Statistical genetics papers

Introductory

  • Bayesian statistical methods for genetic association studies. [NRG, 2009]
  • The role of regulatory variation in complex traits and disease [NRG, 2015]
  • Dissecting the genetics of complex traits using summary association statistics [NRG, 2017]
  • From genome-wide associations to candidate causal variants by statistical fine-mapping [NRG, 2018]
  • The personal and clinical utility of polygenic risk scores [NRG, 2018]

Family-based analysis

  • Parametric and nonparametric linkage analysis: a unified multipoint approach. [AJHG, 1996]
  • The TDT and other family-based tests for linkage disequilibrium and association. [AJHG, 1996]
  • The family based association test method: strategies for studying general genotype-phenotype associations. [EJHG, 2001]

GWAS

  • A brief history of human disease genetics. [Nature, 2020, a good general overview]
  • Genetic mapping in human disease. [Science, 2008]
  • Genome-wide association studies for complex traits: consensus, uncertainty and challenges. [NRG, 2008]
  • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. [WTCCC paper, Nature, 2007]
  • How to interpret a genome-wide association study. [JAMA, 2008]
  • Five years of GWAS discovery. [AJHG, 2012] & 10 Years of GWAS Discovery: Biology, Function, and Translation. [AJHG, 2017]
  • Genome-wide association studies. [Nature Reiews Methods Primers, 2021]

Rare variant association

  • Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. [AJHG, 2008]
  • Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test. [AJHG, 2011]
  • Optimal tests for rare variant effects in sequencing association studies. [Biostatistics, 2012]
  • General Framework for Meta-analysis of Rare Variants in Sequencing Association Studies. [AJHG, 2013] & Meta-analysis of gene-level tests for rare variant association. [Nature Genetics, 2014]

Statistical fine-mapping

  • Identifying Causal Variants at Loci with Multiple Signals of Association. [Genetics, 2014]
  • FINEMAP: efficient variable selection using summary data from genome-wide association studies. [bioinformatics, 2016]
  • Molecular QTL discovery incorporating genomic annotations using Bayesian false discovery rate control. [AoAS, 2016]
  • A simple new approach to variable selection in regression, with application to genetic fine-mapping. [JRSS-B, 2020]
  • Fine-mapping from summary data with the “Sum of Single Effects” model. [PLoS Genetics, 2022]
  • A practical view of fine-mapping and gene prioritization in the post-genome-wide association era. [Open Biology, 2020]

Molecular QTLs

  • A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine. [Trends in Genetics, 2020]
  • Molecular Quantitative Trait Locus Mapping in Human Complex Diseases. [Current Protocols, 2020]

GWAS and functional genomics

  • The role of regulatory variation in complex traits and disease. [Nature Review Genetics 2015]
  • From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases. [Front Genet. 2020]

LD score regression and functional enrichment

  • LD Score regression distinguishes confounding from polygenicity in genome-wide association studies [Nature Genetics, 2015]
  • Partitioning heritability by functional annotation using genomewide association summary statistics. [Nature Genetics, 2015]
  • Functionally-informed fine-mapping and polygenic localization of complex trait heritability [biorxiv, 2019]