Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from t...
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Gespeichert in:

Autor*in:	Alex Rubinsteyn [verfasserIn] Julia Kodysh [verfasserIn] Isaac Hodes [verfasserIn] Sebastien Mondet [verfasserIn] Bulent Arman Aksoy [verfasserIn] John P. Finnigan [verfasserIn] Nina Bhardwaj [verfasserIn] Jeffrey Hammerbacher [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2018

Schlagwörter:	neoantigens personalized vaccine immunoinformatics genomics computational pipeline

Übergeordnetes Werk:	In: Frontiers in Immunology - Frontiers Media S.A., 2011, 8(2018)
Übergeordnetes Werk:	volume:8 ; year:2018

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fimmu.2017.01807

Katalog-ID:	DOAJ015810895

Internformat


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520			\|a This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
650		4	\|a neoantigens
650		4	\|a personalized vaccine
650		4	\|a immunoinformatics
650		4	\|a genomics
650		4	\|a computational pipeline
653		0	\|a Immunologic diseases. Allergy
700	0		\|a Julia Kodysh \|e verfasserin \|4 aut
700	0		\|a Isaac Hodes \|e verfasserin \|4 aut
700	0		\|a Sebastien Mondet \|e verfasserin \|4 aut
700	0		\|a Bulent Arman Aksoy \|e verfasserin \|4 aut
700	0		\|a Bulent Arman Aksoy \|e verfasserin \|4 aut
700	0		\|a John P. Finnigan \|e verfasserin \|4 aut
700	0		\|a John P. Finnigan \|e verfasserin \|4 aut
700	0		\|a Nina Bhardwaj \|e verfasserin \|4 aut
700	0		\|a Nina Bhardwaj \|e verfasserin \|4 aut
700	0		\|a Jeffrey Hammerbacher \|e verfasserin \|4 aut
700	0		\|a Jeffrey Hammerbacher \|e verfasserin \|4 aut
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Indexfelder

