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Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping

As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide associa...

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Autores principales: Crooks, Lucy, Sahana, Goutam, de Koning, Dirk-Jan, Lund, Mogens Sandø, Carlborg, Örjan
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654496/
https://www.ncbi.nlm.nih.gov/pubmed/19278541
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author Crooks, Lucy
Sahana, Goutam
de Koning, Dirk-Jan
Lund, Mogens Sandø
Carlborg, Örjan
author_facet Crooks, Lucy
Sahana, Goutam
de Koning, Dirk-Jan
Lund, Mogens Sandø
Carlborg, Örjan
author_sort Crooks, Lucy
collection PubMed
description As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide association (GWA) efforts to map quantitative trait loci (QTL). Generally the power to detect QTL was high and the Type 1 error was low. Estimates of QTL locations were generally very accurate. Some methods were much better than others at estimating QTL effects, and with some the accuracy depended on simulated effect size or minor allele frequency. There were also indications of bias in the effect estimates. No epistasis was simulated, but the two studies that included searches for epistasis reported several interacting loci, indicating a problem with controlling the Type I error rate in these analyses. Although this study is based on a single dataset, it indicates that there is a need to improve fine mapping and GWA methods with respect to estimation of genetic effects, appropriate choice of significance thresholds and analysis of epistasis.
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spelling pubmed-26544962009-03-13 Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping Crooks, Lucy Sahana, Goutam de Koning, Dirk-Jan Lund, Mogens Sandø Carlborg, Örjan BMC Proc Overview - Dataset Comparison II As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide association (GWA) efforts to map quantitative trait loci (QTL). Generally the power to detect QTL was high and the Type 1 error was low. Estimates of QTL locations were generally very accurate. Some methods were much better than others at estimating QTL effects, and with some the accuracy depended on simulated effect size or minor allele frequency. There were also indications of bias in the effect estimates. No epistasis was simulated, but the two studies that included searches for epistasis reported several interacting loci, indicating a problem with controlling the Type I error rate in these analyses. Although this study is based on a single dataset, it indicates that there is a need to improve fine mapping and GWA methods with respect to estimation of genetic effects, appropriate choice of significance thresholds and analysis of epistasis. BioMed Central 2009-02-23 /pmc/articles/PMC2654496/ /pubmed/19278541 Text en Copyright © 2009 Crooks et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Overview - Dataset Comparison II
Crooks, Lucy
Sahana, Goutam
de Koning, Dirk-Jan
Lund, Mogens Sandø
Carlborg, Örjan
Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title_full Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title_fullStr Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title_full_unstemmed Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title_short Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping
title_sort comparison of analyses of the qtlmas xii common dataset. ii: genome-wide association and fine mapping
topic Overview - Dataset Comparison II
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654496/
https://www.ncbi.nlm.nih.gov/pubmed/19278541
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