scholarly journals Correction to: Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size

2018 ◽  
Vol 30 (1-2) ◽  
pp. 42-42
Author(s):  
John R. Shorter ◽  
Wei Huang ◽  
Ju Youn Beak ◽  
Kunjie Hua ◽  
Daniel M. Gatti ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Trait Mapping ◽  
Quantitative Trait Mapping ◽  
Diversity Outbred ◽  
Heart Size ◽  
Outbred Mice ◽  
Genomic Regions

scholarly journals Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size

2017 ◽  
Vol 29 (1-2) ◽  
pp. 80-89 ◽  
Author(s):  
John R. Shorter ◽  
Wei Huang ◽  
Ju Youn Beak ◽  
Kunjie Hua ◽  
Daniel M. Gatti ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Trait Mapping ◽  
Quantitative Trait Mapping ◽  
Diversity Outbred ◽  
Heart Size ◽  
Outbred Mice ◽  
Genomic Regions

Tree-based quantitative trait mapping in the presence of external covariates

2016 ◽  
Vol 15 (6) ◽  
Author(s):  
Katherine L. Thompson ◽  
Catherine R. Linnen ◽  
Laura Kubatko
Keyword(s):  
Association Mapping ◽  
Quantitative Trait ◽  
Evolutionary History ◽  
Computational Cost ◽  
Covariance Structure ◽  
Complex Data ◽  
Data Types ◽  
Method Performance ◽  
Trait Mapping ◽  
Quantitative Trait Mapping

AbstractA central goal in biological and biomedical sciences is to identify the molecular basis of variation in morphological and behavioral traits. Over the last decade, improvements in sequencing technologies coupled with the active development of association mapping methods have made it possible to link single nucleotide polymorphisms (SNPs) and quantitative traits. However, a major limitation of existing methods is that they are often unable to consider complex, but biologically-realistic, scenarios. Previous work showed that association mapping method performance can be improved by using the evolutionary history within each SNP to estimate the covariance structure among randomly-sampled individuals. Here, we propose a method that can be used to analyze a variety of data types, such as data including external covariates, while considering the evolutionary history among SNPs, providing an advantage over existing methods. Existing methods either do so at a computational cost, or fail to model these relationships altogether. By considering the broad-scale relationships among SNPs, the proposed approach is both computationally-feasible and informed by the evolutionary history among SNPs. We show that incorporating an approximate covariance structure during analysis of complex data sets increases performance in quantitative trait mapping, and apply the proposed method to deer mice data.

scholarly journals Location-Dependent Empirical Thresholds for Quantitative Trait Mapping

2012 ◽  
Vol 2 (9) ◽  
pp. 1035-1039
Author(s):  
Jason LaCombe ◽  
Benjamin McClosky ◽  
Steven Tanksley
Keyword(s):  
Quantitative Trait ◽  
Trait Mapping ◽  
Quantitative Trait Mapping

Quantitative trait mapping in a diallel cross of recombinant inbred lines

2005 ◽  
Vol 16 (5) ◽  
pp. 344-355 ◽  
Author(s):  
Shirng-Wern Tsaih ◽  
Lu Lu ◽  
David C. Airey ◽  
Robert W. Williams ◽  
Gary A. Churchill
Keyword(s):  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Diallel Cross ◽  
Inbred Lines ◽  
Trait Mapping ◽  
Quantitative Trait Mapping

scholarly journals Sequential Use of Transcriptional Profiling, Expression Quantitative Trait Mapping, and Gene Association Implicates MMP20 in Human Kidney Aging

PLoS Genetics ◽  
2009 ◽  
Vol 5 (10) ◽  
pp. e1000685 ◽  
Author(s):  
Heather E. Wheeler ◽  
E. Jeffrey Metter ◽  
Toshiko Tanaka ◽  
Devin Absher ◽  
John Higgins ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Transcriptional Profiling ◽  
Human Kidney ◽  
Gene Association ◽  
Trait Mapping ◽  
Quantitative Trait Mapping

scholarly journals Genetic Architecture Modulates Diet-Induced Hepatic mRNA and miRNA Expression Profiles in Diversity Outbred Mice

Genetics ◽  
2020 ◽  
Vol 216 (1) ◽  
pp. 241-259
Author(s):  
Excel Que ◽  
Kristen L. James ◽  
Alisha R. Coffey ◽  
Tangi L. Smallwood ◽  
Jody Albright ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Mirna Expression ◽  
Quantitative Trait ◽  
Genetic Architecture ◽  
Genetic Regulation ◽  
Phenotypic Variance ◽  
Expression Quantitative Trait Loci ◽  
Diversity Outbred ◽  
Trait Loci ◽  
Outbred Mice

Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here, we performed global hepatic eQTL and microRNA expression quantitative trait loci (mirQTL) analysis in a population of Diversity Outbred mice fed two different diets. We identified several key features of eQTL and mirQTL, namely differences in the mode of genetic regulation (cis or trans) between mRNA and miRNA. Approximately 50% of mirQTL are regulated by a trans-acting factor, compared to ∼25% of eQTL. We note differences in the heritability of mRNA and miRNA expression and variance explained by each eQTL or mirQTL. In general, cis-acting variants affecting mRNA or miRNA expression explain more phenotypic variance than trans-acting variants. Lastly, we investigated the effect of diet on the genetic architecture of eQTL and mirQTL, highlighting the critical effects of environment on both eQTL and mirQTL. Overall, these data underscore the complex genetic regulation of two well-characterized RNA classes (mRNA and miRNA) that have critical roles in the regulation of clinical traits and disease susceptibility.

scholarly journals Genetic architecture modulates diet-induced hepatic mRNA and miRNA expression profiles in Diversity Outbred mice

Genetics ◽  
2021 ◽  
Vol 218 (3) ◽  
Author(s):  
Excel Que ◽  
Kristen L James ◽  
Alisha R Coffey ◽  
Tangi L Smallwood ◽  
Jody Albright ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Mirna Expression ◽  
Quantitative Trait ◽  
Genetic Architecture ◽  
Genetic Regulation ◽  
Phenotypic Variance ◽  
Expression Quantitative Trait Loci ◽  
Diversity Outbred ◽  
Trait Loci ◽  
Outbred Mice

Abstract Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here, we performed global hepatic eQTL and microRNA expression quantitative trait loci (mirQTL) analysis in a population of Diversity Outbred mice fed two different diets. We identified several key features of eQTL and mirQTL, namely differences in the mode of genetic regulation (cis or trans) between mRNA and miRNA. Approximately 50% of mirQTL are regulated by a trans-acting factor, compared to ∼25% of eQTL. We note differences in the heritability of mRNA and miRNA expression and variance explained by each eQTL or mirQTL. In general, cis-acting variants affecting mRNA or miRNA expression explain more phenotypic variance than trans-acting variants. Finally, we investigated the effect of diet on the genetic architecture of eQTL and mirQTL, highlighting the critical effects of environment on both eQTL and mirQTL. Overall, these data underscore the complex genetic regulation of two well-characterized RNA classes (mRNA and miRNA) that have critical roles in the regulation of clinical traits and disease susceptibility

Dissection of heterogeneous phenotypes for quantitative trait mapping

2005 ◽  
Vol 29 (S1) ◽  
pp. S41-S47 ◽  
Author(s):  
Heike Bickeböller ◽  
Julia N. Bailey ◽  
George J. Papanicolaou ◽  
Albert Rosenberger ◽  
Kevin R. Viel
Keyword(s):  
Quantitative Trait ◽  
Trait Mapping ◽  
Quantitative Trait Mapping
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