Systematic characterization of indel variants using a yeast-based protein folding sensor

Introduction

This respository contains all data (except from the raw FASTQ files, which are available at the NCBI Gene Expression Omnibus (GEO) repository (accession number: GSE270811)) and code to repeat the processing and analysis of the CPOP data in Larsen-Ledet et al.: "Systematic characterization of indel variants using a yeast-based protein folding sensor".

Overview of files

Output files

• cpop_data.csv - CPOP scores and standard deviations for DHFR indel, synonymous and nonsense variants.
• cpop_data_pre_rescale - Raw CPOP scores and standard deviations for DHFR indel, synonymous and nonsense variants prior to rescaling.
• cpop_data_ROC_[ins|del].csv - CPOP scores for ROC curves, where duplicated indel variants on protein level have been removed.
• tile[1-5].csv - Counts per tile for DHFR indel, synonymous and nonsense variants for each replicate and condition.

Input files

• [ins|del]_dplddt_ddg.csv - dpLDDT and ddG predictions for DHFR indel variants.
• rSASA.csv - Relative solvent accessible surface area (rSASA) for each residue in DHFR.
• mtx_dist.csv - Distance (Å) of each residue in DHFR to the MTX binding site.
• [ins|del]_esm1b - ESM1b predictions for DHFR indel variants.
• del_sequence_alignment - MSA generated with HHblits of DHFR homologs with deletions per position.

Excel files

• CPOP_primers_annealing.temp..xlsx - Primers and annealing temperatures for the first PCR in amplicon preparation.
• SupplementalFile1.xlsx - All data files combined in a single Excel file.

Processing of raw sequencing data

The function.py file is used to call DHFR variants and calculate CPOP scores. The script takes raw FASTQ files as input. The output is a dataset with CPOP scores and standard deviations for DHFR indel, synonymous and nonsense variants.

Data analysis and plotting

The CPOP_data_analysis.R file is used to produce all plots in the main figures, and the CPOP_data_analysis_supplementary.R file is used to produce all plots in the supplementary figures. Both files take the dataset with CPOP scores and standard deviations as input.

Preprint

https://doi.org/10.1101/2024.07.11.603017