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Supporting information Table 1. Percent of different type misincorporation errors for the three NGS platforms.

Supporting information Table 2. Primers for sequencing sample preparation

Supporting information Figure 1. Sample preparation for Illumina, 454 and Ion Torrent sequencing. For all three sequencing methods we started from total RNA isolated from PBMC. We performed cDNA synthesis with universal bc1R primer and template switch to plug oligo generating identical ends for each molecule. Then universal primers bc2R and M1 were used in the first amplification step. Second amplification step was performed according to the specific requirements for each sequencing platform. V, D, J and C – genomic regions forming mature TCR beta gene; CDR3 – complementarity-determining region 3.

Supporting information Figure 2. Sequence reads length distribution for different NGS platforms. A – 454, B – Ion Torrent, C – Illumina.

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