CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling

Area of Science:

• Immunogenomics
• Molecular Oncology
• T-cell Receptor Biology

Background:

• Mature T-cell lymphomas are characterized by clonal T-cell receptor (TCR) gene rearrangements.
• Molecular methods for T-cell repertoire analysis are crucial for identifying and monitoring these lymphomas.
• Existing methods may lack comprehensive coverage or high throughput.

Purpose of the Study:

• To develop and validate a novel hybrid-capture method for comprehensive T-cell receptor repertoire analysis.
• To characterize T-cell receptor repertoires in lymphoma clinical isolates and related samples.
• To assess the performance of the new method against established techniques.

Main Methods:

• Development of a hybrid-capture method (CapTCR-seq) to enrich DNA sequencing libraries for rearranged TCR genes from all 4 loci in a single reaction.
• Application of CapTCR-seq to 63 lymphoma isolates, 7 peripheral blood mononuclear cell (PBMC) populations, and tumor-infiltrating lymphocytes.
• Validation of dominant TCR gene rearrangements using PCR and Sanger sequencing; comparison with BIOMED-2 methods and commercial assays.

Main Results:

• CapTCR-seq successfully enriched for rearranged TCR genes from all 4 loci.
• Dominant Variable (V) and Joining (J) gene pair rearrangements in lymphoma cells were confirmed.
• Clonality assessment showed good agreement with BIOMED-2 methods (73-77% agreement).
• TCR β locus V and J allele prevalence in PBMCs correlated well with commercial assays (r²=0.94 with Adaptive ImmunoSEQ).

Conclusions:

• CapTCR-seq provides a rapid, high-throughput, and flexible method for characterizing dominant clones within the TCR repertoire.
• This technique enhances quantitative analysis and sensitivity for tumor surveillance in patient samples.
• CapTCR-seq is a valuable tool for T-cell lymphoma research and clinical monitoring.