st_pl_comparison
Comparison of sequencing platforms for TCR sequencing
T cell receptor (TCR) repertoire is a mirror of immune system functioning reflecting many processes caused by infections, autoimmune disorders, therapeutic treatments etc. Next generation sequencing (NGS) is becoming a powerful tool for deep comprehensive analysis of TCR repertoire hence rising some specific questions concerning methodological approaches for sample preparation and correct data interpretation. Here we compare three different NGS platforms - 454, Illumina and Ion Torrent – regarding their application for TCR repertoire sequencing and further data processing. We evaluated the rate and character of sequencing errors for each of three NGS platform and propose an effective algorithm for error correction. The accuracy of individual TCR quantification was tested and we suggest that multiplex primer amplification should be avoided in sample preparation procedure to obtain unbiased and representative TCR repertoire. We conclude that Illumina NGS platform is preferable for TCR repertoire analysis however other two platforms could be suitable for some tasks in study of molecular immunodiversity.