Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of "parental" tubes resulted in "hybrids," whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.

Simultaneous detection and estimation of trait associations with genomic phenotypes

Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such phenotypes very densely. This density often results in spatial structure, in the sense that measurements at nearby sites are very similar. In this article, we consider the task of comparing genomic phenotypes across experimental conditions, cell types, or disease subgroups. We propose a new method, Joint Adaptive Differential Estimation (JADE), which leverages the spatial structure inherent to genomic phenotypes. JADE simultaneously estimates smooth underlying group average genomic phenotype profiles and detects regions in which the average profile differs between groups. We evaluate JADE's performance in several biologically plausible simulation settings. We also consider an application to the detection of regions with differential methylation between mature skeletal muscle cells, myotubes, and myoblasts.

Regularized regression for categorical data

In the last two decades, regularization techniques, in particular penalty-based methods, have become very popular in statistical modelling. Driven by technological developments, most approaches have been designed for high-dimensional problems with metric variables, whereas categorical data has largely been neglected. In recent years, however, it has become clear that regularization is also very promising when modelling categorical data. A specific trait of categorical data is that many parameters are typically needed to model the underlying structure. This results in complex estimation problems that call for structured penalties which are tailored to the categorical nature of the data. This article gives a systematic overview of penalty-based methods for categorical data developed so far and highlights some issues where further research is needed. We deal with categorical predictors as well as models for categorical response variables. The primary interest of this article is to give insight into basic properties of and differences between methods that are important with respect to statistical modelling in practice, without going into technical details or extensive discussion of asymptotic properties.

Identifying pediatric cancer clusters in Florida using loglinear models and generalized lasso penalties

We discuss the identification of pediatric cancer clusters in Florida between 2000 and 2010 using a penalized generalized linear model. More specifically, we introduce a Poisson model for the observed number of cases on each of Florida's ZIP Code Tabulation Areas (ZCTA) and regularize the associated disease rate estimates using a generalized Lasso penalty. Our analysis suggests the presence of a number of pediatric cancer clusters during the period over study, with the largest ones being located around the cities of Jacksonville, Miami, Cape Coral/Fort Meyers and Palm Beach.