ArticleBMC proceedings2010
QTL detection for a medium density SNP panel: comparison of different LD and LA methods.
Article in BMC proceedings, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed, 3 citations in OpenAlex.
- A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state.BMC genomics · 2012Article
- Comparison of analyses of the QTLMAS XIII common dataset. II: QTL analysis.BMC proceedings · 2010Article
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4 authors at 2 institutions in 1 country.
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Abstract
backgroundNew molecular technologies allow high throughput genotyping for QTL mapping with dense genetic maps. Therefore, the interest of linkage analysis models against linkage disequilibrium could be questioned. As these two strategies are very sensitive to marker density, experimental design structures, linkage disequilibrium extent and QTL effect, we propose to investigate these parameters effects on QTL detection.
methodsThe XIIIth QTLMAS workshop simulated dataset was analysed using three linkage disequilibrium models and a linkage analysis model. Interval mapping, multivariate and interaction between QTL analyses were performed using QTLMAP.
resultsThe linkage analysis models identified 13 QTL, from which 10 mapped close of the 18 which were simulated and three other positions being falsely mapped as containing a QTL. Most of the QTLs identified by interval mapping analysis are not clearly detected by any linkage disequilibrium model. In addition, QTL effects are evolving during the time which was not observed using the linkage disequilibrium models.
conclusionsOur results show that for such a marker density the interval mapping strategy is still better than using the linkage disequilibrium only. While the experimental design structure gives a lot of power to both approaches, the marker density and informativity clearly affect linkage disequilibrium efficiency for QTL detection.
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