publication . Article . 2017

Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study

Paul S. de Vries; Maria Sabater-Lleal; Daniel I. Chasman; Stella Trompet; Tarunveer S. Ahluwalia; Alexander Teumer; Marcus E. Kleber; Ming-Huei Chen; Jie Jin Wang; John R. Attia; ...
Open Access English
  • Published: 20 Jan 2017
  • Publisher: PUBLIC LIBRARY SCIENCE
Abstract
<p>An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G im...
Subjects
free text keywords: Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, /dk/atira/pure/researchoutput/pubmedpublicationtype/D052061, Research Support, N.I.H., Extramural, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, /dk/atira/pure/subjectarea/asjc/2700, Medicine(all), /dk/atira/pure/subjectarea/asjc/1300, Biochemistry, Genetics and Molecular Biology(all), /dk/atira/pure/subjectarea/asjc/1100, Agricultural and Biological Sciences(all), Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, Cardiovascular-Disease, Susceptibility Loci, Genetic-Variants, Common Variants, Metaanalysis, Consortium, Imputation, Pressure, Insights, Biology, Research Article, Biology and Life Sciences, Computational Biology, Genome Analysis, Genome-Wide Association Studies, Genetics, Genomics, Human Genetics, Biochemistry, Glycobiology, Glycoproteins, Fibrinogen, Medicine and Health Sciences, Health Care, Health Services Research, Comparative Genomics, Social Sciences, Sociology, Consortia, Research and Analysis Methods, Mathematical and Statistical Techniques, Statistical Methods, Meta-Analysis, Physical Sciences, Mathematics, Statistics (Mathematics), Molecular Biology, Molecular Biology Techniques, Genotyping, Cell Biology, Signal Transduction, Cell Signaling, Genomic Signal Processing, Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, CARDIOVASCULAR-DISEASE, SUSCEPTIBILITY LOCI, GENETIC-VARIANTS, COMMON VARIANTS, METAANALYSIS, CONSORTIUM, IMPUTATION, PRESSURE, INSIGHTS, HapMap Project, Humans, MD Multidisciplinary, General Science & Technology, Haplotype estimation, Imputation (statistics), Biology, Imputation (genetics), International HapMap Project, Bonferroni correction, symbols.namesake, symbols, Genome-wide association study, 1000 Genomes Project
Funded by
NHMRC| Blue Mountains Cohort Study: Long-term (15-year) incidence of eye disease, hearing loss and other public health outcomes
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 457349
  • Funding stream: NHMRC Project Grants
,
NIH| Major Depression: Stage 1 Genomewide Association in Population-Based Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01MH081802-01
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NHMRC| Genes and Environment in the Risk of Early Age-Related Macular Degeneration: A Population-based Case-Control Study
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 512423
  • Funding stream: NHMRC Project Grants
,
NIH| THE FRAMINGHAM HEART STUDY-268025195
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: N01HC025195-005
  • Funding stream: DIVISION OF EPIDEMIOLOGY AND CLINICAL APPLICATIONS
,
NIH| Genome-Wide Association for Loci Influencing CHD and Other Heart, Lung and Blood
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HL087641-02
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
52 references, page 1 of 4

1. International HapMap Consortium. The International HapMap Project. Nature. 2003; 426(6968):789± 96. doi: 10.1038/nature02168 PMID: 14685227

2. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014; 46(11):1173± 86. Epub 2014/10/06. PubMed Central PMCID: PMC4250049. doi: 10.1038/ng.3097 PMID: 25282103

3. Global Lipids Genetics C, Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Gustafsson S, et al. Discovery and refinement of loci associated with lipid levels. Nat Genet. 2013; 45(11):1274±83. Epub 2013/10/ 08. PubMed Central PMCID: PMC3838666. doi: 10.1038/ng.2797 PMID: 24097068

4. Smith NL, Huffman JE, Strachan DP, Huang J, Dehghan A, Trompet S, et al. Genetic predictors of fibrin D-dimer levels in healthy adults. Circulation. 2011; 123(17):1864±72. Epub 2011/04/20. PubMed Central PMCID: PMC3095913. doi: 10.1161/CIRCULATIONAHA.110.009480 PMID: 21502573

5. Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, et al. Genetic studies of body mass index yield new insights for obesity biology. Nature. 2015; 518(7538):197±206. Epub 2015/02/13. PubMed Central PMCID: PMC4382211. doi: 10.1038/nature14177 PMID: 25673413

6. International Consortium for Blood Pressure Genome-Wide Association Studies, Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature. 2011; 478(7367):103±9. Epub 2011/09/13. PubMed Central PMCID: PMC3340926. doi: 10.1038/nature10405 PMID: 21909115 [OpenAIRE]

7. Huang J, Sabater-Lleal M, Asselbergs FW, Tregouet D, Shin SY, Ding J, et al. Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation. Blood. 2012; 120 (24):4873±81. Epub 2012/09/20. PubMed Central PMCID: PMC3520624. doi: 10.1182/blood-2012-06- 436188 PMID: 22990020 [OpenAIRE]

