Statistical and Computational Methods for Genome-Wide Association Analysis

Technological and scientific advances in recent years have revolutionized genomics. For example, decreases in whole genome sequencing (WGS) costs have enabled larger WGS studies as well as larger imputation reference panels, which in turn provide more comprehensive genomic coverage from lower-cost genotyping methods. In addition, new technologies and large collaborative efforts such as ENCODE and GTEx have shed new light on regulatory genomics and the function of non-coding variation, and produced expansive publicly available data sets. These advances have introduced data of unprecedented size and dimension, unique statistical and computational challenges, and numerous opportunities for innovation. In this dissertation, we develop methods to leverage functional genomics data in post-GWAS analysis, to expedite routine computations with increasingly large genetic data sets, and to address limitations of current imputation reference panels for understudied populations. In Chapter 2, we propose strategies to improve imputation and increase power in GWAS of understudied populations. Genotype imputation is instrumental in GWAS, providing increased genomic coverage from low-cost genotyping arrays. Imputation quality depends crucially on reference panel size and the genetic distance between reference and target haplotypes. Current reference panels provide excellent imputation quality in many European populations, but lower quality in non-European, admixed, and isolate populations. We consider a GWAS strategy in which a subset of participants is sequenced and the rest are imputed using a reference panel that comprises the sequenced participants together with individuals from an external reference panel. Using empirical data from the HRC and TOPMed WGS Project, simulations, and asymptotic analysis, we identify powerful and cost-effective study designs for GWAS of non-European, admixed, and isolated populations. In Chapter 3, we develop efficient methods to estimate linkage disequilibrium (LD) with large data sets. Motivated by practical and logistical constraints, a variety of statistical methods and tools have been developed for analysis of GWAS summary statistics rather than individual-level data. These methods often rely on LD estimates from an external reference panel, which are ideally calculated on-the-fly rather than precomputed and stored. We develop efficient algorithms to estimate LD exploiting sparsity and haplotype structure and implement our methods in an open-source C++ tool, emeraLD. We benchmark performance using genotype data from the 1KGP, HRC, and UK Biobank, and find that emeraLD is up to two orders of magnitude faster than existing tools while using comparable or less memory. In Chapter 4, we develop methods to identify causative genes and biological mechanisms underlying associations in post-GWAS analysis by leveraging regulatory and functional genomics databases. Many gene-based association tests can be viewed as instrumental variable methods in which intermediate phenotypes, e.g. tissue-specific expression or protein alteration, are hypothesized to mediate the association between genotype and GWAS trait. However, LD and pleiotropy can confound these statistics, which complicates their mechanistic interpretation. We develop a hierarchical Bayesian model that accounts for multiple potential mechanisms underlying associations using functional genomic annotations derived from GTEx, Roadmap/ENCODE, and other sources. We apply our method to analyze twenty-five complex traits using GWAS summary statistics from UK Biobank, and provide an open-source implementation of our methods. In Chapter 5, we review our work, discuss its relevance and prospects as new resources emerge, and suggest directions for future research.PHDBiostatisticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147697/1/corbinq_1.pd

A Framework For Detecting Noncoding Rare-Variant associations of Large-Scale Whole-Genome Sequencing Studies

Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 toPMed samples. We also analyze five non-lipid toPMed traits

The Science Case for Io Exploration

Io is a priority destination for solar system exploration, as it is the best natural laboratory to study the intertwined processes of tidal heating, extreme volcanism, and atmosphere-magnetosphere interactions. Io exploration is relevant to understanding terrestrial worlds (including the early Earth), ocean worlds, and exoplanets across the cosmos

Recommendations for Addressing Priority Io Science in the Next Decade

Io is a priority destination for solar system exploration. The scope and importance of science questions at Io necessitates a broad portfolio of research and analysis, telescopic observations, and planetary missions - including a dedicated New Frontiers class Io mission

Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis.

Gene-based association tests aggregate genotypes across multiple variants for each gene, providing an interpretable gene-level analysis framework for genome-wide association studies (GWAS). Early gene-based test applications often focused on rare coding variants; a more recent wave of gene-based methods, e.g. TWAS, use eQTLs to interrogate regulatory associations. Regulatory variants are expected to be particularly valuable for gene-based analysis, since most GWAS associations to date are non-coding. However, identifying causal genes from regulatory associations remains challenging and contentious. Here, we present a statistical framework and computational tool to integrate heterogeneous annotations with GWAS summary statistics for gene-based analysis, applied with comprehensive coding and tissue-specific regulatory annotations. We compare power and accuracy identifying causal genes across single-annotation, omnibus, and annotation-agnostic gene-based tests in simulation studies and an analysis of 128 traits from the UK Biobank, and find that incorporating heterogeneous annotations in gene-based association analysis increases power and performance identifying causal genes

PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

Abstract We propose a new computational framework, probabilistic transcriptome-wide association study (PTWAS), to investigate causal relationships between gene expressions and complex traits. PTWAS applies the established principles from instrumental variables analysis and takes advantage of probabilistic eQTL annotations to delineate and tackle the unique challenges arising in TWAS. PTWAS not only confers higher power than the existing methods but also provides novel functionalities to evaluate the causal assumptions and estimate tissue- or cell-type-specific gene-to-trait effects. We illustrate the power of PTWAS by analyzing the eQTL data across 49 tissues from GTEx (v8) and GWAS summary statistics from 114 complex traits.http://deepblue.lib.umich.edu/bitstream/2027.42/173857/1/13059_2020_Article_2026.pd

Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

Meta-analysis of whole genome sequencing/whole exome sequencing (WGS/WES) studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare variants associated with complex phenotypes. Existing rare variant meta-analysis approaches are not scalable to biobank-scale WGS data. Here we present MetaSTAAR, a powerful and resource-efficient rare variant meta-analysis framework for large-scale WGS/WES studies. MetaSTAAR accounts for relatedness and population structure, can analyze both quantitative and dichotomous traits and boosts the power of rare variant tests by incorporating multiple variant functional annotations. Through meta-analysis of four lipid traits in 30,138 ancestrally diverse samples from 14 studies of the Trans Omics for Precision Medicine (TOPMed) Program, we show that MetaSTAAR performs rare variant meta-analysis at scale and produces results comparable to using pooled data. Additionally, we identified several conditionally significant rare variant associations with lipid traits. We further demonstrate that MetaSTAAR is scalable to biobank-scale cohorts through meta-analysis of TOPMed WGS data and UK Biobank WES data of ~200,000 samples