pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

被引：325

作者：

Hundal, Jasreet ^{[1
]}

Carreno, Beatriz M. ^{[2
]}

Petti, Allegra A. ^{[1
]}

Linette, Gerald P. ^{[2
]}

Griffith, Obi L. ^{[1
,2
,4
,5
]}

Mardis, Elaine R. ^{[1
,3
,4
,5
,6
]}

Griffith, Malachi ^{[1
,4
,5
]}

机构：

[1] Washington Univ, Sch Med, McDonnell Genome Inst, St Louis, MO USA

[2] Washington Univ, Sch Med, Dept Med, Div Oncol, St Louis, MO 63110 USA

[3] Washington Univ, Sch Med, Dept Med, Div Genom & Bioinformat, St Louis, MO 63110 USA

[4] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA

[5] Washington Univ, Sch Med, Siteman Canc Ctr, St Louis, MO USA

[6] Washington Univ, Sch Med, Dept Mol Microbiol, St Louis, MO 63110 USA

来源：

GENOME MEDICINE | 2016年 / 8卷

关键词：

EXOME ANALYSIS REVEALS; PREDICTION; ANTIGENS; DISCOVERY; BINDING; CANCER; IDENTIFICATION; IMMUNOTHERAPY; RECOGNITION; NETMHCPAN;

D O I：

10.1186/s13073-016-0264-5

中图分类号：

Q3 [遗传学];

学科分类号：

071007 [遗传学];

摘要：

Cancer immunotherapy has gained significant momentum from recent clinical successes of checkpoint blockade inhibition. Massively parallel sequence analysis suggests a connection between mutational load and response to this class of therapy. Methods to identify which tumor-specific mutant peptides (neoantigens) can elicit anti-tumor T cell immunity are needed to improve predictions of checkpoint therapy response and to identify targets for vaccines and adoptive T cell therapies. Here, we present a flexible, streamlined computational workflow for identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA-and RNA-Seq).

引用

页数：11

共 46 条

[1]

Bhasin M, 2006, J BIOSCIENCE, V1, P31

[2]

TUMOR-ANTIGENS RECOGNIZED BY T-LYMPHOCYTES [J].

BOON, T ;

CEROTTINI, JC ;

VANDENEYNDE, B ;

VANDERBRUGGEN, P ;

VANPEL, A .

ANNUAL REVIEW OF IMMUNOLOGY, 1994, 12 :337-365

[3]

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells [J].

Carreno, Beatriz M. ;

Magrini, Vincent ;

Becker-Hapak, Michelle ;

Kaabinejadian, Saghar ;

Hundal, Jasreet ;

Petti, Allegra A. ;

Ly, Amy ;

Lie, Wen-Rong ;

Hildebrand, William H. ;

Mardis, Elaine R. ;

Linette, Gerald P. .

SCIENCE, 2015, 348 (6236) :803-808

[4]

Exploiting the Mutanome for Tumor Vaccination [J].

Castle, John C. ;

Kreiter, Sebastian ;

Diekmann, Jan ;

Loewer, Martin ;

Van de Roemer, Niels ;

de Graaf, Jos ;

Selmi, Abderraouf ;

Diken, Mustafa ;

Boegel, Sebastian ;

Paret, Claudia ;

Koslowski, Michael ;

Kuhn, Andreas N. ;

Britten, Cedrik M. ;

Huber, Christoph ;

Tuereci, Oezlem ;

Sahin, Ugur .

CANCER RESEARCH, 2012, 72 (05) :1081-1091

[5]

Dodt Matthias, 2012, Biology (Basel), V1, P895, DOI 10.3390/biology1030895

[6]

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity [J].

Duan, Fei ;

Duitama, Jorge ;

Al Seesi, Sahar ;

Ayres, Cory M. ;

Corcelli, Steven A. ;

Pawashe, Arpita P. ;

Blanchard, Tatiana ;

McMahon, David ;

Sidney, John ;

Sette, Alessandro ;

Baker, Brian M. ;

Mandoiu, Ion I. ;

Srivastava, Pramod K. .

