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A HapMap harvest of insights into the genetics of common disease
Open accessAbstract
The International HapMap Project was designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases. This expectation has been amply fulfilled with just the initial output of genome-wide association studies, identifying nearly 100 loci for nearly 40 common diseases and traits. These associations provided new insights into pathophysiology, suggesting previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. In addition, HapMap-based discoveries have shed new light on the impact of evolutionary pressures on the human genome, suggesting multiple loci important for adapting to disease-causing pathogens and new environments. In this review we examine the origin, development, and current status of the HapMap; its prospects for continued evolution; and its current and potential future impact on biomedical science.
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“A relevant example is evident in genomics research, in which data pooling has, e.g., enabled knowledge of disease-related loci to be expanded substantially [e.g.Lambert et al. (2013); Manolio et al. (2008); Schizophrenia Working Group of the Psychiatric Genomics (2014)], findings which would not have been possible without the sample sizes offered through data-sharing.”
From New directions in hypnosis research: strategies for advancing the cognitive and clinical neuroscience of hypnosis (2017) · cites this paper as Manolio et al. 2008
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In the citing paper
“Research in other fields has benefited substantially from datasharing initiatives.”
From New directions in hypnosis research: strategies for advancing the cognitive and clinical neuroscience of hypnosis (2017) · cites this paper as Manolio et al. 2008
In the citing paper
“GWAS has successfully identified thousands of common variants99”
From Rare and common variants: twenty arguments (2012) · cites this paper as [99]
In the citing paper
“As of June 2011, the NHGRI GWAS catalog lists 1,449 genome-wide significant associations with 237 traits and diseases, spread across all chromosome except the Y99.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [99]
In the citing paper
“Despite the success of genome wide association (GWA) studies in identifying common single nucleotide variants (SNVs) that contribute to complex diseases1, the vast majority of genetic variants contributing to disease susceptibility are yet to be discovered.”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [1]
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“gif" NDATA ITEM> ]> In the past 3 years, genome-wide association (GWA) studies have identified over 200 common marker alleles that are associated with over seventy common diseases and trait”
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“5 (2), and may not be useful for clinical prediction (7, 8).”
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“As a result, many novel susceptibility loci have been identified from the marginal association analysis of SNPs with disease risk.(1) However, there is far more information in the data that researchers are just beginning to explore.”
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“Genome wide association studies using indirect mapping have been successful in localizing genes which are associated with complex diseases when common variants are the underlying cause of disease etiology [1,2].”
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“The recent efforts of genome-wide association studies have been fruitful [Manolio, Brooks and Collins, 2008] in the identification of novel genetic variants predisposing to a variety of complex traits.”
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McBride, C. M., Bowen, D. J., Brody, L. C., Condit, C. M., Croyle, R. T., GWINN, M. L., Khoury, M. J., Koehly, L. M., Korf, B. R., Marteau, T. M., et al. (2010) · American Journal of Preventive Medicine · doi:10.1016/j.amepre.2010.01.027 · Cited by 141
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“In individuals with SHH-associated diseases such as HPE, poor genotype-phenotype correlations may therefore result from the combination of multiple genes of small additive or epistatic effect contributing to overall severity (Hardy and Singleton, 2009; Manolio et al., 2009).”
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“Genome-wide association studies (GWAS) using single SNP analysis have been very successful in identifying loci for various quantitative traits and diseases (Manolio et al. 2008).”
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“3) similar to those identified in several common diseases such as diabetes or different cancers [29] where larger samples are easier to collect.”
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InfluentialUsing Genome-Wide Association Studies to Identify Genes Important in Serious Adverse Drug Reactions
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“sity genome-wide association (GWA) studies to date have demonstrated the success and robustness of this approach in identifying genetic variants or regions associated with nearly 40 complex diseases or traits (59), including complex lung diseases such as asthma (69).”
