Literature DB >> 24793455

Towards error-free profiling of immune repertoires.

Mikhail Shugay1, Olga V Britanova2, Ekaterina M Merzlyak2, Maria A Turchaninova2, Ilgar Z Mamedov3, Timur R Tuganbaev4, Dmitriy A Bolotin4, Dmitry B Staroverov4, Ekaterina V Putintseva4, Karla Plevova5, Carsten Linnemann6, Dmitriy Shagin7, Sarka Pospisilova5, Sergey Lukyanov7, Ton N Schumacher6, Dmitriy M Chudakov8.   

Abstract

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.

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Year:  2014        PMID： 24793455     DOI： 10.1038/nmeth.2960

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  23 in total

1.  Counting absolute numbers of molecules using unique molecular identifiers.

Authors:  Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

2.  MiTCR: software for T-cell receptor sequencing data analysis.

Authors:  Dmitriy A Bolotin; Mikhail Shugay; Ilgar Z Mamedov; Ekaterina V Putintseva; Maria A Turchaninova; Ivan V Zvyagin; Olga V Britanova; Dmitriy M Chudakov
Journal:  Nat Methods       Date:  2013-07-28       Impact factor: 28.547

Review 3.  Single-cell sequencing-based technologies will revolutionize whole-organism science.

Authors:  Ehud Shapiro; Tamir Biezuner; Sten Linnarsson
Journal:  Nat Rev Genet       Date:  2013-07-30       Impact factor: 53.242

4.  Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.

Authors:  René L Warren; J Douglas Freeman; Thomas Zeng; Gina Choe; Sarah Munro; Richard Moore; John R Webb; Robert A Holt
Journal:  Genome Res       Date:  2011-02-24       Impact factor: 9.043

5.  Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires.

Authors:  Chen Wang; Yi Liu; Lan T Xu; Katherine J L Jackson; Krishna M Roskin; Tho D Pham; Jonathan Laserson; Eleanor L Marshall; Katie Seo; Ji-Yeun Lee; David Furman; Daphne Koller; Cornelia L Dekker; Mark M Davis; Andrew Z Fire; Scott D Boyd
Journal:  J Immunol       Date:  2013-12-11       Impact factor: 5.422

6.  Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire.

Authors:  Phuong Nguyen; Jing Ma; Deqing Pei; Caroline Obert; Cheng Cheng; Terrence L Geiger
Journal:  BMC Genomics       Date:  2011-02-11       Impact factor: 3.969

7.  Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.

Authors:  Jacob Glanville; Wenwu Zhai; Jan Berka; Dilduz Telman; Gabriella Huerta; Gautam R Mehta; Irene Ni; Li Mei; Purnima D Sundar; Giles M R Day; David Cox; Arvind Rajpal; Jaume Pons
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-29       Impact factor: 11.205

8.  Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.

Authors:  Peter J Campbell; Erin D Pleasance; Philip J Stephens; Ed Dicks; Richard Rance; Ian Goodhead; George A Follows; Anthony R Green; P Andy Futreal; Michael R Stratton
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-22       Impact factor: 11.205

9.  IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis.

Authors:  Xavier Brochet; Marie-Paule Lefranc; Véronique Giudicelli
Journal:  Nucleic Acids Res       Date:  2008-05-24       Impact factor: 16.971

10.  PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.

Authors:  Johanna Brodin; Mattias Mild; Charlotte Hedskog; Ellen Sherwood; Thomas Leitner; Björn Andersson; Jan Albert
Journal:  PLoS One       Date:  2013-07-23       Impact factor: 3.240
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  192 in total

1.  TCRβ repertoire of CD4+ and CD8+ T cells is distinct in richness, distribution, and CDR3 amino acid composition.

Authors:  Hoi Ming Li; Toyoko Hiroi; Yongqing Zhang; Alvin Shi; Guobing Chen; Supriyo De; E Jeffrey Metter; William H Wood; Alexei Sharov; Joshua D Milner; Kevin G Becker; Ming Zhan; Nan-ping Weng
Journal:  J Leukoc Biol       Date:  2015-09-22       Impact factor: 4.962

2.  Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information.

Authors:  Aleksandr Kovaltsuk; Konrad Krawczyk; Sebastian Kelm; James Snowden; Charlotte M Deane
Journal:  J Immunol       Date:  2018-11-05       Impact factor: 5.422

Review 3.  Comparative analysis of murine T-cell receptor repertoires.

Authors:  Mark Izraelson; Tatiana O Nakonechnaya; Bruno Moltedo; Evgeniy S Egorov; Sofya A Kasatskaya; Ekaterina V Putintseva; Ilgar Z Mamedov; Dmitriy B Staroverov; Irina I Shemiakina; Maria Y Zakharova; Alexey N Davydov; Dmitriy A Bolotin; Mikhail Shugay; Dmitriy M Chudakov; Alexander Y Rudensky; Olga V Britanova
Journal:  Immunology       Date:  2017-11-27       Impact factor: 7.397

Review 4.  B cells, plasma cells and antibody repertoires in the tumour microenvironment.

Authors:  George V Sharonov; Ekaterina O Serebrovskaya; Diana V Yuzhakova; Olga V Britanova; Dmitriy M Chudakov
Journal:  Nat Rev Immunol       Date:  2020-01-27       Impact factor: 53.106

5.  A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing.

Authors:  Trisha A Rettig; Michael J Pecaut; Stephen K Chapes
Journal:  FASEB Bioadv       Date:  2018-08-30

6.  RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis.

Authors:  Shuqiang Li; Jing Sun; Rosa Allesøe; Krishnalekha Datta; Yun Bao; Giacomo Oliveira; Juliet Forman; Roger Jin; Lars Rønn Olsen; Derin B Keskin; Sachet A Shukla; Catherine J Wu; Kenneth J Livak
Journal:  Nat Protoc       Date:  2019-07-24       Impact factor: 13.491

7.  High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library.

Authors:  Jinsung Noh; Okju Kim; Yushin Jung; Haejun Han; Jung-Eun Kim; Soohyun Kim; Sanghyub Lee; Jaeseong Park; Rae Hyuck Jung; Sang Il Kim; Jaejun Park; Jerome Han; Hyunho Lee; Duck Kyun Yoo; Amos C Lee; Euijin Kwon; Taehoon Ryu; Junho Chung; Sunghoon Kwon
Journal:  MAbs       Date:  2019-02-12       Impact factor: 5.857

8.  How to deduplicate PCR.

Authors:  Vivien Marx
Journal:  Nat Methods       Date:  2017-04-27       Impact factor: 28.547

Review 9.  Applications of Immunogenomics to Cancer.

Authors:  X Shirley Liu; Elaine R Mardis
Journal:  Cell       Date:  2017-02-09       Impact factor: 41.582

10.  Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8+ TCR Repertoires to Immunodominant Viral Antigens.

Authors:  Guobing Chen; Xinbo Yang; Annette Ko; Xiaoping Sun; Mingming Gao; Yongqing Zhang; Alvin Shi; Roy A Mariuzza; Nan-Ping Weng
Journal:  Cell Rep       Date:  2017-04-18       Impact factor: 9.423
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