While the machinery of quantitative genetics can blissfully function in complete ignorance of any of the underlying genetic details, we are certainly interested (at least one some level) on the genetic basis of trait variation. At the most practical level, if a gene of major effect is segregating in our population of interest, we would certainly like to not only to be aware of this, but also to...

Expression quantitative trait loci (eQTL) mapping holds great promise in elucidating gene regulations and predicting gene networks associated with complex phenotypes. We propose a systems biology approach by incorporating prior pathway information into an eQTL mapping framework, to identify novel pathway regulators that mediate pathway expression changes. We model gene expressions in a predefin...

UNLABELLED : Commonly used multiplicity adjustments fail to control the error rate for reported findings in many expression quantitative trait loci (eQTL) studies. TreeQTL implements a hierarchical multiple testing procedure which allows control of appropriate error rates defined relative to a grouping of the eQTL hypotheses. AVAILABILITY AND IMPLEMENTATION The R package TreeQTL is available ...

In 2001, Sen and Churchill reported a general Bayesian framework for quantitative trait loci (QTL) mapping in inbred line crosses. The framework is a powerful one, as many QTL mapping methods can be represented as special cases and many important considerations are accommodated. These considerations include accounting for covariates, nonstandard crosses, missing genotypes, genotyping errors, mu...

Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. We developed a genomic quantitative genetic approach to overcome this problem, allowing us to e...

Recent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as allele frequency and effect size. One lesser-known aspect of complex traits is the extent of allelic heterogeneity (AH) arising from multiple causal variants at a locus. We developed a computational method to infer the probability ...

Ontogenetic variation in the causal components of phenotypic variability and covariability is described for body weight and tail length in mice derived from a full 7 x 7 diallel cross. Age-related changes in additive, dominance, sex-linked and maternal variance and covariance between 14 and 70 days of age are described. Age-specific variance components at time t are conditioned on the causal ge...

This article presents a method to combine QTL results from different independent analyses. This method provides a modified Akaike criterion that can be used to decide how many QTL are actually represented by the QTL detected in different experiments. This criterion is computed to choose between models with one, two, three, etc., QTL. Simulations are carried out to investigate the quality of the...

Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression ...

MOTIVATION In most quantitative trait locus (QTL) mapping studies, phenotypes are assumed to follow normal distributions. Deviations from this assumption may affect the accuracy of QTL detection and lead to detection of spurious QTLs. To improve the robustness of QTL mapping methods, we replaced the normal distribution for residuals in multiple interacting QTL models with the normal/independent...