author_variant	a r ar j k jk i h ih s m sm b a a baa b a a baa j p f jpf j p f jpf n b nb n b nb j h jh j h jh
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allfields	10.3389/fimmu.2017.01807 doi (DE-627)DOAJ015810895 (DE-599)DOAJ5976529a96fd4d6c9419a82fea91d16e DE-627 ger DE-627 rakwb eng RC581-607 Alex Rubinsteyn verfasserin aut Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations. neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy Julia Kodysh verfasserin aut Isaac Hodes verfasserin aut Sebastien Mondet verfasserin aut Bulent Arman Aksoy verfasserin aut Bulent Arman Aksoy verfasserin aut John P. Finnigan verfasserin aut John P. Finnigan verfasserin aut Nina Bhardwaj verfasserin aut Nina Bhardwaj verfasserin aut Jeffrey Hammerbacher verfasserin aut Jeffrey Hammerbacher verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 8(2018) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:8 year:2018 https://doi.org/10.3389/fimmu.2017.01807 kostenfrei https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e kostenfrei http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2018
spelling	10.3389/fimmu.2017.01807 doi (DE-627)DOAJ015810895 (DE-599)DOAJ5976529a96fd4d6c9419a82fea91d16e DE-627 ger DE-627 rakwb eng RC581-607 Alex Rubinsteyn verfasserin aut Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations. neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy Julia Kodysh verfasserin aut Isaac Hodes verfasserin aut Sebastien Mondet verfasserin aut Bulent Arman Aksoy verfasserin aut Bulent Arman Aksoy verfasserin aut John P. Finnigan verfasserin aut John P. Finnigan verfasserin aut Nina Bhardwaj verfasserin aut Nina Bhardwaj verfasserin aut Jeffrey Hammerbacher verfasserin aut Jeffrey Hammerbacher verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 8(2018) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:8 year:2018 https://doi.org/10.3389/fimmu.2017.01807 kostenfrei https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e kostenfrei http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2018
allfields_unstemmed	10.3389/fimmu.2017.01807 doi (DE-627)DOAJ015810895 (DE-599)DOAJ5976529a96fd4d6c9419a82fea91d16e DE-627 ger DE-627 rakwb eng RC581-607 Alex Rubinsteyn verfasserin aut Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations. neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy Julia Kodysh verfasserin aut Isaac Hodes verfasserin aut Sebastien Mondet verfasserin aut Bulent Arman Aksoy verfasserin aut Bulent Arman Aksoy verfasserin aut John P. Finnigan verfasserin aut John P. Finnigan verfasserin aut Nina Bhardwaj verfasserin aut Nina Bhardwaj verfasserin aut Jeffrey Hammerbacher verfasserin aut Jeffrey Hammerbacher verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 8(2018) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:8 year:2018 https://doi.org/10.3389/fimmu.2017.01807 kostenfrei https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e kostenfrei http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2018
allfieldsGer	10.3389/fimmu.2017.01807 doi (DE-627)DOAJ015810895 (DE-599)DOAJ5976529a96fd4d6c9419a82fea91d16e DE-627 ger DE-627 rakwb eng RC581-607 Alex Rubinsteyn verfasserin aut Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations. neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy Julia Kodysh verfasserin aut Isaac Hodes verfasserin aut Sebastien Mondet verfasserin aut Bulent Arman Aksoy verfasserin aut Bulent Arman Aksoy verfasserin aut John P. Finnigan verfasserin aut John P. Finnigan verfasserin aut Nina Bhardwaj verfasserin aut Nina Bhardwaj verfasserin aut Jeffrey Hammerbacher verfasserin aut Jeffrey Hammerbacher verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 8(2018) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:8 year:2018 https://doi.org/10.3389/fimmu.2017.01807 kostenfrei https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e kostenfrei http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2018
allfieldsSound	10.3389/fimmu.2017.01807 doi (DE-627)DOAJ015810895 (DE-599)DOAJ5976529a96fd4d6c9419a82fea91d16e DE-627 ger DE-627 rakwb eng RC581-607 Alex Rubinsteyn verfasserin aut Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations. neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy Julia Kodysh verfasserin aut Isaac Hodes verfasserin aut Sebastien Mondet verfasserin aut Bulent Arman Aksoy verfasserin aut Bulent Arman Aksoy verfasserin aut John P. Finnigan verfasserin aut John P. Finnigan verfasserin aut Nina Bhardwaj verfasserin aut Nina Bhardwaj verfasserin aut Jeffrey Hammerbacher verfasserin aut Jeffrey Hammerbacher verfasserin aut In Frontiers in Immunology Frontiers Media S.A., 2011 8(2018) (DE-627)657998354 (DE-600)2606827-8 16643224 nnns volume:8 year:2018 https://doi.org/10.3389/fimmu.2017.01807 kostenfrei https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e kostenfrei http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full kostenfrei https://doaj.org/toc/1664-3224 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2018
language	English
source	In Frontiers in Immunology 8(2018) volume:8 year:2018
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institution	findex.gbv.de
topic_facet	neoantigens personalized vaccine immunoinformatics genomics computational pipeline Immunologic diseases. Allergy
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container_title	Frontiers in Immunology
authorswithroles_txt_mv	Alex Rubinsteyn @@aut@@ Julia Kodysh @@aut@@ Isaac Hodes @@aut@@ Sebastien Mondet @@aut@@ Bulent Arman Aksoy @@aut@@ John P. Finnigan @@aut@@ Nina Bhardwaj @@aut@@ Jeffrey Hammerbacher @@aut@@
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callnumber-first	R - Medicine
author	Alex Rubinsteyn
spellingShingle	Alex Rubinsteyn misc RC581-607 misc neoantigens misc personalized vaccine misc immunoinformatics misc genomics misc computational pipeline misc Immunologic diseases. Allergy Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
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topic_title	RC581-607 Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial neoantigens personalized vaccine immunoinformatics genomics computational pipeline
topic	misc RC581-607 misc neoantigens misc personalized vaccine misc immunoinformatics misc genomics misc computational pipeline misc Immunologic diseases. Allergy
topic_unstemmed	misc RC581-607 misc neoantigens misc personalized vaccine misc immunoinformatics misc genomics misc computational pipeline misc Immunologic diseases. Allergy
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title	Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
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title_full	Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
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author_browse	Alex Rubinsteyn Julia Kodysh Isaac Hodes Sebastien Mondet Bulent Arman Aksoy John P. Finnigan Nina Bhardwaj Jeffrey Hammerbacher
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title_sort	computational pipeline for the pgv-001 neoantigen vaccine trial
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title_auth	Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
abstract	This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
abstractGer	This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
abstract_unstemmed	This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
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title_short	Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
url	https://doi.org/10.3389/fimmu.2017.01807 https://doaj.org/article/5976529a96fd4d6c9419a82fea91d16e http://journal.frontiersin.org/article/10.3389/fimmu.2017.01807/full https://doaj.org/toc/1664-3224
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author2	Julia Kodysh Isaac Hodes Sebastien Mondet Bulent Arman Aksoy John P. Finnigan Nina Bhardwaj Jeffrey Hammerbacher
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up_date	2024-07-03T17:13:01.401Z
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Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

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