satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

Genome Biology

Method

Ian Hoskins¹  Can Cenik¹  Frederick P. Roth²  Atina Cote²  Song Sun² 

[1]Department of Molecular Biosciences, University of Texas at Austin, 78712, Austin, TX, USA

[2]The Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada

[3]Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada

关键词: MAVE;    DMS;    Mutagenesis;    Variant calling;    SNP;    MNP;    CBS;    Codon optimality;   

DOI  :  10.1186/s13059-023-02922-z

 received in 2022-04-26, accepted in 2023-04-04,  发布年份 2023

来源: Springer

【 摘 要 】

The impact of millions of individual genetic variants on molecular phenotypes in coding sequences remains unknown. Multiplexed assays of variant effect (MAVEs) are scalable methods to annotate relevant variants, but existing software lacks standardization, requires cumbersome configuration, and does not scale to large targets. We present satmut_utils as a flexible solution for simulation and variant quantification. We then benchmark MAVE software using simulated and real MAVE data. We finally determine mRNA abundance for thousands of cystathionine beta-synthase variants using two experimental methods. The satmut_utils package enables high-performance analysis of MAVEs and reveals the capability of variants to alter mRNA abundance.

【 授权许可】

CC BY   
© The Author(s) 2023

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