8. Huang J, Huffman JE, Yamakuchi M, Trompet S, Asselbergs FW, Sabater-Lleal M, et al. Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2. Arterioscler Thromb Vasc Biol. 2014; 34(5):1093±101. Epub 2014/03/ 01. PubMed Central PMCID: PMC4009733. doi: 10.1161/ATVBAHA.113.302088 PMID: 24578379 [OpenAIRE]

9. Estrada K, Styrkarsdottir U, Evangelou E, Hsu YH, Duncan EL, Ntzani EE, et al. Genome-wide metaanalysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet. 2012; 44(5):491±501. Epub 2012/04/17. PubMed Central PMCID: PMC3338864. doi: 10.1038/ ng.2249 PMID: 22504420 [OpenAIRE]

10. CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet. 2013; 45(1):25±33. Epub 2012/12/04. PubMed Central PMCID: PMC3679547. doi: 10.1038/ng.2480 PMID: 23202125

11. Dehghan A, Dupuis J, Barbalic M, Bis JC, Eiriksdottir G, Lu C, et al. Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels. Circulation. 2011; 123(7):731±8. Epub 2011/02/09. PubMed Central PMCID: PMC3147232. doi: 10.1161/ CIRCULATIONAHA.110.948570 PMID: 21300955 [OpenAIRE]

12. Smith NL, Chen MH, Dehghan A, Strachan DP, Basu S, Soranzo N, et al. Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium. Circulation. 2010; 121 (12):1382±92. Epub 2010/03/17. PubMed Central PMCID: PMC2861278. doi: 10.1161/ CIRCULATIONAHA.109.869156 PMID: 20231535

13. Loth DW, Artigas MS, Gharib SA, Wain LV, Franceschini N, Koch B, et al. Genome-wide association analysis identifies six new loci associated with forced vital capacity. Nat Genet. 2014; 46(7):669±77. Epub 2014/06/16. PubMed Central PMCID: PMC4140093. doi: 10.1038/ng.3011 PMID: 24929828 [OpenAIRE]

14. Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, et al. Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A. 2014; 111(4):E455±64. Epub 2014/01/21. PubMed Central PMCID: PMC3910587. doi: 10.1073/pnas.1322563111 PMID: 24443550 [OpenAIRE]

15. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56±65. PubMed Central PMCID: PMC3498066. doi: 10.1038/nature11632 PMID: 23128226

52 references, page 1 of 4
Abstract
<p>An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G im...
Subjects
free text keywords: Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, /dk/atira/pure/researchoutput/pubmedpublicationtype/D052061, Research Support, N.I.H., Extramural, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, /dk/atira/pure/subjectarea/asjc/2700, Medicine(all), /dk/atira/pure/subjectarea/asjc/1300, Biochemistry, Genetics and Molecular Biology(all), /dk/atira/pure/subjectarea/asjc/1100, Agricultural and Biological Sciences(all), Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, Cardiovascular-Disease, Susceptibility Loci, Genetic-Variants, Common Variants, Metaanalysis, Consortium, Imputation, Pressure, Insights, Biology, Research Article, Biology and Life Sciences, Computational Biology, Genome Analysis, Genome-Wide Association Studies, Genetics, Genomics, Human Genetics, Biochemistry, Glycobiology, Glycoproteins, Fibrinogen, Medicine and Health Sciences, Health Care, Health Services Research, Comparative Genomics, Social Sciences, Sociology, Consortia, Research and Analysis Methods, Mathematical and Statistical Techniques, Statistical Methods, Meta-Analysis, Physical Sciences, Mathematics, Statistics (Mathematics), Molecular Biology, Molecular Biology Techniques, Genotyping, Cell Biology, Signal Transduction, Cell Signaling, Genomic Signal Processing, Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, CARDIOVASCULAR-DISEASE, SUSCEPTIBILITY LOCI, GENETIC-VARIANTS, COMMON VARIANTS, METAANALYSIS, CONSORTIUM, IMPUTATION, PRESSURE, INSIGHTS, HapMap Project, Humans, MD Multidisciplinary, General Science & Technology, Haplotype estimation, Imputation (statistics), Biology, Imputation (genetics), International HapMap Project, Bonferroni correction, symbols.namesake, symbols, Genome-wide association study, 1000 Genomes Project
Funded by
NHMRC| Blue Mountains Cohort Study: Long-term (15-year) incidence of eye disease, hearing loss and other public health outcomes
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 457349
  • Funding stream: NHMRC Project Grants
,
NIH| Major Depression: Stage 1 Genomewide Association in Population-Based Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01MH081802-01
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NHMRC| Genes and Environment in the Risk of Early Age-Related Macular Degeneration: A Population-based Case-Control Study
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 512423
  • Funding stream: NHMRC Project Grants
,
NIH| THE FRAMINGHAM HEART STUDY-268025195
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: N01HC025195-005
  • Funding stream: DIVISION OF EPIDEMIOLOGY AND CLINICAL APPLICATIONS
,
NIH| Genome-Wide Association for Loci Influencing CHD and Other Heart, Lung and Blood
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HL087641-02
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
52 references, page 1 of 4

