Comparision of analysis of the QTLMAS XII common dataset: II: genome-wide association and fine mapping

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  • Lucy Crooks, Swedish University of Agricultural Sciences, Sverige
  • Goutam Sahana
  • Dirk-Jan de Koning, University of Edinburgh, Storbritannien
  • Mogens Sandø Lund
  • Örjan Carlborg, Swedish University of Agricultural Sciences, Sverige
  • Biostatistik
  • Institut for Genetik og Bioteknologi
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
TidsskriftBMC Proceedings
NummerSuppl 1
Antal sider13
StatusUdgivet - 2009
BegivenhedEuropean workshop on QTL mapping and marker assisted selection - Uppsala, Sverige
Varighed: 15 maj 200816 aug. 2008
Konferencens nummer: 12th


KonferenceEuropean workshop on QTL mapping and marker assisted selection

Bibliografisk note

Udgivelsesdato: 23. February
Volumne: 3

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