, M. G., Abecasis, G. R., Moffatt, M. F., & Cookson, W. (2013) · Genome Research · doi:10.1101/gr.142521.112 · Cited by 151
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets
Barenboim, M., Zoltick, B. J., Guo, Y., & Weinberger, D. R. (2010) · Human Mutation · doi:10.1002/humu.21349 · Cited by 150
Fluorescent silver nanoclusters as DNA probes
Obliosca, J. M., Liu, C., & Yeh, H. (2013) · Nanoscale · doi:10.1039/c3nr01601c · Cited by 150
Goulielmos, G. N., Zervou, M. I., Vazgiourakis, V., Ghodke‐Puranik, Y., Garyfallos, A., & Niewold, T. B. (2018) · Gene · doi:10.1016/j.gene.2018.05.041 · Cited by 148
Polygenic Scores to Assess Atherosclerotic Cardiovascular Disease Risk
Aragam, K. G., & Natarajan, P. (2020) · Circulation Research · doi:10.1161/circresaha.120.315928 · Cited by 148
Creating artificial human genomes using generative neural networks
Yelmen, B., Decelle, A., Ongaro, L., Marnetto, D., Tallec, C., Montinaro, F., Furtlehner, C., Pagani, L., & Jay, F. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009303 · Cited by 148
GWAS for executive function and processing speed suggests involvement of the CADM2 gene
Ibrahim-Verbaas, C. A., Bressler, J., Debette, S., Schuur, M., Smith, A. V., Bis, J. C., Davies, G., Trompet, S., Smith, J. A., Wolf, C., et al. (2016) · Molecular Psychiatry · doi:10.1038/mp.2015.37 · Cited by 147
Neuditschko, M., Khatkar, M. S., & Raadsma, H. W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048375 · Cited by 147
Reaching new heights: insights into the genetics of human stature
Weedon, M. N., & Frayling, T. M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.09.006 · Cited by 147
Berg, I. L., Neumann, R., Sarbajna, S., Odenthal-Hesse, L., Butler, N. J., & Jeffreys, A. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109531108 · Cited by 147
Khoury, M. J., & Wacholder, S. (2008) · American Journal of Epidemiology · doi:10.1093/aje/kwn351 · Cited by 147
Demography and the Age of Rare Variants
Mathieson, I., & McVean, G. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004528 · Cited by 147
Chen, Y., Cunningham, F. M., Ríos, D., McLaren, W. M., Smith, J. A., Yates, B., Spudich, G. M., Brent, S., Kulesha, E., Marín-García, P., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-293 · Cited by 146
Genetic structure characterization of Chileans reflects historical immigration patterns
Eyheramendy, S., Martínez, F. I., Manevy, F., Vial, C., & Repetto, G. M. (2015) · Nature Communications · doi:10.1038/ncomms7472 · Cited by 146
A second generation genetic map for rainbow trout (Oncorhynchus mykiss)
Rexroad, C. E., Palti, Y., Gahr, S. A., & Vallejo, R. L. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-74 · Cited by 146
Catalina, M. D., Owen, K. A., Labonte, A. C., Grammer, A. C., & Lipsky, P. E. (2019) · Journal of Autoimmunity · doi:10.1016/j.jaut.2019.102359 · Cited by 146
The Recombinational Anatomy of a Mouse Chromosome
Paigen, K., Szatkiewicz, J. P., Sawyer, K., Leahy, N., Parvanov, E. D., Ng, S. H. S., Graber, J. H., Broman, K. W., & Petkov, P. M. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000119 · Cited by 146
Stein, J. L., Hua, X., Morra, J. H., Lee, S., Hibar, D. P., Ho, A. J., Leow, A. D., Toga, A. W., Sul, J. H., Kang, H. M., et al. (2010) · NeuroImage · doi:10.1016/j.neuroimage.2010.02.068 · Cited by 145
Kumar, V., Wijmenga, C., & Withoff, S. (2012) · Seminars in Immunopathology · doi:10.1007/s00281-012-0312-1 · Cited by 145
The Complex Admixture History and Recent Southern Origins of Siberian Populations
Pugach, I., Matveev, R., Va, S., Makarov, S., Novgorodov, I. N., Осаковский, В. Л., Stoneking, M., & Pakendorf, B. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw055 · Cited by 145
Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Baker, Z., Schumer, M. E., Haba, Y., Bashkirova, L., Holland, C., Rosenthal, G. G., & Przeworski, M. (2017) · eLife · doi:10.7554/elife.24133 · Cited by 145
Wallace, D. C. (2008) · Genetics · doi:10.1534/genetics.104.91769 · Cited by 145
JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia
Boztuǧ, K., Järvinen, P. M., Salzer, E., Racek, T., Mönch, S., Garncarz, W., Gertz, E. M., Schäffer, A. A., Antonopoulos, A., Haslam, S. M., et al. (2014) · Nature Genetics · doi:10.1038/ng.3069 · Cited by 144
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region
