Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data.

Abstract

T cell receptors (TCRs) serve key roles in the adaptive immune system by enabling recognition and response to pathogens and irregular cells. Various methods have been developed for TCR construction from single-cell RNA sequencing (scRNA-seq) datasets, each with its unique characteristics. Yet, a comprehensive evaluation of their relative performance under different conditions remains elusive. In this study, we conducted a benchmark analysis utilizing experimental single-cell immune profiling datasets. Additionally, we introduced a novel simulator, YASIM-scTCR (Yet Another SIMulator for single-cell TCR), capable of generating scTCR-seq reads containing diverse TCR-derived sequences with different sequencing depths and read lengths. Our results consistently showed that TRUST4 and MiXCR outperformed others across multiple datasets, while DeRR also demonstrated considerable accuracy. We also discovered that the sequencing depth inherently imposes a critical constraint on successful TCR construction from scRNA-seq data. In summary, we present a benchmark study to aid researchers in choosing the appropriate method for reconstructing TCR from scRNA-seq data.