JOURNAL OF EXPERIMENTAL MEDICINE, 2014, 211 (11) :2231-2248

[7]

Prediction of CD8+ Epitopes in Leishmania braziliensis Proteins Using EPIBOT: In Silico Search and In Vivo Validation [J].

Duarte, Angelo ;

Queiroz, Artur T. L. ;

Tosta, Rafael ;

Carvalho, Augusto M. ;

Barbosa, Carlos Henrique ;

Bellio, Maria ;

de Oliveira, Camila I. ;

Barral-Netto, Manoel .

PLOS ONE, 2015, 10 (04)

[8]

Ensembl 2013 [J].

Flicek, Paul ;

Ahmed, Ikhlak ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Garcia-Giron, Carlos ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Komorowska, Monika ;

Kulesha, Eugene ;

Longden, Ian ;

Maurel, Thomas ;

McLaren, William M. ;

Muffato, Matthieu ;

Nag, Rishi ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Pritchard, Emily ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sheppard, Daniel ;

Sobral, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Trevanion, Stephen ;

White, Simon ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Johnson, Nathan ;

Kinsella, Rhoda .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D48-D55

[9]

Genome Modeling System: A Knowledge Management Platform for Genomics [J].

Griffith, Malachi ;

Griffith, Obi L. ;

Smith, Scott M. ;

Ramu, Avinash ;

Callaway, Matthew B. ;

Brummett, Anthony M. ;

Kiwala, Michael J. ;

Coffman, Adam C. ;

Regier, Allison A. ;

Oberkfell, Ben J. ;

Sanderson, Gabriel E. ;

Mooney, Thomas P. ;

Nutter, Nathaniel G. ;

Belter, Edward A. ;

Du, Feiyu ;

Long, Robert L. ;

Abbott, Travis E. ;

Ferguson, Ian T. ;

Morton, David L. ;

Burnett, Mark M. ;

Weible, James V. ;

Peck, Joshua B. ;

Dukes, Adam ;

McMichael, Joshua F. ;

Lolofie, Justin T. ;

Derickson, Brian R. ;

Hundal, Jasreet ;

Skidmore, Zachary L. ;

Ainscough, Benjamin J. ;

Dees, Nathan D. ;

Schierding, William S. ;

Kandoth, Cyriac ;

Kim, Kyung H. ;

Lu, Charles ;

Harris, Christopher C. ;

Maher, Nicole ;

Maher, Christopher A. ;

Magrini, Vincent J. ;

Abbott, Benjamin S. ;

Chen, Ken ;

Clark, Eric ;

Das, Indraniel ;

Fan, Xian ;

Hawkins, Amy E. ;

Hepler, Todd G. ;

Wylie, Todd N. ;

Leonard, Shawn M. ;

Schroeder, William E. ;

Shi, Xiaoqi ;

Carmichael, Lynn K. .

PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (07)

[10]

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens [J].

Gubin, Matthew M. ;

Zhang, Xiuli ;

Schuster, Heiko ;

Caron, Etienne ;

Ward, Jeffrey P. ;

Noguchi, Takuro ;

Ivanova, Yulia ;

Hundal, Jasreet ;

Arthur, Cora D. ;

Krebber, Willem-Jan ;

Mulder, Gwenn E. ;

Toebes, Mireille ;

Vesely, Matthew D. ;

Lam, Samuel S. K. ;

Korman, Alan J. ;

Allison, James P. ;

Freeman, Gordon J. ;

Sharpe, Arlene H. ;

Pearce, Erika L. ;

Schumacher, Ton N. ;

Aebersold, Ruedi ;

Rammensee, Hans-Georg ;

Melief, Cornelis J. M. ;

Mardis, Elaine R. ;

Gillanders, William E. ;

Artyomov, Maxim N. ;

Schreiber, Robert D. .

NATURE, 2014, 515 (7528) :577-+

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