BulkLMM: Real-time genome scans for multiple quantitative traits using linear mixed models

• Published in: bioRxiv
• Main Authors: Yu, Zifan, Farage, Gregory, Williams, Robert W, Broman, Karl W, Sen, Śaunak
• Format: Journal Article Paper
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 21.12.2023; Cold Spring Harbor Laboratory
• Edition: 1.1
• Subjects: Bioinformatics; Genomes; Phenotyping; Proteomes; Julia; Linear Mixed Models; Genome Scan; Parallel; Computing; Parallel Computing
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2023.12.20.572698

Genetic studies often collect data using high-throughput phenotyping. That has led to the need for fast genomewide scans for large number of traits using linear mixed models (LMMs). Computing the scans one by one on each trait is time consuming. We have developed new algorithms for performing genome scans on a large number of quantitative traits using LMMs, BulkLMM, that speeds up the computation by orders of magnitude compared to one trait at a time scans. On a mouse BXD Liver Proteome data with more than 35,000 traits and 7,000 markers, BulkLMM completed in a few seconds. We use vectorized, multi-threaded operations and regularization to improve optimization, and numerical approximations to speed up the computations. Our software implementation in the Julia programming language also provides permutation testing for LMMs and is available at https://github.com/senresearch/BulkLMM.jl.