A Statistical Framework for QTL Hotspot Detectio‪n‬ PaperPlayer biorxiv genetics

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Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.08.13.249342v1?rss=1

Authors: Kao, C.-H., Wu, P.-Y., Yang, M.-H.

Abstract:
Quantitative trait loci (QTL) hotspots (genomic locations enriched in QTL) are a common and notable feature when collecting many QTL for various traits in many areas of biological studies. The QTL hotspots are important and attractive since they are highly informative and may harbor genes for the quantitative traits. So far, the current statistical methods for QTL hotspot detection use either the individual-level data from the genetical genomics experiments or the summarized data from public QTL databases to proceed with the detection analysis. These detection methods attempt to address some of the concerns, including the correlation structure among traits, the magnitude of LOD scores within a hotspot and computational cost, that arise during the process of QTL hotspot detection. In this article, we describe a statistical framework that can handle both types of data as well as address all the concerns at a time for QTL hotspot detection. Our statistical framework directly operates on the QTL matrix and hence has a very cheap computation cost, and is deployed to take advantage of the QTL mapping results for assisting the detection analysis. Two special devices, trait grouping and top profile, are introduced into the framework. The trait grouping attempts to group the closely linked or pleiotropic traits together to take care of the true linkages and cope with the underestimation of hotspot thresholds due to non-genetic correlations (arising from ignoring the correlation structure among traits), so as to have the ability to obtain much stricter thresholds and dismiss spurious hotspots. The top profile is designed to outline the LOD-score pattern of a hotspot across the different hotspot architectures, so that it can serve to identify and characterize the types of QTL hotspots with varying sizes and LOD score distributions. Real examples, numerical analysis and simulation study are performed to validate our statistical framework, investigate the detection properties, and also compare with the current methods in QTL hotspot detection. The results demonstrate that the proposed statistical framework can effectively accommodate the correlation structure among traits, identify the types of hotspots and still keep the notable features of easy implementation and fast computation for practical QTL hotspot detection.

Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2020.08.13.249342v1?rss=1

Authors: Kao, C.-H., Wu, P.-Y., Yang, M.-H.

Abstract:
Quantitative trait loci (QTL) hotspots (genomic locations enriched in QTL) are a common and notable feature when collecting many QTL for various traits in many areas of biological studies. The QTL hotspots are important and attractive since they are highly informative and may harbor genes for the quantitative traits. So far, the current statistical methods for QTL hotspot detection use either the individual-level data from the genetical genomics experiments or the summarized data from public QTL databases to proceed with the detection analysis. These detection methods attempt to address some of the concerns, including the correlation structure among traits, the magnitude of LOD scores within a hotspot and computational cost, that arise during the process of QTL hotspot detection. In this article, we describe a statistical framework that can handle both types of data as well as address all the concerns at a time for QTL hotspot detection. Our statistical framework directly operates on the QTL matrix and hence has a very cheap computation cost, and is deployed to take advantage of the QTL mapping results for assisting the detection analysis. Two special devices, trait grouping and top profile, are introduced into the framework. The trait grouping attempts to group the closely linked or pleiotropic traits together to take care of the true linkages and cope with the underestimation of hotspot thresholds due to non-genetic correlations (arising from ignoring the correlation structure among traits), so as to have the ability to obtain much stricter thresholds and dismiss spurious hotspots. The top profile is designed to outline the LOD-score pattern of a hotspot across the different hotspot architectures, so that it can serve to identify and characterize the types of QTL hotspots with varying sizes and LOD score distributions. Real examples, numerical analysis and simulation study are performed to validate our statistical framework, investigate the detection properties, and also compare with the current methods in QTL hotspot detection. The results demonstrate that the proposed statistical framework can effectively accommodate the correlation structure among traits, identify the types of hotspots and still keep the notable features of easy implementation and fast computation for practical QTL hotspot detection.

Copy rights belong to original authors. Visit the link for more info

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