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.

Základní údaje

Originální název

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

Autoři

TURCHANINOVA, M. A. (643 Rusko); Alexey Nikolayevich DAVYDOV (643 Rusko, domácí); O. V. BRITANOVA (643 Rusko); Mikhail SHUGAY (643 Rusko); Vasileios BIKOS (300 Řecko, domácí); Evgeny EGOROV (643 Rusko, domácí); V. I. KIRGIZOVA (643 Rusko); E. M. MERZLYAK (643 Rusko); D. B. STAROVEROV (643 Rusko); D. A. BOLOTIN (643 Rusko); Ilgar MAMEDOV (643 Rusko, domácí); Mark IZRAELSON (643 Rusko, domácí); M. D. LOGACHEVA (643 Rusko); O. KLADOVA (643 Rusko); Karla PLEVOVÁ (203 Česká republika, domácí); Šárka POSPÍŠILOVÁ (203 Česká republika, domácí) a Dmitriy CHUDAKOV (643 Rusko, garant, domácí)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 10.032

Kód RIV

RIV/00216224:14740/16:00088911

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1038/nprot.2016.093

UT WoS

000382164800004

EID Scopus

2-s2.0-84981170197

Klíčová slova anglicky

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

Štítky

rivok

Změněno: 22. 3. 2017 10:08, Mgr. Eva Špillingová

Anotace

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.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

NV15-30015A, projekt VaV

Název: 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 a Dmitriy CHUDAKOV. High-quality full-length immunoglobulin profiling with unique molecular barcoding. NATURE PROTOCOLS. LONDON: NATURE PUBLISHING GROUP, 2016, roč. 11, č. 9, s. 1599-1616. ISSN 1754-2189. Dostupné z: https://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 = {https://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 a Dmitriy CHUDAKOV. High-quality full-length immunoglobulin profiling with unique molecular barcoding. \textit{NATURE PROTOCOLS}. LONDON: NATURE PUBLISHING GROUP, 2016, roč.~11, č.~9, s.~1599-1616. ISSN~1754-2189. Dostupné z: https://doi.org/10.1038/nprot.2016.093.

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