Biology subjects

He, T.

Publications and source records attributed to He, T..

5 recordsLinked to original sources

bioRxiv2018

A Simple Approximation To The Bias Of Gene-Environment Interactions In Case/Control Studies With Silent Disease

One of the most important research areas in case-control Genome-Wide Association Studies is to determine how the effect of a genotype varies across the environment or to measure the gene-environment interaction (GxE). We consider the scenario when some of the \"healthy\" controls actually have the disease and when the frequency of these latent cases varies by the environmental variable of interest. In this scenario, performing logistic regression of clinically defined case status on the genetic variant, environmental variable, and their interaction will result in biased estimates of GxE interaction. Here, we derive a general theoretical approximation to the bias in the estimates of the GxE interaction and show, through extensive simulation, that this approximation is accurate in finite samples. Moreover, we apply this approximation to evaluate the bias in the effect estimates of the genetic variants related to mitochondrial proteins a large-scale Prostate Cancer study.

genetics↗

bioRxiv2018

Accurate Nonlinear Mapping between MNI Volumetric and FreeSurfer Surface Coordinate Systems

The results of most neuroimaging studies are reported in volumetric (e.g., MNI152) or surface (e.g., fsaverage) coordinate systems. Accurate mappings between volumetric and surface coordinate systems can facilitate many applications, such as projecting fMRI group analyses from MNI152/Colin27 to fsaverage for visualization, or projecting resting-state fMRI parcellations from fsaverage to MNI152/Colin27 for volumetric analysis of new data. However, there has been surprisingly little research on this topic. Here, we evaluated three approaches for mapping data between MNI152/Colin27 and fsaverage coordinate systems by simulating the above applications: projection of group-average data from MNI152/Colin27 to fsaverage and projection of fsaverage parcellations to MNI152/Colin27. Two of the approaches are currently widely used. A third approach (registration fusion) was previously proposed, but not widely adopted. Two implementations of the registration fusion (RF) approach were considered, with one implementation utilizing the Advanced Normalization Tools (ANTs). We found that RF-ANTs performed the best for mapping between fsaverage and MNI152/Colin27, even for new subjects registered to MNI152/Colin27 using a different software tool (FSL FNIRT). This suggests that RF-ANTs would be useful even for researchers not using ANTs. Finally, it is worth emphasizing that the most optimal approach for mapping data to a coordinate system (e.g., fsaverage) is to register individual subjects directly to the coordinate system, rather than via another coordinate system. Only in scenarios where the optimal approach is not possible (e.g., mapping previously published results from MNI152 to fsaverage), should the approaches evaluated in this manuscript be considered. In these scenarios, we recommend RF-ANTs (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion).

neuroscience↗

bioRxiv2018

An optimal kernel-based method for gene set association analysis

Single-variant based genome-wide association studies have successfully detected many genetic variants that are associated with many complex traits. However, their power is limited due to weak marginal signals and ignoring potential complex interactions among genetic variants. Set-based strategy was proposed to provide a remedy where multiple genetic variants in a given set (e.g., gene or pathway) are jointly evaluated, so that the systematic effect of the set is considered. Among many, the kernel-based testing (KBT) framework is one of the most popular and powerful methods in set-based association studies. Given a set of candidate kernels, method has been proposed to choose the one with the smallest p-value. Such a method, however, can yield inflated type I error, especially when the number of variants in a set is large. Alternatively one can get p-values by permutations which, however, could be very time consuming. In this work, we proposed an efficient testing procedure that can not only control type I error rate but also generate power close to the one obtained under the optimal kernel. Our method is built upon the KBT framework and is based on asymptotic results under a high-dimensional setting. Hence it can efficiently deal with the case where the number of variants in a set is much larger than the sample size. Both simulation and real data analysis demonstrate the advantages of the method compared with its counterparts.

genetics↗

bioRxiv2018

Predictive remapping of visual features beyond saccadic targets

Visual stability is thought to be mediated by predictive remapping of the relevant object information from its current, pre-saccadic locations to its future, post-saccadic location on the retina. However, it is heavily debated whether and what feature information is predictively remapped during the pre-saccadic interval. Using an orientation adaptation paradigm, we investigated whether predictive remapping occurs for stimulus features and whether adaptation itself is remapped. We found strong evidence for predictive remapping of a stimulus presented shortly before saccade onset, but no remapping of adaptation. Furthermore, we establish that predictive remapping also occurs for stimuli that are not saccade targets, pointing toward a forward remapping process operating across the whole visual field. Together, our findings suggest that predictive feature remapping of object information plays an important role in mediating visual stability.

neuroscience↗

bioRxiv2017

Contribution of transition and stabilization processes to speciation is a function of the ancestral trait state and selective environment in Hakea

Currently the origin and trajectories of novel traits are emphasised in evolutionary studies, the role of stabilization is neglected, and interpretations are often post hoc rather than as hypothesised responses to stated agents of selection. Here we evaluated the impact of changing environmental conditions on trait evolution and stabilization and their relative contribution to diversification in a prominent Australian genus, Hakea (Proteaceae). We assembled a time-based phylogeny for Hakea, reconstructed its ancestral traits for six attributes and determined their evolutionary trajectories in response to the advent or increasing presence of fire, seasonality, aridity, nectar-feeding birds and (in)vertebrate herbivores/granivores. The ancestral Hakea arose 18 million years ago (Ma) and was broad-leaved, non-spinescent, insect-pollinated, had medium-sized, serotinous fruits and resprouted after fire. Of the 190 diversification events that yielded the 82 extant species analysed, 8-50% involved evolution, stabilization or re-evolution (reversal) of individual novel traits. Needle leaves appeared 14 Ma and increased through the Neogene/Quaternary coinciding with intensifying seasonality and aridity. Spinescence arose 12 Ma consistent with the advent of vertebrate herbivores. Bird-pollination appeared 14 Ma in response to advent of the Meliphagidae in the early Miocene. Small and large woody fruits evolved from 12 Ma as alternative defenses against granivory. Fire-caused death evolved 14 Ma, accounting for 50% of subsequent events, as fire became less stochastic. Loss of serotiny began in the late Miocene as non-fireprone habitats became available but only contributed 8% of events. Innovation and subsequent stabilization of functional traits promoted the overall species diversification rate in Hakea by 15 times such that only three species now retain the ancestral phenotype. Our approach holds great promise for understanding the processes responsible for speciation of organisms when the ancestral condition can be identified and the likely selective agents are understood.

ecology↗