Deep profiling of antibody and T cell–receptor repertoires by means of high-throughput sequencing has become an attractive approach for adaptive immunity studies, but its power is substantially compromised by the accumulation of PCR and sequencing errors. Here we report MIGEC (molecular identifier groups–based error correction), a strategy for high-throughput sequencing data analysis. MIGEC allows for nearly absolute error correction while fully preserving the natural diversity of complex immune repertoires.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Sequence Read Archive
Robins, H.S. et al. Blood 114, 4099–4107 (2009).
Warren, R.L. et al. Genome Res. 21, 790–797 (2011).
Venturi, V. et al. J. Immunol. 186, 4285–4294 (2011).
Mamedov, I.Z. et al. EMBO Mol. Med. 3, 201–207 (2011).
Klarenbeek, P.L. et al. PLoS Pathog. 8, e1002889 (2012).
Britanova, O.V. et al. Bone Marrow Transplant. 47, 1479–1481 (2012).
Bashford-Rogers, R.J. et al. Genome Res. 23, 1874–1884 (2013).
Putintseva, E.V. et al. Front. Immunol. 4, 463 (2013).
Britanova, O.V. et al. J. Immunol. 192, 2689–2698 (2014).
Wang, C. et al. J. Immunol. 192, 603–611 (2014).
Nguyen, P. et al. BMC Genomics 12, 106 (2011).
Bolotin, D.A. et al. Eur. J. Immunol. 42, 3073–3083 (2012).
Campbell, P.J. et al. Proc. Natl. Acad. Sci. USA 105, 13081–13086 (2008).
Logan, A.C. et al. Proc. Natl. Acad. Sci. USA 108, 21194–21199 (2011).
Kivioja, T. et al. Nat. Methods 9, 72–74 (2012).
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K.W. & Vogelstein, B. Proc. Natl. Acad. Sci. USA 108, 9530–9535 (2011).
Douek, D.C. et al. J. Immunol. 168, 3099–3104 (2002).
Bolotin, D.A. et al. Nat. Methods 10, 813–814 (2013).
Shapiro, E., Biezuner, T. & Linnarsson, S. Nat. Rev. Genet. 14, 618–630 (2013).
Brodin, J. et al. PLoS ONE 8, e70388 (2013).
Brochet, X., Lefranc, M.-P. & Giudicelli, V. Nucleic Acids Res. 36, W503–W508 (2008).
Ye, J., Ma, N., Madden, T.L. & Ostell, J.M. Nucleic Acids Res. 41, W34–W40 (2013).
Glanville, J. et al. Proc. Natl. Acad. Sci. USA 106, 20216–20221 (2009).
We are grateful to M. Eisenstein for the English editing. This work was supported by the Molecular and Cell Biology program RAS, Russian Foundation for Basic Research 12-04-33139 (to D.M.C.), 13-04-00998 (to O.V.B.) and 14-04-01247 (to E.M.M.), Russian President grant MD-3044.2014.4 (to D.M.C.) and European Regional Development Fund (CZ.1.05/1.1.00/02.0068).
The authors declare no competing financial interests.
About this article
Cite this article
Shugay, M., Britanova, O., Merzlyak, E. et al. Towards error-free profiling of immune repertoires. Nat Methods 11, 653–655 (2014). https://doi.org/10.1038/nmeth.2960
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
BMC Bioinformatics (2022)
A comprehensive model based on temporal dynamics of peripheral T cell repertoire for predicting post-treatment distant metastasis of nasopharyngeal carcinoma
Cancer Immunology, Immunotherapy (2022)
Exosome-based detection of EGFR T790M in plasma and pleural fluid of prospectively enrolled non-small cell lung cancer patients after first-line tyrosine kinase inhibitor therapy
Cancer Cell International (2021)
Nature Methods (2021)
Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2
Nature Communications (2021)