Armstrong, D. L., Zidovetzki, R., Alarcón-Riquelme, M. E., Tsao, B. P., Criswell, L. A., Kimberly, R. P., Harley, J. B., Sivils, K. L. M., Vyse, T. J., Gaffney, P. M., et al. (2014) · Genes and Immunity · doi:10.1038/gene.2014.23 · Cited by 144
Pouladi, M. A., Stanek, L. M., Xie, Y., Franciosi, S., Southwell, A. L., Deng, Y., Butland, S. L., Zhang, W., Cheng, S. H., Shihabuddin, L. S., et al. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds037 · Cited by 144
Pathway-Based Analysis Tools for Complex Diseases: A Review
Lv, J., Zuo, X., Su, W., Zhao, X., Yuan, M., Han, L., Zhao, X., Chen, Y., & Rao, S. (2014) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2014.10.002 · Cited by 143
Genetic determinants of Tibetan high-altitude adaptation
Simonson, T. S., McClain, D. A., Jorde, L. B., & Prchal, J. T. (2011) · Human Genetics · doi:10.1007/s00439-011-1109-3 · Cited by 143
Complementary Alu sequences mediate enhancer–promoter selectivity
Liang, L., Cao, C., Ji, L., Cai, Z., Wang, D., Ye, R., Chen, J., Yu, X., Zhou, J., Bai, Z., et al. (2023) · Nature · doi:10.1038/s41586-023-06323-x · Cited by 147
Yang, Q., Wu, H., Guo, C., & Fox, C. S. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20497 · Cited by 142
Leveraging Genetic Variability across Populations for the Identification of Causal Variants
Zaitlen, N., Paşaniuc, B., Gur, T., Ziv, E., & Halperin, E. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.11.016 · Cited by 142
Adaptations to new environments in humans: the role of subtle allele frequency shifts
Hancock, A. M., Alkorta‐Aranburu, G., Witonsky, D., & Rienzo, A. D. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2010.0032 · Cited by 142
Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans
Crawford, J. E., Amaru, R., Song, J., Julian, C. G., Racimo, F., Cheng, J. Y., Guo, X., Yao, J., Ambale‐Venkatesh, B., Lima, J. A. C., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.09.023 · Cited by 142
Metadata
- Authors
- The International HapMap Consortium
- Venue
- Nature
- Published
- 2007-10
- Volume
- 449
- Issue
- 7164
- Pages
- 851-861
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2689609
- OpenAlex
- W2119279196
- Cited by
- 4,438
- References
- 60
- Citations by year
- 2026: 53 · 2025: 67 · 2024: 77 · 2023: 71 · 2022: 114 · 2021: 129 · 2020: 111 · 2019: 133 · 2018: 150 · 2017: 153 · 2016: 162 · 2015: 232 · 2014: 275 · 2013: 317 · 2012: 412
- FWCI
- 270.06
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Deep Blue (University of Michigan) (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Leicester Research Archive (University of Leicester) (submittedVersion)
- Funders
- W. M. Keck Foundation
- Genome Canada
- Wellcome Trust (081682, 077011, 077008, 077046)
- Ministry of Education, Culture, Sports, Science and Technology
- National Natural Science Foundation of China
- University Grants Committee
- Chinese Academy of Sciences
- Beijing Normal University
- Ministry of Science and Technology of the People's Republic of China
- Innovation and Technology Commission
- National Institutes of Health
- Engineering and Physical Sciences Research Council
- National Institute on Alcohol Abuse and Alcoholism
- National Institute on Aging
- National Institute of Mental Health
- National Institute on Drug Abuse
- National Human Genome Research Institute
- National Eye Institute
- National Cancer Institute
- National Institute on Deafness and Other Communication Disorders
- National Institute of General Medical Sciences
- National Institute of Allergy and Infectious Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases
- National Institute of Neurological Disorders and Stroke
- National Institute of Environmental Health Sciences
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
- National Institute of Biomedical Imaging and Bioengineering
- National Institute of Dental and Craniofacial Research
- National Center for Research Resources
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- single nucleotide polymorphisms, linkage disequilibrium, SNP genotyping, imputation, recombination hotspots, recombination rate, genetic differentiation, natural selection, non-synonymous SNPs, genetic ancestry, genome-wide association study, Lassa virus, skin pigmentation, hair follicle development
- MeSH terms
- Female, Haplotypes, Homozygote, Humans, Male, Recombination, Genetic, Selection, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Racial Groups
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