1. International HapMap Consortium. The International HapMap Project. Nature. 2003; 426(6968):789± 96. doi: 10.1038/nature02168 PMID: 14685227

2. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014; 46(11):1173± 86. Epub 2014/10/06. PubMed Central PMCID: PMC4250049. doi: 10.1038/ng.3097 PMID: 25282103

3. Global Lipids Genetics C, Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Gustafsson S, et al. Discovery and refinement of loci associated with lipid levels. Nat Genet. 2013; 45(11):1274±83. Epub 2013/10/ 08. PubMed Central PMCID: PMC3838666. doi: 10.1038/ng.2797 PMID: 24097068

4. Smith NL, Huffman JE, Strachan DP, Huang J, Dehghan A, Trompet S, et al. Genetic predictors of fibrin D-dimer levels in healthy adults. Circulation. 2011; 123(17):1864±72. Epub 2011/04/20. PubMed Central PMCID: PMC3095913. doi: 10.1161/CIRCULATIONAHA.110.009480 PMID: 21502573

5. Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, et al. Genetic studies of body mass index yield new insights for obesity biology. Nature. 2015; 518(7538):197±206. Epub 2015/02/13. PubMed Central PMCID: PMC4382211. doi: 10.1038/nature14177 PMID: 25673413

6. International Consortium for Blood Pressure Genome-Wide Association Studies, Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature. 2011; 478(7367):103±9. Epub 2011/09/13. PubMed Central PMCID: PMC3340926. doi: 10.1038/nature10405 PMID: 21909115 [OpenAIRE]

7. Huang J, Sabater-Lleal M, Asselbergs FW, Tregouet D, Shin SY, Ding J, et al. Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation. Blood. 2012; 120 (24):4873±81. Epub 2012/09/20. PubMed Central PMCID: PMC3520624. doi: 10.1182/blood-2012-06- 436188 PMID: 22990020 [OpenAIRE]

8. Huang J, Huffman JE, Yamakuchi M, Trompet S, Asselbergs FW, Sabater-Lleal M, et al. Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2. Arterioscler Thromb Vasc Biol. 2014; 34(5):1093±101. Epub 2014/03/ 01. PubMed Central PMCID: PMC4009733. doi: 10.1161/ATVBAHA.113.302088 PMID: 24578379 [OpenAIRE]

9. Estrada K, Styrkarsdottir U, Evangelou E, Hsu YH, Duncan EL, Ntzani EE, et al. Genome-wide metaanalysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet. 2012; 44(5):491±501. Epub 2012/04/17. PubMed Central PMCID: PMC3338864. doi: 10.1038/ ng.2249 PMID: 22504420 [OpenAIRE]

10. CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet. 2013; 45(1):25±33. Epub 2012/12/04. PubMed Central PMCID: PMC3679547. doi: 10.1038/ng.2480 PMID: 23202125

11. Dehghan A, Dupuis J, Barbalic M, Bis JC, Eiriksdottir G, Lu C, et al. Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels. Circulation. 2011; 123(7):731±8. Epub 2011/02/09. PubMed Central PMCID: PMC3147232. doi: 10.1161/ CIRCULATIONAHA.110.948570 PMID: 21300955 [OpenAIRE]

12. Smith NL, Chen MH, Dehghan A, Strachan DP, Basu S, Soranzo N, et al. Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium. Circulation. 2010; 121 (12):1382±92. Epub 2010/03/17. PubMed Central PMCID: PMC2861278. doi: 10.1161/ CIRCULATIONAHA.109.869156 PMID: 20231535

13. Loth DW, Artigas MS, Gharib SA, Wain LV, Franceschini N, Koch B, et al. Genome-wide association analysis identifies six new loci associated with forced vital capacity. Nat Genet. 2014; 46(7):669±77. Epub 2014/06/16. PubMed Central PMCID: PMC4140093. doi: 10.1038/ng.3011 PMID: 24929828 [OpenAIRE]

14. Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, et al. Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A. 2014; 111(4):E455±64. Epub 2014/01/21. PubMed Central PMCID: PMC3910587. doi: 10.1073/pnas.1322563111 PMID: 24443550 [OpenAIRE]

15. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56±65. PubMed Central PMCID: PMC3498066. doi: 10.1038/nature11632 PMID: 23128226

52 references, page 1 of 4
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publication . Article . 2017

Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study

Paul S. de Vries; Maria Sabater-Lleal; Daniel I. Chasman; Stella Trompet; Tarunveer S. Ahluwalia; Alexander Teumer; Marcus E. Kleber; Ming-Huei Chen; Jie Jin Wang; John R. Attia; ...