Databases

• GWAS Catalog
• HapMap
• PDB

Supplementary Readings

To be populated as we progress through the course.

Chapter 1: SNPs and Haplotypes: Linkage Disequilibrium and the Haplotype Phasing Problem

• 5 Years of GWAS
• 10 Years of GWAS
• 15 Years of GWAS
• Balding GWAS Tutorial
• GWAS for Common Diseases and Complex Traits
• How to Interpret a GWAS
• Assessment of Risk and Disease Using GWAS
• A Haplotype Map of the Human Genome
• Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population

Chapter 2: Protein Folding, Misfolding, and Disease

• Miyazawa-Jernigan Amino Acid Contact Potentials
• Highly Accurate Protein Structure Predication with AlphaFold
• Historical Progress in the Protein Folding Problem
• A Survey of the Protein Folding Problem
• A Survey of the Combinatorial Protein Folding

Chapter 3: MCMC and Spectral Graph Theory, with Applications to Population Stratification

• The Original Metropolis Paper
• Perspective on the Initial Metropolis Paper
• The Beginning of the Monte-Carlo Method
• The MCMC Revolution
• Rapidly Mixing Markov Chains with Applications in CS and Physics

Chapter 4: Missing Heritability, Genetic Heterogeneity, and Rare and Common Genetic Variants

• A Comparison of Linkage Disequilibrium Measures for Fine-Scale Mapping

Chapter 5: Polygenic Risk Scores and GWAS

Final Project Ideas

• Epistatic Interactions in GWAS
  • Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease
  • Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits (L Crawford)
• Variable Selection in Deep Learning Models for GWAS
  • A Spike and Slab Restricted Boltzmann Machine
  • Concrete Autoencoders for Differentiable Feature Selection and Reconstruction
  • The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables
  • Categorical Reparameterization with Gumbel-Softmax
• Bayesian Variable Selection and Regression Analysis in GWAS and Fine Mapping Studies
  • varbvs: Fast Variable Selection for Large-scale Regression (M Stephens)
  • A simple new approach to variable selection in regression, with application to genetic fine mapping (M Stephens)
  • Bayesian Variable Selection Regression for Genome-Wide Association Studies and Other Large-Scale Problems
• Gene Sets and GWAS: From selecting SNPs to selecting Genes and Pathways
  • Bayesian large-scale multiple regression with summary statistics from genome-wide association studies (RSS by M Stephens)
  • Analysing biological pathways in genome-wide association studies
  • Pathway analysis of genomic data: concepts, methods, and prospects for future development
  • Leveraging models of cell regulation and GWAS data in integrative network-based association studies
• Random Forests, Decision Trees, and GWAS
  • An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings
• GWAS using Ancestral Recombination Graphs (combinatorial approach to GWAS using haplotypes)
  • Coalescent-Based Association Mapping and Fine Mapping of Complex Trait Loci
  • Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs
• ARGs and Haplotype Phasing
  • Genealogical Trees, Coalescent Theory and the Analysis of Genetic Polymorphisms
  • Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs
  • Coalescent-Based Association Mapping and Fine Mapping of Complex Trait Loci
• Tag SNPs - Unifying LD-select/Tagger and Informativeness - Dominating Set Optimization
  • Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium
  • Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies
  • Linkage Disequilibrium in Humans: Models and Data
• Minimum Informative Subset Selection Algorithm and Transferability
  • Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium
  • Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies
  • Supplemental 1
  • Supplemental 2
  • The Portability of tagSNPs Across Populations: A Worldwide Survey
• Codon Bias in GWAS
  • Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium
  • Genotype Imputation with Thousands of Genomes
  • The Codon Adaptation Index: A Measure of Directional Synonymous Codon Usage Bias and Its Potential Applications
• Identity by Descent in GWAS
  • A Fast, Powerful Method for Detecting Identity by Descent
  • Whole Population, Genome-Wide Mapping of Hidden Relatedness
• Rigorous Algorithms for Global Maximum Likelihood Phasing, EM, and Generalized Likelihoods
  • Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population
• Long-Range Haplotype Phasing – “The Power of Amnesia” Variable-Length Markov Chain
  • Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies by Use of Localized Haplotype Clustering
  • The Power of Amnesia: Learning Probabilistic Automata with Variable Memory Length
• Long-Range Haplotype Phasing – The deCODE Algorithm
  • Detection of Sharing by Descent, Long-Range Phasing, and Haplotype Imputation
• Cryptic Population Structure
  • Genetic Heterogeneity in Human Disease
• Immunogenomics
  • Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity
  • Comparative Immunopeptidomics of Humans and Their Pathogens
• Detecting Recombination Rates and the Li-Stephens Framework
  • Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
• Fast Detection of Identical by Descent Relatedness
  • A Fast, Powerful Method for Detecting Identity by Descent
  • Whole Population, Genome-Wide Mapping of Hidden Relatedness
• Parents of Origin Genetic Variation
  • Parental Origin of Sequence Variants Associated with Complex Diseases
• Transferability of Tagging SNPs Across Populations
  • The Portability of tagSNPs Across Populations: A Worldwide Survey
• Generalized Family and Pedigree-Based Statistical Tests for Association
  • Family-Based Tests of Association in the Presence of Linkage
• Crypto-GWAS and the Maximum Non-Identifiability Problem
  • Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays
  • The Limits of Individual Identification from Sample Allele Frequencies: Theory and Statistical Analysis
• Pedigree Inference from Genotypes/Haplotypes
  • Pedigree Reconstruction Using Identity by Descent
  • Efficient Maximum Likelihood Pedigree Reconstruction
• Viral Quasispecies Reconstruction and Polyploid Haplotype Assembly
  • QColors: An Algorithm for Conservative Viral Quasispecies Reconstruction from Short and Non-Contiguous Next Generation Sequencing Reads
  • Haplotype Assembly in Polyploid Genomes and Identical by Descent Shared Tracts
• Haplotype and Genome Assembly of Metagenomes
  • Genovo: De Novo Assembly for Metagenomes
  • A Bioinformatician’s Guide to Metagenomics
  • Haplotype Assembly in Polyploid Genomes and Identical by Descent Shared Tracts

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