Powerful Method for Including Genotype Uncertainty in Tests of Hardy-Weinberg Equilibrium

The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both simulated and real genotypes

Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries

Traditional Hardy-Weinberg equilibrium (HWE) tests (the χ2 test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in datasets comprised of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and evaluate the impact of population heterogeneity and genotype uncertainty on the standard HWE tests and alternative methods using simulated and real sequence datasets. Our results demonstrate that ignoring population structure or genotype uncertainty in HWE tests can inflate false positive rates by many orders of magnitude. Our evaluations demonstrate different tradeoffs between false positives and statistical power across the methods, with RUTH consistently amongst the best across all evaluations. RUTH is implemented as a practical and scalable software tool to rapidly perform HWE tests across millions of markers and hundreds of thousands of individuals while supporting standard VCF/BCF formats. RUTH is publicly available at https://www.github.com/statgen/ruth

gap: Genetic Analysis Package

A preliminary attempt at collecting tools and utilities for genetic data as an R package called gap is described. Genomewide association is then described as a specific example, linking the work of Risch and Merikangas (1996), Long and Langley (1997) for family-based and population-based studies, and the counterpart for case-cohort design established by Cai and Zeng (2004). Analysis of staged design as outlined by Skol et al. (2006) and associate methods are discussed. The package is flexible, customizable, and should prove useful to researchers especially in its application to genomewide association studies.

Haplotype reconstruction error as a classical misclassification problem

Statistically reconstructing haplotypes from single nucleotide polymorphism (SNP) genotypes, can lead to falsely classified haplotypes. This can be an issue when interpreting haplotype association results or when selecting subjects with certain haplotypes for subsequent functional studies. It was our aim to quantify haplotype reconstruction error and to provide tools for it. By numerous simulation scenarios, we systematically investigated several error measures, including discrepancy, error rate, and R(2), and introduced the sensitivity and specificity to this context. We exemplified several measures in the KORA study, a large population-based study from Southern Germany. We find that the specificity is slightly reduced only for common haplotypes, while the sensitivity was decreased for some, but not all rare haplotypes. The overall error rate was generally increasing with increasing number of loci, increasing minor allele frequency of SNPs, decreasing correlation between the alleles and increasing ambiguity. We conclude that, with the analytical approach presented here, haplotype-specific error measures can be computed to gain insight into the haplotype uncertainty. This method provides the information, if a specific risk haplotype can be expected to be reconstructed with rather no or high misclassification and thus on the magnitude of expected bias in association estimates. We also illustrate that sensitivity and specificity separate two dimensions of the haplotype reconstruction error, which completely describe the misclassification matrix and thus provide the prerequisite for methods accounting for misclassification

Statistical and Computational Methods for Analyzing and Visualizing Large-Scale Genomic Datasets

Advances in large-scale genomic data production have led to a need for better methods to process, interpret, and organize this data. Starting with raw sequencing data, generating results requires many complex data processing steps, from quality control, alignment, and variant calling to genome wide association studies (GWAS) and characterization of expression quantitative trait loci (eQTL). In this dissertation, I present methods to address issues faced when working with large-scale genomic datasets. In Chapter 2, I present an analysis of 4,787 whole genomes sequenced for the study of age-related macular degeneration (AMD) as a follow-up fine-mapping study to previous work from the International AMD Genomics Consortium (IAMDGC). Through whole genome sequencing, we comprehensively characterized genetic variants associated with AMD in known loci to provide additional insights on the variants potentially responsible for the disease by leveraging 60,706 additional controls. Our study improved the understanding of loci associated with AMD and demonstrated the advantages and disadvantages of different approaches for fine-mapping studies with sequence-based genotypes. In Chapter 3, I describe a novel method and a software tool to perform Hardy-Weinberg equilibrium (HWE) tests for structured populations. In sequence-based genetic studies, HWE test statistics are important quality metrics to distinguish true genetic variants from artifactual ones, but it becomes much less informative when it is applied to a heterogeneous and/or structured population. As next generation sequencing studies contain samples from increasingly diverse ancestries, we developed a new HWE test which addresses both the statistical and computational challenges of modern large-scale sequencing data and implemented the method in a publicly available software tool. Moreover, we extensively evaluated our proposed method with alternative methods to test HWE in both simulated and real datasets. Our method has been successfully applied to the latest variant calling QC pipeline in the TOPMed project. In Chapter 4, I describe PheGET, a web application to interactively visualize Expression Quantitative Trait Loci (eQTLs) across tissues, genes, and regions to aid functional interpretations of regulatory variants. Tissue-specific expression has become increasingly important for understanding the links between genetic variation and disease. To address this need, the Genotype-Tissue Expression (GTEx) project collected and analyzed a treasure trove of expression data. However, effectively navigating this wealth of data to find signals relevant to researchers has become a major challenge. I demonstrate the functionalities of PheGET using the newest GTEx data on our eQTL browser website at https://eqtl.pheweb.org/, allowing the user to 1) view all cis-eQTLs for a single variant; 2) view and compare single-tissue, single-gene associations within any genomic region; 3) find the best eQTL signal in any given genomic region or gene; and 4) customize the plotted data in real time. PheGET is designed to handle and display the kind of complex multidimensional data often seen in our post-GWAS era, such as multi-tissue expression data, in an intuitive and convenient interface, giving researchers an additional tool to better understand the links between genetics and disease.PHDBiostatisticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162918/1/amkwong_1.pd

