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Ellen Oostenbach

ORCID: 0009-0004-8497-1943
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A5095657040
Research Areas
  • Immunotherapy and Immune Responses
  • Monoclonal and Polyclonal Antibodies Research
  • Cancer Immunotherapy and Biomarkers
  • vaccines and immunoinformatics approaches

Princess Máxima Center
 2024

 The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing cancers to identify collection neo-open reading frame peptides (NOP) expressed in tumors. We termed this NOPs tumor framome. represent tumor-specific that are different from wild-type proteins may be strongly immunogenic. describe a class hidden derive structural genomic variants involving an upstream protein coding gene driving...

10.1158/2326-6066.cir-23-0158 article EN Cancer Immunology Research 2024-04-04
 Figure S10 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S10: A) NOP expression compared to normal genes.</p>

10.1158/2326-6066.25964373.v1 preprint EN cc-by 2024-06-04
 Figure S15 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S15: Tetramer gating strategy.</p>

10.1158/2326-6066.25964355.v1 preprint NO cc-by 2024-06-04
 Figure S7 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S7: Protein mass spectrometry results for A375 NOPs.</p>

10.1158/2326-6066.25964331.v1 preprint EN cc-by 2024-06-04
 Figure S16 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S16: Expansion of FRM-specific CD8T cells after priming with relevant peptide in PBMC from healthy individuals.</p>

10.1158/2326-6066.25964352 preprint EN cc-by 2024-06-04
 Figure S14 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S14: A375 immunopeptidomics.</p>

10.1158/2326-6066.25964358 preprint EN cc-by 2024-06-04
 Figure S1 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S1: RNA-guided tumor genome reconstruction.</p>

10.1158/2326-6066.25964376 preprint EN cc-by 2024-06-04
 Figure S4 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S4: Overview of somatic mutation statistics for tumor samples analyzed by WGS in this study.</p>

10.1158/2326-6066.25964343 preprint EN cc-by 2024-06-04
 Figure S16 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S16: Expansion of FRM-specific CD8T cells after priming with relevant peptide in PBMC from healthy individuals.</p>

10.1158/2326-6066.25964352.v1 preprint EN cc-by 2024-06-04
 Figure S8 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S8: Comparison of EasyFuse short-read fusion gene caller with long-read and WGS guided NOP identification.</p>

10.1158/2326-6066.25964328.v1 preprint EN cc-by 2024-06-04
 Figure S11 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S11: Example of a hidden NOP resulting from complex chromosomal rearrangement in tumor sample LUN022.</p>

10.1158/2326-6066.25964370.v1 preprint EN cc-by 2024-06-04
 Figure S13 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S13: In silico determined immunogenic properties of NOPs.</p>

10.1158/2326-6066.25964364.v1 preprint EN 2024-06-04
 Figure S8 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S8: Comparison of EasyFuse short-read fusion gene caller with long-read and WGS guided NOP identification.</p>

10.1158/2326-6066.25964328 preprint EN cc-by 2024-06-04
 Data from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<div>Abstract<p>Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing cancers to identify collection neo-open reading frame peptides (NOP) expressed in tumors. We termed this NOPs tumor framome. represent tumor-specific that are different from wild-type proteins may be strongly immunogenic. describe a class hidden derive structural genomic variants involving an upstream...

10.1158/2326-6066.c.7267923.v1 preprint EN 2024-06-04
 Figure S5 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S5: Long-read transcript sequencing statistics.</p>

10.1158/2326-6066.25964340 preprint EN cc-by 2024-06-04
 Figure S7 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S7: Protein mass spectrometry results for A375 NOPs.</p>

10.1158/2326-6066.25964331 preprint EN cc-by 2024-06-04
 Figure S11 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S11: Example of a hidden NOP resulting from complex chromosomal rearrangement in tumor sample LUN022.</p>

10.1158/2326-6066.25964370 preprint EN cc-by 2024-06-04
 Figure S6 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S6: Comparison of long and short read RNA gene expression quantification transcript coverage bias.</p>

10.1158/2326-6066.25964337 preprint EN cc-by 2024-06-04
 Figure S1 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S1: RNA-guided tumor genome reconstruction.</p>

10.1158/2326-6066.25964376.v1 preprint EN cc-by 2024-06-04
 Data from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<div>Abstract<p>Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing cancers to identify collection neo-open reading frame peptides (NOP) expressed in tumors. We termed this NOPs tumor framome. represent tumor-specific that are different from wild-type proteins may be strongly immunogenic. describe a class hidden derive structural genomic variants involving an upstream...

10.1158/2326-6066.c.7267923 preprint EN 2024-06-04
 Figure S13 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S13: In silico determined immunogenic properties of NOPs.</p>

10.1158/2326-6066.25964364 preprint EN cc-by 2024-06-04
 Figure S5 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S5: Long-read transcript sequencing statistics.</p>

10.1158/2326-6066.25964340.v1 preprint EN cc-by 2024-06-04
 Figure S9 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
OPENALEX - Publications 
Michael V. Martin Salvador Aguilar-Rosas Katka Franke Mark Pieterse Jamie van Langelaar and 31 more Renée Schreurs Maarten F. Bijlsma Marc G. Besselink Jan Köster Wim Timens Mustafa Khasraw David M. Ashley Stephen T. Keir Christian H. Ottensmeier Emma V. King Joanne Verheij Cynthia Waasdorp Peter J.M. Valk Sem A.G. Engels Ellen Oostenbach Jip T. van Dinter Damon A. Hofman Juk Yee Mok Wim J.E. van Esch Hanneke Wilmink Kim Monkhorst Henk M.W. Verheul Dennis Poel T. Jeroen N. Hiltermann Léon C.L.T. van Kempen Harry J.M. Groen Joachim G.J.V. Aerts Sebastiaan van Heesch Bob Löwenberg Ronald H.A. Plasterk Wigard P. Kloosterman

<p>Figure S9: Results of NOP identification using simulated sequencing data.</p>

10.1158/2326-6066.25964325.v1 preprint EN cc-by 2024-06-04
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