Dissecting the Functional Impacts of Non-Coding Genetic Variation

A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease susceptibility. Although scientists have identified genetic causes for over 4,000 monogenic diseases, the underlying mechanisms of many highly prevalent multifactorial inheritance disorders such as diabetes, obesity, and cardiovascular disease remain largely unknown. Identifying genetic mechanisms for complex traits has been challenging because most of the variants are located outside of protein-coding regions, and determining the effects of such non-coding variants remains difficult. In this dissertation, I evaluate the hypothesis that such non-coding variants contribute to human traits and diseases by altering the regulation of genes rather than the sequence of those genes. I will specifically focus on studies to determine the functional impacts of genetic variation associated with two related complex traits: gestational hyperglycemia and fetal adiposity. At the genomic locus associated with maternal hyperglycemia, we found that genetic variation in regulatory elements altered the expression of the HKDC1 gene. Furthermore, we demonstrated that HKDC1 phosphorylates glucose in vitro and in vivo, thus demonstrating that HKDC1 is a fifth human hexokinase gene. At the fetal-adiposity associated locus, we identified variants that likely alter VEPH1 expression in preadipocytes during differentiation. To make such studies of regulatory variation high-throughput and routine, we developed POP-STARR, a novel high throughput reporter assay that can empirically measure the effects of regulatory variants directly from patient DNA. By combining targeted genome capture technologies with STARR-seq, we assayed thousands of haplotypes from 760 individuals in a single experiment. We subsequently used POP-STARR to identify three key features of regulatory variants: that regulatory variants typically have weak effects on gene expression; that the effects of regulatory variants are often coordinated with respect to disease-risk, suggesting a general mechanism by which the weak effects can together have phenotypic impact; and that nucleotide transversions have larger impacts on enhancer activity than transitions. Together, the findings presented here demonstrate successful strategies for determining the regulatory mechanisms underlying genetic associations with human traits and diseases, and value of doing so for driving novel biological discovery.

Adaptive Mixture Modelling Metropolis Methods for Bayesian Analysis of Non-linear State-Space Models.

We describe a strategy for Markov chain Monte Carlo analysis of non-linear, non-Gaussian state-space models involving batch analysis for inference on dynamic, latent state variables and fixed model parameters. The key innovation is a Metropolis-Hastings method for the time series of state variables based on sequential approximation of filtering and smoothing densities using normal mixtures. These mixtures are propagated through the non-linearities using an accurate, local mixture approximation method, and we use a regenerating procedure to deal with potential degeneracy of mixture components. This provides accurate, direct approximations to sequential filtering and retrospective smoothing distributions, and hence a useful construction of global Metropolis proposal distributions for simulation of posteriors for the set of states. This analysis is embedded within a Gibbs sampler to include uncertain fixed parameters. We give an example motivated by an application in systems biology. Supplemental materials provide an example based on a stochastic volatility model as well as MATLAB code.

The centrality of event scale: a measure of integrating a trauma into one's identity and its relation to post-traumatic stress disorder symptoms.

We introduce a new scale that measures how central an event is to a person's identity and life story. For the most stressful or traumatic event in a person's life, the full 20-item Centrality of Event Scale (CES) and the short 7-item scale are reliable (alpha's of .94 and .88, respectively) in a sample of 707 undergraduates. The scale correlates .38 with PTSD symptom severity and .23 with depression. The present findings are discussed in relation to previous work on individual differences related to PTSD symptoms. Possible connections between the CES and measures of maladaptive attributions and rumination are considered along with suggestions for future research.

Memorability as a measure of processing: a unit analysis of prose and list learning.

The percentage of subjects recalling each unit in a list or prose passage is considered as a dependent measure. When the same units are recalled in different tasks, processing is assumed to be the same; when different units are recalled, processing is assumed to be different. Two collections of memory tasks are presented, one for lists and one for prose. The relations found in these two collections are supported by an extensive reanalysis of the existing prose memory literature. The same set of words were learned by 13 different groups of subjects under 13 different conditions. Included were intentional free-recall tasks, incidental free recall following lexical decision, and incidental free recall following ratings of orthographic distinctiveness and emotionality. Although the nine free-recall tasks varied widely with regard to the amount of recall, the relative probability of recall for the words was very similar among the tasks. Imagery encoding and recognition produced relative probabilities of recall that were different from each other and from the free-recall tasks. Similar results were obtained with a prose passage. A story was learned by 13 different groups of subjects under 13 different conditions. Eight free-recall tasks, which varied with respect to incidental or intentional learning, retention interval, and the age of the subjects, produced similar relative probabilities of recall, whereas recognition and prompted recall produced relative probabilities of recall that were different from each other and from the free-recall tasks. A review of the prose literature was undertaken to test the generality of these results. Analysis of variance is the most common statistical procedure in this literature. If the relative probability of recall of units varied across conditions, a units by condition interaction would be expected. For the 12 studies that manipulated retention interval, an average of 21% of the variance was accounted for by the main effect of retention interval, 17% by the main effect of units, and only 2% by the retention interval by units interaction. Similarly, for the 12 studies that varied the age of the subjects, 6% of the variance was accounted for by the main effect of age, 32% by the main effect of units, and only 1% by the interaction of age by units.(ABSTRACT TRUNCATED AT 400 WORDS)