These authors contributed equally to this work.
Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms
Article first published online: 24 SEP 2012
© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
European Journal of Immunology
Volume 42, Issue 11, pages 3073–3083, November 2012
How to Cite
Bolotin, D. A., Mamedov, I. Z., Britanova, O. V., Zvyagin, I. V., Shagin, D., Ustyugova, S. V., Turchaninova, M. A., Lukyanov, S., Lebedev, Y. B. and Chudakov, D. M. (2012), Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms. Eur. J. Immunol., 42: 3073–3083. doi: 10.1002/eji.201242517
See accompanying Commentary: http:/dx.doi.org/10.1002/eji.201242999
- Issue published online: 29 OCT 2012
- Article first published online: 24 SEP 2012
- Accepted manuscript online: 18 JUL 2012 01:47AM EST
- Manuscript Accepted: 10 JUL 2012
- Manuscript Revised: 14 JUN 2012
- Manuscript Received: 6 MAR 2012
- Molecular and Cell Biology program of the Russian Academy of Sciences
- Russian Science Support Foundation
- Russian Foundation for Basic Research. Grant Numbers: 10-04-01771-а, 11-04-12042-ofi-m
- President of the Russian Federation. Grant Number: MK- 575.2011.4
Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.
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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