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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...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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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. |
format | Text |
id | pubmed-2654496 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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