TCR profiling

TCR profiling service

cat.# CS061, CS062

- Unbiased TCR beta profiling due to unique cDNA construction and amplification technology
- Usage of RNA as a starting material allows exclusion of nonfunctional TCR beta genes
- A wide variety of data analysis options with Evrogen's TCRBase software

TCR profiling service yields comprehensive, quantitative data on T-Cell Receptor (TCR) diversity in human blood (or other tissues). This information reflects immune system status or changes in immune system parameters under conditions of an autoimmune disease or infection. TCR clonality is mainly determined by a hypervariable, complementary-determining region 3 (CDR3) of the TCR beta chain. Next generation sequencing (NGS) technologies enable detailed characterization of the TCR repertoire, as well as precise identification and fate tracking of individual T-cell clones through mass TCR beta sequencing.

TCR profiling service includes two stages: (1) specially developed unbiased cDNA synthesis and amplification procedure allowing isolation of TCR beta sequences with preserved quantitative ratios and (2) bioinformatics analysis of NGS output.

Stage I

cDNA is made from customer-supplied total or poly(A)+ RNA using propriety protocol allowing amplification of whole repertoire of TCR beta genes and providing unbiased ready-to-sequence DNA samples. Starting from RNA is preferable because it allows the exclusion of a significant portion of rearranged but nonfunctional TCR beta genes, which is not possible when dealing with a DNA library.

Stage II

Level 1: the NGS sequencer output is processed with Evrogen TCRBase software, especially developed to elaborate raw data and generate quantitative results on TCR diversity in a clear, intelligible way. The analysis includes:

• Multistep sequence error removal
• Referring each sequence read to a particular V and J family
• Clusterization of clonal sequences, i.e. sequence reads with identical V, J and CDR3 (the relative amount of each clonal sequence corresponds to the actual abundance of the T cell clone)
• Virtual CDR3 length spectratyping for each of V and J gene segments
• Calculating a relative abundance of the V and J gene segments
• Input data quality statistics, including sequence error rates

Please, find more information on TCRBase algorithm and program output in a simplified Stage II Report (PDF) description. If a more complex, in-depth bioinformatics analysis is desirable (e.g. a cross-comparison of a number of datasets), please consider level 2.

Level 2 is an extended custom-tailored sequencing analysis service. Additional available features include:

• Virtual clonotyping
• GeneBank BLAST search for each clone, providing you with extended information on the entire sequence
• Multiple dataset cross-comparisons with Cross-Identity algorithm