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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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“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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“This has allowed various studies to find associations for several genes—not previously reported as genetic risk factors— with target diseases, including diabetes (Manolio et al. 2008).”
BackgroundAge of onset and effect size in genome‐wide association studies
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“This threshold was based on commonly accepted cut points for small effect sizes in GWAS (Manolio et al., 2008; Hindorff et al., 2009).”
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“While these efforts have resulted in the identification of more than 350 genes (1), additional genes of unknown or presumably unrelated function likely play critical roles in cancer development and progression (2).”
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“More recently, with the development of high-throughput genotyping platforms and a comprehensive map of human haplotypes, genome-wide association studies (GWAS) have evolved into a powerful tool for investigating the genetic architecture of human complex diseases (Manolio et al. 2008).”
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“Improved haplotype mapping of the human genome is an important step in this direction [4,5].”
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Deletion of Jazf1 gene causes early growth retardation and insulin resistance in mice
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“However, while these GWAS approaches have discovered statistically robust associations between many DNA sequence variants and traits (38, 39) including T2D (5, 40, 41), the predictive value of any single variant for assessing an individual’s disease risk has generally been disappointing as each of the identified genes…”
BackgroundWhole Genome Analysis of Venous Thromboembolism: the Trans-Omics for Precision Medicine Program
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“The International HapMap project (http:// www. hapmap. org/) measured the LD between SNPs in numerous common racial and ethnic populations (Goldberg et al. 2015; Manolio et al. 2008).”
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“and many of the associations found in GWAS identify novel candidate genes [18, 19].”
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“more than 40 different common diseases (2).”
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“Genome-wide association studies (GWAS) have identified hundreds of genetic loci at which common variation confers disease susceptibility (1,2).”
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“More recently, genetic variation has been estimated using genetic marker information and, in particular, in genome-wide association studies (GWASs) (Manolio et al., 2008; Welter et al., 2014), which have identified thousands of genetic variants that are associated with dozens of common diseases.”
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“Rather, with data from the Human Genome Project and the HapMap project, we now know something about the structure of most genes in the human genome (Manolio et al., 2008).”
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“Because the GWAS is hypothesis-free, it is proving to be a great success in understanding unknown and unexpected molecular aspects of many human common diseases.(4) Thye et al combined the GWAS results of two large African cohortsdone cohort from Ghana comprising 1740 controls and 921 cases, and another from The Gambi…”
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“Recent studies on common diseases using these state-of-the-art techniques confirmed the complexity of their underlying genetic architecture (13, 14).”
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“Association studies based on haplotypes of multiple markers could increase the efficiency of mapping and characterizing disease-causing genes (34); however, we still found no association between multiple haplotypes of CUBN, FUT6, MUT genes, and the risk”
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Leitsalu, L., Hercher, L., & Metspalu, A. (2011) · Journal of Genetic Counseling · doi:10.1007/s10897-011-9424-3 · Cited by 8
“…power of genomic information in general is limited at present, and the idea that genome screens will have sufficient validity and utility to improve medical care in the next few years remains contentious (Altshuler et al. 2008; Janssens & van Duijn, 2009; Manolio et al. 2008; Ormond et al., 2010).”
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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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