Multi-resolution localization of causal variants across the genome

• Published in: Nature communications Vol. 11; no. 1; pp. 1093 - 10
• Main Authors: Sesia, Matteo, Katsevich, Eugene, Bates, Stephen, Candès, Emmanuel, Sabatti, Chiara
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.02.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2415; 631/208/205/2138; 631/208/726/649; 631/208/728; Algorithms; Chromosome Mapping - methods; Computer applications; Datasets as Topic; Feasibility Studies; Gene mapping; Genome, Human - genetics; Genome-wide association studies; Genome-Wide Association Study - methods; Genomes; Genomics - methods; Genotypes; Humanities and Social Sciences; Humans; Linkage Disequilibrium; Localization; Mapping; Markov chains; Models, Genetic; multidisciplinary; Multifactorial Inheritance - genetics; Phenotypes; Polymorphism, Single Nucleotide - genetics; Quantitative Trait Loci - genetics; Science; Science (multidisciplinary); Software; Statistical analysis; Statistical methods; Statistics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-14791-2

In the statistical analysis of genome-wide association data, it is challenging to precisely localize the variants that affect complex traits, due to linkage disequilibrium, and to maximize power while limiting spurious findings. Here we report on KnockoffZoom : a flexible method that localizes causal variants at multiple resolutions by testing the conditional associations of genetic segments of decreasing width, while provably controlling the false discovery rate. Our method utilizes artificial genotypes as negative controls and is equally valid for quantitative and binary phenotypes, without requiring any assumptions about their genetic architectures. Instead, we rely on well-established genetic models of linkage disequilibrium. We demonstrate that our method can detect more associations than mixed effects models and achieve fine-mapping precision, at comparable computational cost. Lastly, we apply KnockoffZoom to data from 350k subjects in the UK Biobank and report many new findings. GWAS analysis currently relies mostly on linear mixed models, which do not account for linkage disequilibrium (LD) between tested variants. Here, Sesia et al. propose KnockoffZoom, a non-parametric statistical method for the simultaneous discovery and fine-mapping of causal variants, assuming only that LD is described by hidden Markov models (HMMs).