Gattaca: Base-Pair Resolution Mutation Tracking for Somatic Evolution Studies using Agent-based Models. (17th March 2022)

• Record Type: Journal Article
• Authors: Schenck, Ryan O.; Brosula, Gabriel; West, Jeffrey; Leedham, Simon; Shibata, Darryl; Anderson, Alexander R.A.
• Editors: Townsend, Jeffrey
• Is Part Of: Molecular biology and evolution. Volume 39:Number 4(2022)
• Publication Date: 2022-03-17
• Subjects: somatic evolution -- computational tool -- mechanistic modeling; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msac058
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: Research over the past two decades has made substantial inroads into our understanding of somatic mutations. Recently, these studies have focused on understanding their presence in homeostatic tissue. In parallel, agent-based mechanistic models have emerged as an important tool for understanding somatic mutation in tissue; yet no common methodology currently exists to provide base-pair resolution data for these models. Here, we present Gattaca as the first method for introducing and tracking somatic mutations at the base-pair resolution within agent-based models that typically lack nuclei. With nuclei that incorporate human reference genomes, mutational context, and sequence coverage/error information, Gattaca is able to realistically evolve sequence data, facilitating comparisons between in silico cell tissue modeling with experimental human somatic mutation data. This user-friendly method, incorporated into each in silico cell, allows us to fully capture somatic mutation spectra and evolution.