FUME-TCRseq

• Formalin-fixed paraffin embedded (FFPE)-suitable Unique Molecular idEntifier-based TCRseq (FUMETCRseq) is multiplex PCR-based and uses 38 primers against the TCR V genes. 
• FUME-TCRseq incorporates unique molecular identifiers (UMIs) for the correction of amplification bias and sequencing errors. It has great potential for commercial development, being very low cost compared to existing methods, quicker, able to detect more clonotypes, and able to analyse low-quality RNA samples.
• Developed by Prof. Trevor Graham, Dr. Annie Baker (ICR), and Prof. Benny Chain (UCL).

The diversity of the TCR repertoire means that sequencing is technically challenging, particularly for samples with low-quality, degraded nucleic acids. Current methods have significant weaknesses, including relatively long preparation times, high cost and high failure rate for poor quality samples.

The research team has performed spatially-resolved FUME-TCRseq of colorectal cancers using microdissected archival samples, revealing the shifting T-cell landscapes at the transition to an invasive phenotype, and between tumour subclones containing distinct driver alterations.

FUME-TCRseq proved effective at accurately measuring T cell repertoires with as little as 100ng RNA input. FUME-TCRseq requires no specialist equipment and is very low cost compared to existing methods, meaning that it will be accessible to most genomic and molecular biology laboratories.

FUME-TCRseq reveals the strength, breadth and clonal dynamics of the adaptive immune response to pathogens or cancer. FUME-TCRseq can also unlock the analysis of archival FFPE tissue, facilitating longitudinal analysis of T-cell dynamics in clinical samples. This can help in tracking immune responses through disease course and treatment.