High-quality full-length immunoglobulin profiling with unique
molecular barcoding

J 2016

High-quality full-length immunoglobulin profiling with unique molecular barcoding

TURCHANINOVA, M. A., Alexey Nikolayevich DAVYDOV, O. V. BRITANOVA, Mikhail SHUGAY, Vasileios BIKOS et. al.

Basic information

Original name

High-quality full-length immunoglobulin profiling with unique molecular barcoding

Authors

TURCHANINOVA, M. A. (643 Russian Federation), Alexey Nikolayevich DAVYDOV (643 Russian Federation, belonging to the institution), O. V. BRITANOVA (643 Russian Federation), Mikhail SHUGAY (643 Russian Federation), Vasileios BIKOS (300 Greece, belonging to the institution), Evgeny EGOROV (643 Russian Federation, belonging to the institution), V. I. KIRGIZOVA (643 Russian Federation), E. M. MERZLYAK (643 Russian Federation), D. B. STAROVEROV (643 Russian Federation), D. A. BOLOTIN (643 Russian Federation), Ilgar MAMEDOV (643 Russian Federation, belonging to the institution), Mark IZRAELSON (643 Russian Federation, belonging to the institution), M. D. LOGACHEVA (643 Russian Federation), O. KLADOVA (643 Russian Federation), Karla PLEVOVÁ (203 Czech Republic, belonging to the institution), Šárka POSPÍŠILOVÁ (203 Czech Republic, belonging to the institution) and Dmitriy CHUDAKOV (643 Russian Federation, guarantor, belonging to the institution)

Edition

NATURE PROTOCOLS, LONDON, NATURE PUBLISHING GROUP, 2016, 1754-2189

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 10.032

RIV identification code

RIV/00216224:14740/16:00088911

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/nprot.2016.093

UT WoS

000382164800004

Keywords in English

ZEBRAFISH ANTIBODY REPERTOIRE; B-CELL REPERTOIRE; RHEUMATOID-ARTHRITIS; IMMUNE REPERTOIRES; MULTIPLEX PCR; MEMORY; VACCINATION; RESPONSES; REVEALS; DEEP

Abstract

V originále

High-throughput sequencing analysis of hypermutating immunoglobulin (IG) repertoires remains a challenging task. Here we present a robust protocol for the full-length profiling of human and mouse IG repertoires. This protocol uses unique molecular identifiers (UMIs) introduced in the course of cDNA synthesis to control bottlenecks and to eliminate PCR and sequencing errors. Using asymmetric 400+100-nt paired-end Illumina sequencing and UMI-based assembly with the new version of the MIGEC software, the protocol allows up to 750-nt lengths to be sequenced in an almost error-free manner. This sequencing approach should also be applicable to various tasks beyond immune repertoire studies. In IG profiling, the achieved length of high-quality sequence covers the variable region of even the longest chains, along with the fragment of a constant region carrying information on the antibody isotype. The whole protocol, including preparation of cells and libraries, sequencing and data analysis, takes 5 to 6 d.

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

NV15-30015A, research and development project

Name: Analýza klonální heterogenity chronické lymfocytární leukemie pomoci sekvenování nové generace genu pro B-buněčný receptor. Národní studie.

Citovat

TURCHANINOVA, M. A., Alexey Nikolayevich DAVYDOV, O. V. BRITANOVA, Mikhail SHUGAY, Vasileios BIKOS, Evgeny EGOROV, V. I. KIRGIZOVA, E. M. MERZLYAK, D. B. STAROVEROV, D. A. BOLOTIN, Ilgar MAMEDOV, Mark IZRAELSON, M. D. LOGACHEVA, O. KLADOVA, Karla PLEVOVÁ, Šárka POSPÍŠILOVÁ and Dmitriy CHUDAKOV. High-quality full-length immunoglobulin profiling with unique molecular barcoding. NATURE PROTOCOLS. LONDON: NATURE PUBLISHING GROUP, 2016, vol. 11, No 9, p. 1599-1616. ISSN 1754-2189. Available from: https://dx.doi.org/10.1038/nprot.2016.093.