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BackgroundInfluentialModeling Molecular and Cellular Aspects of Human Disease Using the Nematode Caenorhabditis elegans
Silverman, G. A., Luke, C. J., Bhatia, S. R., Long, O. S., Vetica, A. C., Perlmutter, D. H., & Pak, S. C. (2008) · Pediatric Research · doi:10.1203/pdr.0b013e31819009b0 · Cited by 100
Holmans, P. (2010) · Advances in genetics · doi:10.1016/b978-0-12-380862-2.00007-2 · Cited by 101
The role of large pedigrees in an era of high-throughput sequencing
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“However, early optimistic predictions about the impact of these discoveries (Manolio et al. 2008) became more guarded for two reasons: (1) most GWAS studies have only lead to associations, with identification and verification of the actual risk variants a rare outcome (Hindorff et al.”
BackgroundYeager, M., Xiao, N., Hayes, R. B., Bouffard, P., Desany, B. A., Burdett, L. A., Orr, N., Matthews, C., Qi, L., Crenshaw, A., et al. (2008) · Human Genetics · doi:10.1007/s00439-008-0535-3 · Cited by 100
“Genome-wide association studies with su Y ciently large replication components are rapidly identifying regions of the genome that are convincingly associated with risk of cancer and other diseases (Manolio et al. 2008; Rahim et al. 2008).”
BackgroundHypothesis-Driven Candidate Gene Association Studies: Practical Design and Analytical Considerations
Jørgensen, T., Ruczinski, I., Kessing, B. D., Smith, M. W., Shugart, Y. Y., & Alberg, A. J. (2009) · American Journal of Epidemiology · doi:10.1093/aje/kwp242 · Cited by 109
Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State
Stevens, E. L., Heckenberg, G., Roberson, E. D. O., Baugher, J. D., Downey, T. J., & Pevsner, J. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002287 · Cited by 99
“SNPs are used as proxies for the unobserved sequence variants in the surrounding DNA, allowing measurement of the flow of genetic material through populations [1].”
BackgroundMethodLou, H., Yeager, M., Li, H., Bosquet, J. G., Hayes, R. B., Orr, N., Yu, K. F., Hutchinson, A. A., Jacobs, K. B., Kraft, P. L., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902104106 · Cited by 98
“So far, GWAS have discovered over 400 genomic regions in over 75 diseases or human traits (6).”
BackgroundGenetic factors in contact allergy-review and future goals
Schnuch, A., Westphal, G., Mößner, R., Uter, W. J. C., & Reich, K. (2010) · Contact Dermatitis · doi:10.1111/j.1600-0536.2010.01800.x · Cited by 98
Researching Genetic Versus Nongenetic Determinants of Disease: A Comparison and Proposed Unification
Ioannidis, J. P. A., Loy, E. Y., Poulton, R., & Chia, K. S. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000247 · Cited by 95
“Hundreds of new genetic associations with disease risk have been discovered recently (2), and full genome sequencing in population studies is currently under way.”
BackgroundBreast Cancer in the Personal Genomics Era
Ellsworth, R. E., Decewicz, D. J., Shriver, C. D., & Ellsworth, D. L. (2010) · Current Genomics · doi:10.2174/138920210791110951 · Cited by 97
“Whole-genome association studies have identified some DNA variants contributing to breast cancer risk that provide new insights into the pathophysiology of disease and may ultimately prove useful for developing targeted interventions [146], but many variants will never have clinical utility.”
BackgroundChen, C., Chen, C., Moyzis, R., Stern, H., He, Q., Li, H., Li, J., Zhu, B., & Dong, Q. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021636 · Cited by 95
“Thus it is necessary to examine the combined effects of multiple gene loci [21,22].”
BackgroundImpact of the ADHD-susceptibility gene CDH13 on development and function of brain networks
Rivero, O., Sich, S., Popp, S., Schmitt, A. G., Franke, B., & Lesch, K. (2012) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2012.06.009 · Cited by 97
“The completion of the Human Genome Project and the 1000 Genomes Project pilot studies have been instrumental for the re-conceptionalization of genetic studies of complex traits (Manolio et al., 2008; Lupski et al., 2011).”
