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Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study
- Source :
- PLoS One (print), 12(1):e0167742. Public Library of Science, de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLoS ONE, vol. 12, no. 1, e0167742, pp. e0167742 . https://doi.org/10.1371/journal.pone.0167742, De Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, De Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, De Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study ', PLoS ONE, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, De Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, De Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, De Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study ', PL o S One, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, de Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLOS ONE, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, PLoS ONE, 12(1), de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, de Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLoS ONE, vol. 12, no. 1, pp. e0167742 . https://doi.org/10.1371/journal.pone.0167742, PLoS ONE, 12(1):e0167742. Public Library of Science, PloS one, vol 12, iss 1, PLoS ONE, Vol 12, Iss 1, p e0167742 (2017), PLoS ONE
- Publication Year :
- 2017
- Publisher :
- Public Library of Science, 2017.
-
Abstract
- 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 imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.
- Subjects :
- Netherlands Twin Register (NTR)
0301 basic medicine
Glycobiology
Social Sciences
lcsh:Medicine
Genome-wide association study
030105 genetics & heredity
Biochemistry
Mathematical and Statistical Techniques
Sociology
Cell Signaling
Consortia
GENETIC-VARIANTS
Medicine and Health Sciences
IMPUTATION
International HapMap Project
lcsh:Science
Genetics
Multidisciplinary
COMMON VARIANTS
Genomics
Multidisciplinary Sciences
INSIGHTS
CARDIOVASCULAR-DISEASE
Physical Sciences
symbols
Science & Technology - Other Topics
Health Services Research
Genomic Signal Processing
Statistics (Mathematics)
Research Article
Signal Transduction
Genotyping
SUSCEPTIBILITY LOCI
General Science & Technology
BIOLOGY
Single-nucleotide polymorphism
HapMap Project
Computational biology
PRESSURE
Biology
Research and Analysis Methods
03 medical and health sciences
symbols.namesake
MD Multidisciplinary
Genome-Wide Association Studies
Journal Article
Humans
Statistical Methods
1000 Genomes Project
Molecular Biology Techniques
Molecular Biology
METAANALYSIS
Glycoproteins
Science & Technology
lcsh:R
Human Genome
CONSORTIUM
Biology and Life Sciences
Computational Biology
Fibrinogen
Human Genetics
Cell Biology
Comparative Genomics
Genome Analysis
Health Care
030104 developmental biology
Bonferroni correction
lcsh:Q
Haplotype estimation
Mathematics
Imputation (genetics)
Meta-Analysis
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Database :
- OpenAIRE
- Journal :
- PLoS One (print), 12(1):e0167742. Public Library of Science, de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLoS ONE, vol. 12, no. 1, e0167742, pp. e0167742 . https://doi.org/10.1371/journal.pone.0167742, De Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, De Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, De Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study ', PLoS ONE, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, De Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, De Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, De Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, De Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study ', PL o S One, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, de Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLOS ONE, vol. 12, no. 1, e0167742 . https://doi.org/10.1371/journal.pone.0167742, PLoS ONE, 12(1), de Vries, P S, Sabater-Lleal, M, Chasman, D I, Trompet, S, Ahluwalia, T S, Teumer, A, Kleber, M E, Chen, M-H, Wang, J J, Attia, J R, Marioni, R E, Steri, M, Weng, L-C, Pool, R, Grossmann, V, Brody, J A, Venturini, C, Tanaka, T, Rose, L M, Oldmeadow, C, Mazur, J, Basu, S, Frånberg, M, Yang, Q, Ligthart, S, Hottenga, J J, Rumley, A, Mulas, A, de Craen, A J M, Grotevendt, A, Taylor, K D, Delgado, G E, Kifley, A, Lopez, L M, Berentzen, T L, Mangino, M, Bandinelli, S, Morrison, A C, Hamsten, A, Tofler, G, de Maat, M P M, Draisma, H H M, Lowe, G D, Zoledziewska, M, Sattar, N, Lackner, K J, Völker, U, McKnight, B, Huang, J, Holliday, E G, McEvoy, M A, Starr, J M, Hysi, P G, Hernandez, D G, Guan, W, Rivadeneira, F, McArdle, W L, Slagboom, P E, Zeller, T, Psaty, B M, Uitterlinden, A G, de Geus, E J C, Stott, D J, Binder, H, Hofman, A, Franco, O H, Rotter, J I, Ferrucci, L, Spector, T D, Deary, I J, März, W, Greinacher, A, Wild, P S, Cucca, F, Boomsma, D I, Watkins, H, Tang, W, Ridker, P M, Jukema, J W, Scott, R J, Mitchell, P, Hansen, T, O'Donnell, C J, Smith, N L, Strachan, D P & Dehghan, A 2017, ' Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study ', PLoS ONE, vol. 12, no. 1, pp. e0167742 . https://doi.org/10.1371/journal.pone.0167742, PLoS ONE, 12(1):e0167742. Public Library of Science, PloS one, vol 12, iss 1, PLoS ONE, Vol 12, Iss 1, p e0167742 (2017), PLoS ONE
- Accession number :
- edsair.doi.dedup.....b6e37d2f1380f91bb68e70f2c58266d3