@article{1362658,
   author = {Turchaninova, M. A. and Davydov, Alexey Nikolayevich and Britanova, O. V. and Shugay, Mikhail and Bikos, Vasileios and Egorov, Evgeny and Kirgizova, V. I. and Merzlyak, E. M. and Staroverov, D. B. and Bolotin, D. A. and Mamedov, Ilgar and Izraelson, Mark and Logacheva, M. D. and Kladova, O. and Plevová, Karla and Pospíšilová, Šárka and Chudakov, Dmitriy},
   article_location = {LONDON},
   article_number = {9},
   doi = {http://dx.doi.org/10.1038/nprot.2016.093},
   keywords = {ZEBRAFISH ANTIBODY REPERTOIRE; B-CELL REPERTOIRE; RHEUMATOID-ARTHRITIS; IMMUNE REPERTOIRES; MULTIPLEX PCR; MEMORY; VACCINATION; RESPONSES; REVEALS; DEEP},
   language = {eng},
   issn = {1754-2189},
   journal = {NATURE PROTOCOLS},
   title = {High-quality full-length immunoglobulin profiling with unique molecular barcoding},
   url = {http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.093.html#access},
   volume = {11},
   year = {2016}
}

TY  - JOUR
ID  - 1362658
AU  - Turchaninova, M. A. - Davydov, Alexey Nikolayevich - Britanova, O. V. - Shugay, Mikhail - Bikos, Vasileios - Egorov, Evgeny - Kirgizova, V. I. - Merzlyak, E. M. - Staroverov, D. B. - Bolotin, D. A. - Mamedov, Ilgar - Izraelson, Mark - Logacheva, M. D. - Kladova, O. - Plevová, Karla - Pospíšilová, Šárka - Chudakov, Dmitriy
PY  - 2016
TI  - High-quality full-length immunoglobulin profiling with unique molecular barcoding
JF  - NATURE PROTOCOLS
VL  - 11
IS  - 9
SP  - 1599-1616
EP  - 1599-1616
PB  - NATURE PUBLISHING GROUP
SN  - 17542189
KW  - ZEBRAFISH ANTIBODY REPERTOIRE
KW  - B-CELL REPERTOIRE
KW  - RHEUMATOID-ARTHRITIS
KW  - IMMUNE REPERTOIRES
KW  - MULTIPLEX PCR
KW  - MEMORY
KW  - VACCINATION
KW  - RESPONSES
KW  - REVEALS
KW  - DEEP
UR  - http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.093.html#access
L2  - http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.093.html#access
N2  - High-throughput sequencing analysis of hypermutating immunoglobulin (IG) repertoires remains a challenging task. Here we present a robust protocol for the full-length profiling of human and mouse IG repertoires. This protocol uses unique molecular identifiers (UMIs) introduced in the course of cDNA synthesis to control bottlenecks and to eliminate PCR and sequencing errors. Using asymmetric 400+100-nt paired-end Illumina sequencing and UMI-based assembly with the new version of the MIGEC software, the protocol allows up to 750-nt lengths to be sequenced in an almost error-free manner. This sequencing approach should also be applicable to various tasks beyond immune repertoire studies. In IG profiling, the achieved length of high-quality sequence covers the variable region of even the longest chains, along with the fragment of a constant region carrying information on the antibody isotype. The whole protocol, including preparation of cells and libraries, sequencing and data analysis, takes 5 to 6 d.
ER  -

TURCHANINOVA, M. A., Alexey Nikolayevich DAVYDOV, O. V. BRITANOVA, Mikhail SHUGAY, Vasileios BIKOS, Evgeny EGOROV, V. I. KIRGIZOVA, E. M. MERZLYAK, D. B. STAROVEROV, D. A. BOLOTIN, Ilgar MAMEDOV, Mark IZRAELSON, M. D. LOGACHEVA, O. KLADOVA, Karla PLEVOVÁ, Šárka POSPÍŠILOVÁ and Dmitriy CHUDAKOV. High-quality full-length immunoglobulin profiling with unique molecular barcoding. \textit{NATURE PROTOCOLS}. LONDON: NATURE PUBLISHING GROUP, 2016, vol.~11, No~9, p.~1599-1616. ISSN~1754-2189. Available from: https://dx.doi.org/10.1038/nprot.2016.093.

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