Molecular diagnostics in transplantation
Naesens, M., & Sarwal, M. (2010) · Nature Reviews Nephrology · doi:10.1038/nrneph.2010.113 · Cited by 95
“Genome-wide association (GWA) studies, which use accessible tools for high-throughput genotyping, have now become a standard method for disease gene discovery”
BackgroundBuilding towards precision medicine: empowering medical professionals for the next revolution
McGrath, S., & Ghersi, D. (2016) · BMC Medical Genomics · doi:10.1186/s12920-016-0183-8 · Cited by 98
“phisms (SNP), which are “sites in the genome sequence of 3 billion nucleotide bases where individuals differ by a single base” [21].”
BackgroundXiong, L., Catoire, H., Dion, P. A., Gaspar, C., Lafrenière, R. G., Girard, S., Levchenko, А., Rivière, J., Fiori, L. M., St‐Onge, J., et al. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddn443 · Cited by 96
Genome-Wide Association Studies in Nephrology Research
Köttgen, A. (2010) · American Journal of Kidney Diseases · doi:10.1053/j.ajkd.2010.05.018 · Cited by 92
The American cranberry: first insights into the whole genome of a species adapted to bog habitat
Polashock, J. J., Zelzion, E., Fajardo, D. A., Zalapa, J. E., Georgi, L. L., Bhattacharya, D., & Vorsa, N. (2014) · BMC Plant Biology · doi:10.1186/1471-2229-14-165 · Cited by 96
Ziogas, D. E., & Roukos, D. H. (2009) · Annals of Surgical Oncology · doi:10.1245/s10434-009-0436-2 · Cited by 92
“Over the last 2 years, GWAS have identified more than 100 new chromosomal regions at which more than 165 novel DNA variants influence risk of common human diseases and clinical phenotypes.(75) Nevertheless, at the present time, despite initial optimism, the clinical implication of these risk variants is being debated.”
BackgroundSystems pharmacology and genome medicine: a future perspective
Wist, A. D., Berger, S., & Iyengar, R. (2009) · Genome Medicine · doi:10.1186/gm11 · Cited by 90
“Genome-wide association studies have become popular over the past few years [12], although their ability to predict disease susceptibility is only beginning to be determined.”
BackgroundMolloy, A. M., Brody, L. C., Mills, J. L., Scott, J. M., & Kirke, P. N. (2009) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.20566 · Cited by 89
“This variation map, known as the HapMap, can be used to scan the genome for genes associated with specific diseases (Manolio et al., 2008).”
MethodDirect-to-consumer personalized genomic testing
Bloss, C. S., Darst, B. F., Topol, E. J., & Schork, N. J. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr349 · Cited by 89
“These tests are based on high-throughput genome-wide genotyping technologies and findings from genome-wide association studies (7).”
BackgroundFareed, M., & Afzal, M. (2012) · Egyptian Journal of Medical Human Genetics · doi:10.1016/j.ejmhg.2012.08.001 · Cited by 84
“GWA studies in which hundreds of thousands of single-nucleotide polymorphisms (SNPs) are tested for association with a disease in hundreds or thousands of persons have revolutionized the search for genetic influences on complex traits [23,24].”
BackgroundRueckert, E. H., Barker, D., Ruderfer, D. M., Bergen, S. E., O’Dushlaine, C. T., Luce, C. J., Sheridan, S. D., Theriault, K. M., Chambert, K., Moran, J. L., et al. (2012) · Molecular Psychiatry · doi:10.1038/mp.2012.104 · Cited by 87
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“…fact that GWAs have provided convincing evidence for identifying important genetic variants influencing a wide variety of common diseases and traits (Manolio et al., 2008; Seng & Seng, 2008), a lot of the genetic heritability cannot be explained by the (major) genetic loci discovered so far…”
BackgroundIoannidis, J. P. A. (2009) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.108.833392 · Cited by 85
Is there still a need for candidate gene approaches in the era of genome-wide association studies?