Using GWAS Data to Identify Copy Number Variants Contributing to Common Complex Diseases

Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional variation. Consequently, most modern genome-wide association studies test CNVs along with SNPs, after inferring copy number status from the data generated by high-throughput genotyping platforms. Here we give an overview of CNV genomics in humans, highlighting patterns that inform methods for identifying CNVs. We describe how genotyping signals are used to identify CNVs and provide an overview of existing statistical models and methods used to infer location and carrier status from such data, especially the most commonly used methods exploring hybridization intensity. We compare the power of such methods with the alternative method of using tag SNPs to identify CNV carriers. As such methods are only powerful when applied to common CNVs, we describe two alternative approaches that can be informative for identifying rare CNVs contributing to disease risk. We focus particularly on methods identifying de novo CNVs and show that such methods can be more powerful than case-control designs. Finally we present some recommendations for identifying CNVs contributing to common complex disorders.Comment: Published in at http://dx.doi.org/10.1214/09-STS304 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Robust joint analysis allowing for model uncertainty in two-stage genetic association studies

<p>Abstract</p> <p>Background</p> <p>The cost efficient two-stage design is often used in genome-wide association studies (GWASs) in searching for genetic loci underlying the susceptibility for complex diseases. Replication-based analysis, which considers data from each stage separately, often suffers from loss of efficiency. Joint test that combines data from both stages has been proposed and widely used to improve efficiency. However, existing joint analyses are based on test statistics derived under an assumed genetic model, and thus might not have robust performance when the assumed genetic model is not appropriate.</p> <p>Results</p> <p>In this paper, we propose joint analyses based on two robust tests, MERT and MAX3, for GWASs under a two-stage design. We developed computationally efficient procedures and formulas for significant level evaluation and power calculation. The performances of the proposed approaches are investigated through the extensive simulation studies and a real example. Numerical results show that the joint analysis based on the MAX3 test statistic has the best overall performance.</p> <p>Conclusions</p> <p>MAX3 joint analysis is the most robust procedure among the considered joint analyses, and we recommend using it in a two-stage genome-wide association study.</p

Haplotype analysis of case-control data using haplologit: New features

In haplotype-association studies, the risk of a disease is often determined not only by the presence of certain haplotypes but also by their interactions with various environmental factors. The detection of such interactions with case-control data is a challenging task and often requires very large samples. This prompted the development of more efficient estimation methods for analyzing case-control genetic data. The haplologit command implements efficient semiparametric methods, recently proposed in the literature, for fitting haplotype-environment models in the very important special cases of 1) a rare disease, 2) a single candidate gene in Hardy-Weinberg equilibrium, and 3) independence of genetic and environmental factors. In this presentation, I will describe new features of the haplologit command.

DNA Evidence: Probability, Population Genetics, and the Courts

To help meet the challenge of presenting properly performed DNA tests within the post-Daubert legal framework, this article outlines the statistical procedures that have been employed or proposed to provide judges and juries with quantitative measures of probative value, describes more fully how the courts have dealt with these procedures, and evaluates the opinions and the statistical analyses from the standpoint of the law of evidence. Specifically, the article outlines the procedure used to declare whether two samples of DNA match, and how shrinking the size of the match window, as some defendants have urged, will decrease the risk of false matches, but will also exclude highly probative evidence of identity. It also demonstrates that a defendant\u27s effort to show that a smaller match window would not permit the declaration of a match is irrelevant or misleading. Additionally, the article explains procedures for estimating the frequency of the incriminating genetic characteristics in various populations. These procedures have been the subject of an acrimonious debate, both in the courts and in the press, about the effect of population structure. The population structure objection, which has proved so effective in court, applies most strongly to only a limited class of case, and therefore, courts have erred in excluding DNA evidence on the theory that the scientific community advocates that the most conservative procedures must be used in all cases. Finally, the article identifies more fundamental problems in the use of population frequency estimates, and advocates supplementary and alternative procedures that are essential if quantitative statements of the probative value of DNA evidence are to be admissible