Genome-wide genetic association of complex traits in heterogeneous stock mice

By W. Valdar, Leah C. Solberg, D. Gauguier, Stephanie Burnett, P. Klenerman, W. Cookson, Martin S. Taylor, J. N. P. Rawlins, Richard Mott, J. Flint. Nature Genetics, 2006

596 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be0f3e105b8a7891e731e20b6948f5a4b6e77edc

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population (2011, methodology): “We carried out two distinct initial GWA analyses: a single forward regression search on each chromosome separately using the full RIL dataset, and forward regression for each chromosome within each of 100 subsample data sets containing 80% of the RILs in each famil”
Missing heritability and strategies for finding the underlying causes of complex disease (2010, background): “; however, apparently equally complex phenotypes (such as cell counts of red and white blood cells, variation in high and low density lipoproteins and obesity) have a much more complex genetic architecture due to the joint action of very many loci of small effec”
Mouse genomic variation and its effect on phenotypes and gene regulation (2011, unknown): “90 4,198,324 (44,837) 823,688 (24,502) 28,691 (1,474) AKR/J 107.”
Genome-wide association study of leaf architecture in the maize nested association mapping population (2011, methodology): “For leaf quantitative traits, we used a subsampling-based multiple SNP model to carry out association mapping (Online Methods) based on a method successfully applied to GWAS in mic”
Genomic Selection in Plant Breeding (2011, background): “VanRaden et al. (2009) designated bulls born between 1952 and 1998 as the training set and bulls born between 1999 and 2002 as the validation set so that no sons were present in the training set, as per a real breeding program.”
Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies (2017, methodology): “We tested the genetic associations between genetic variables with 44 different traits such as days to germination , days to ﬂowering , lesioning etc. 2) Heterogeneous Stock Mice: The heterogeneous stock mice dataset contains measurements from around 700 mice, with 100,000 genetic variables [34].”
Genomic selection in plant breeding: from theory to practice. (2010, background): “QTL analysis of this population did not result in a ‘case of missing heritability’ [62].”
Using Genetic Distance to Infer the Accuracy of Genomic Prediction (2015, background): “The heterogeneous mice population from [42] consists of 1940 individuals genotyped with 12545 SNPs; among the recorded traits, we consider growth rate and weight.”
The genetics of inbreeding depression (2009, background): “Sophisticated analyses of QTL-fine-mapping experiments, starting with experimentally tractable numbers of founding genotypes, may soon allow nearly single-gene resolution of QTLs, and they should have the power to detect mutations that have effects of just a few per cent and that are present in just”
Accuracy of Predicting the Genetic Risk of Disease Using a Genome-Wide Approach (2008, unknown): “However, when a disease is of complex inheritance, the genetic risk of the disease may be associated with many loci, each explaining only a small portion of the genetic variance [1,2].”
Polygenic Modeling with Bayesian Sparse Linear Mixed Models (2012, methodology): “In addition to the WTCCC dataset, we also assess perdition performance using a mouse dataset [67], which has been widely used to compare various phenotype prediction methods [37–39].”
A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana (2009, methodology): “QTL study in mice [30] where it was shown by simulation to be a”
Prediction of individual genetic risk to disease from genome-wide association studies. (2007, background): “In species where it is possible to measure the number of loci influencing a trait, around 10–50 loci have been identified, most individually counting for only a few percent, and together accounting for <50% of the genetic variation (Henderson et al. 2004; Jacobsson et al. 2005; Valdar et al. 2006).”
Accounting for linkage disequilibrium in genome-wide association studies: A penalized regression method (2013, methodology): “This data resource, which also includes pedigree information, was based on an advanced intercross mating among 8 inbred strains over 50 generations of random mating [17].”
Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree (2009, methodology): “These results are in agreement with previous reports (Valdar et al. 2006b and Legarra et al. 382 G. de los Campos et al. 2008 for the mouse data and Crossa et al. 2007 for the wheat data) for these traits and populations.”
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses (2012, unknown): “Our understanding of the genetic basis of gene expression has been developed by studying species such as yeast 3–5 , worms 6 , mice 7,8 and humans 9–12 .”