Wilkening, S., Chen, B., Bermejo, J. L., & Canzian, F. (2009) · Genomics · doi:10.1016/j.ygeno.2008.12.011 · Cited by 84
“[2].”
Pooled Association Tests for Rare Genetic Variants: A Review and Some New Results
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Yu, W., Wulf, A., Liu, T., Khoury, M. J., & GWINN, M. L. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-528 · Cited by 83
“Recently, publications based on GWAS have become a leading source of replicated genetic associations [26].”
BackgroundKang, Y. H., Şakiroğlu, M., Krom, N., Stanton‐Geddes, J., Wang, M., Lee, Y., Young, N. D., & Udvardi, M. K. (2015) · Plant Cell & Environment · doi:10.1111/pce.12520 · Cited by 88
“In the search for genes underlying variation in a population, genome-wide association studies (GWAS) have proven to be a powerful tool in both humans (Cardon & Abecasis 2003; Gibbs et al. 2003;Altshuler et al. 2005;Manolio et al. 2008) and plants, including Arabidopsis (Buckler & Gore 2007; Atwell et al.”
BackgroundSo, H., Kwan, J. S. H., Cherny, S. S., & Sham, P. C. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.04.001 · Cited by 81
“However, because of the recent progress in genome-wide association studies (GWAS), an increasing number of susceptibility variants for complex diseases are being identified.(1,2) The genotyping of these variants is expected to contribute to risk prediction.”
3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk
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From Darwin's Finches to Canaries in the Coal Mine — Mining the Genome for New Biology
Hunter, D. J., Altshuler, D., & Rader, D. J. (2008) · New England Journal of Medicine · doi:10.1056/nejmp0804318 · Cited by 80
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“Over the past several years, GWAS assaying several hundred thousand to a few million SNPs in thousands of individuals have successfully identified numerous genetic variants that were significantly associated with over two hundred human complex diseases/traits [1,2].”
BackgroundConsumers' Views of Direct-to-Consumer Genetic Information
McBride, C. M., Wade, C. H., & Kaphingst, K. A. (2010) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141604 · Cited by 78
Schizophrenia genetics: advancing on two fronts
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Ethical Data Release in Genome-Wide Association Studies in Developing Countries
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“Genome-wide association (GWA) studies provide a powerful way of getting at this problem by identifying genetic variants determining resistance or susceptibility to common diseases [2–4].”
BackgroundEvaluation of risk prediction updates from commercial genome-wide scans
Mihăescu, R., van Hoek, M., Sijbrands, E. J. G., Uitterlinden, A. G., Witteman, J. C. M., Albert Hofman, D., van Duijn, C. M., & Janssens, A. C. J. W. (2009) · Genetics in Medicine · doi:10.1097/gim.0b013e3181b13a4f · Cited by 77
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Metadata
- Authors
- Manolio, T. A., Brooks, L. D., & Collins, F. S.
- Affiliations
- National Human Genome Research Institute (US)
- Venue
- Journal of Clinical Investigation
- Published
- 2008-05-01
- Volume
- 118
- Issue
- 5
- Pages
- 1590-1605
- ISSN
- 0021-9738 (ISSN-L)
- PMC
- PMC2336881
- OpenAlex
- W2101983393
- Cited by
- 889
- References
- 136
- Citations by year
- 2026: 6 · 2025: 13 · 2024: 10 · 2023: 10 · 2022: 14 · 2021: 16 · 2020: 14 · 2019: 22 · 2018: 23 · 2017: 30 · 2016: 30 · 2015: 34 · 2014: 55 · 2013: 53 · 2012: 88
- FWCI
- 14.78
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- Locations
- Journal of Clinical Investigation (publishedVersion, public-domain)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- HapMap, human genetic variation, genome-wide association study, disease pathophysiology, therapeutic target, genetic risk
- MeSH terms
- Chromosome Mapping, Genetics, Population, Haplotypes, Humans, Genetic Variation, Linkage Disequilibrium, Genome, Human, Evolution, Molecular, Genetic Predisposition to Disease, Databases, Genetic
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