Screening and early cancer detection via protease-activatable receptor T cells

This code was used for data analysis in a study published by Phuengkham et al in Cell Reports. Most of the code comprises amplicon sequencing analysis for a custom variant library of synthetic receptors, which are displayed by T cells enabling cell sorting and genomic DNA sequencing to identify activated receptors. This approach was used to screen synthetic receptors in vitro against recombinant proteases and in vivo in xenograft tumor models. For in vitro analysis, a bootstrapping method was used to filter on variants with highest library coverage and remove variants most likely to be affected by sampling bias, followed by quantification of amplicon frequencies. For in vivo analysis, amplicon frequencies were quantified based on counts of unique molecular identifiers to reduce effects of PCR bias and sequencing noise. This project also includes code used for non-targeted quantification of all amplicons detected by sequencing, which was used to quantify circulating tumor DNA variants as a benchmark for the tumor detection sensitivity of T cells expressing synthetic receptors.