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Immune clonotypes

Immune Clonotypes

Data Type

Independently from gene expression analysis, bulk RNA sequencing can be used to reconstruct the lineages of B- and T- cells present in a sample by de novo reconstruction of BCR and TCR loci. The TRUST4 tool used in this workflow is described by the authors as:

A computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length.

User Guide

Workflow Repository: github.com/FredHutch/pw-bulk-rna-immune-clonotypes

Citations:

  • TRUST4: Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021 Jun;18(6):627-630. doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13. PMID: 33986545.