Cargando…

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

BACKGROUND: Dense SNP genotypes are often combined with complex trait phenotypes to map causal variants, study genetic architecture and provide genomic predictions for individuals with genotypes but no phenotype. A single method of analysis that jointly fits all genotypes in a Bayesian mixture model...

Descripción completa

Detalles Bibliográficos
Autores principales:	MacLeod, I. M., Bowman, P. J., Vander Jagt, C. J., Haile-Mariam, M., Kemper, K. E., Chamberlain, A. J., Schrooten, C., Hayes, B. J., Goddard, M. E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2016
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769584/ https://www.ncbi.nlm.nih.gov/pubmed/26920147 http://dx.doi.org/10.1186/s12864-016-2443-6

Ejemplares similares

Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions
por: Kemper, Kathryn E, et al.
Publicado: (2015)

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants
por: Nguyen, Tuan V., et al.
Publicado: (2023)

Correction: In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants
por: Nguyen, Tuan V., et al.
Publicado: (2023)

Genome position specific priors for genomic prediction
por: Brøndum, Rasmus Froberg, et al.
Publicado: (2012)

A multi-trait Bayesian method for mapping QTL and genomic prediction
por: Kemper, Kathryn E., et al.
Publicado: (2018)

Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery
por: Herridge, Rowan P, et al.
Publicado: (2011)

Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle
por: van den Berg, I., et al.
Publicado: (2019)

Prior knowledge guided eQTL mapping for identifying candidate genes
por: Wang, Yunli, et al.
Publicado: (2016)

Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping
por: Wang, Tingting, et al.
Publicado: (2017)

Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery
por: Guan, Xin, et al.
Publicado: (2020)

Mutant alleles differentially shape fitness and other complex traits in cattle
por: Xiang, Ruidong, et al.
Publicado: (2021)

Searching QTL by gene expression: analysis of diabesity
por: Brown, Aaron C, et al.
Publicado: (2005)

Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle
por: Dorji, Jigme, et al.
Publicado: (2022)

Sensitivity of genomic selection to using different prior distributions
por: Verbyla, Klara L, et al.
Publicado: (2010)

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis
por: Coffman, Cynthia J, et al.
Publicado: (2003)

Genome-wide fine-mapping identifies pleiotropic and functional variants that predict many traits across global cattle populations
por: Xiang, Ruidong, et al.
Publicado: (2021)

Automated quantitative trait locus analysis (AutoQTL)
por: Freda, Philip J., et al.
Publicado: (2023)

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues
por: Xiang, Ruidong, et al.
Publicado: (2018)

A note on QTL detecting for censored traits
por: Fang, Yixin
Publicado: (2006)

Extensive variation between tissues in allele specific expression in an outbred mammal
por: Chamberlain, Amanda J., et al.
Publicado: (2015)

Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon
por: Vasemägi, Anti, et al.
Publicado: (2010)

Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk
por: Liu, Zhiqian, et al.
Publicado: (2019)

A practical approach for minimising inbreeding and maximising genetic gain in dairy cattle
por: Haile-Mariam, Mekonnen, et al.
Publicado: (2007)

A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping
por: Wang, Tingting, et al.
Publicado: (2016)

Prior knowledge driven Granger causality analysis on gene regulatory network discovery
por: Yao, Shun, et al.
Publicado: (2015)

Data-driven assessment of eQTL mapping methods
por: Michaelson, Jacob J, et al.
Publicado: (2010)

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits
por: Wang, Min, et al.
Publicado: (2018)

RNA-Seq optimization with eQTL gold standards
por: Ellis, Shannon E, et al.
Publicado: (2013)

Improving Genomic Prediction of Crossbred and Purebred Dairy Cattle
por: Khansefid, Majid, et al.
Publicado: (2020)

MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments
por: Veyrieras, Jean-Baptiste, et al.
Publicado: (2007)

SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data
por: Hu, Yue, et al.
Publicado: (2020)

Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks
por: Song, Fei, et al.
Publicado: (2022)

A pilot study to estimate the population size of endangered Galápagos marine iguanas using drones
por: Varela-Jaramillo, Andrea, et al.
Publicado: (2023)

Accuracy of genomic breeding values in multi-breed dairy cattle populations
por: Hayes, Ben J, et al.
Publicado: (2009)

Impact of QTL properties on the accuracy of multi-breed genomic prediction
por: Wientjes, Yvonne CJ, et al.
Publicado: (2015)

Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses
por: Wang, Xiaoqiang, et al.
Publicado: (2012)

Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria
por: Joubert, Fourie, et al.
Publicado: (2009)

Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect
por: van den Berg, Irene, et al.
Publicado: (2017)

Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle
por: Gonzalez-Recio, Oscar, et al.
Publicado: (2015)

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits
por: Xiang, Ruidong, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_69up2rmn5hi70lj0umncc2gv1q