ArticleCell2020
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
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Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07686744 (A Phase I Clinical Trial of Personalized Neoantigen Peptide Vaccine in Combination With Pembrolizumab for the Safety and Efficacy in Patients With Advanced, Recurrent or Refractory Renal Cell Carcinoma), which is not on this map. Cited by 356 papers.
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356citing papers in PubMed
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
NCT07686744 phase1not yet recruitingnot on this mapstarted 2026, after this paper: background citation
A Phase I Clinical Trial of Personalized Neoantigen Peptide Vaccine in Combination With Pembrolizumab for the Safety and Efficacy in Patients With Advanced, Recurrent or Refractory Renal Cell Carcinoma
Who cites it
356 citing papers in PubMed.
- Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product.Scientific reports · 2025Trial
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- Toward next-generation therapeutic HPV vaccines: A review on expanding the antigen repertoire and an integrated bioinformatics selection framework.Human vaccines & immunotherapeutics · 2026Review
- Neoantigen cancer vaccines for gastrointestinal tumors: opportunities and challenges.MedScience · 2026Review
- Predicting Neoantigen Immunogenicity frombioRxiv : the preprint server for biology · 2026Article
- Cancers modulate processing and presentation of p53 neoantigens to evade T cell detection.Immunity · 2026Article
- Current landscape and future directions of neoantigen vaccines: A new era of personalized cancer immunotherapy.Innovation (Cambridge (Mass.)) · 2026Review
- From Universal Aspiration to Precision Immunization: A Hypothesis Framework for Antigen-Defined, HLA-Restricted Cancer Vaccines.Vaccines · 2026Review
- Current and future therapies for triple-negative breast cancer.Journal of hematology & oncology · 2026Review
- Artificial intelligence in oncology: linking biological discovery to clinical utility.Molecular cancer · 2026Review
- T-cell receptor repertoires against HLA class I-restricted minor histocompatibility antigens are highly diverse with a small subset of public clonotypes.Journal for immunotherapy of cancer · 2026Article
- Past achievements and future perspectives of personalized vaccines and the role of dendritic cells.Immunologic research · 2026Review
- Take Five: harmonization in personalized cancer vaccines for cancer immunotherapy.Experimental & molecular medicine · 2026Review
- Highlight of 2025: From binding prediction to molecular design-computational advances in TCR-pMHC prediction and targeting.Immunology and cell biology · 2026Review
- Technical review of artificial intelligence in TCR-T therapy.Journal of the National Cancer Center · 2026Review
- Quantum convolutional HLA immunogenic peptide prediction (Q-CHIPP): Next-generation neoantigen prediction with quantum neural network.Science advances · 2026Article
- Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer.Cell reports. Medicine · 2026Article
- Article
- Cancer epitope prediction tools and analysis pipelines in CEDAR.Nucleic acids research · 2026Article
- In vivo engineering tumor cells to a universal "all-in-one" cancer vaccine with full antigen spectrum.Science advances · 2026Article
296 more citing papers are in PubMed but not listed here.
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Authors and funding
37 authors.
Daniel K WellsParker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Electronic address: dwells@parkerici.org.
Marit M van BuurenDivision of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; T Cell Immunology, Biopharmaceutical New Technologies (BioNTech) Corporation, BioNTech US, Cambridge, MA, USA.
Kristen K DangComputational Oncology, Sage Bionetworks, Seattle, WA, USA.
Vanessa M Hubbard-LuceyAnna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA.
Kathleen C F SheehanDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
Katie M CampbellDivision of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Andrew LambComputational Oncology, Sage Bionetworks, Seattle, WA, USA.
Jeffrey P WardDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
John SidneyDivision of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
Ana B BlazquezDivision of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Andrew J RechParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.
Jesse M ZaretskyDivision of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Begonya Comin-AnduixParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Surgery, David Geffen School of Medicine, Johnson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Alphonsus H C NgInstitute for Systems Biology, Seattle, WA, USA.
William ChourDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Thomas V YuComputational Oncology, Sage Bionetworks, Seattle, WA, USA.
Hira RizviDruckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA.
Jia M ChenDivision of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
Patrice ManningParker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
Gabriela M SteinerParker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
Xengie C DoanComputational Oncology, Sage Bionetworks, Seattle, WA, USA.
Tumor Neoantigen Selection Alliance
Taha MerghoubParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
Justin GuinneyComputational Oncology, Sage Bionetworks, Seattle, WA, USA; Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
Adam KolomParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA.
Cheryl SelinskyParker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
Antoni RibasParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Matthew D HellmannParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Druckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
Nir HacohenBroad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA.
Alessandro SetteDivision of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
James R HeathParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Institute for Systems Biology, Seattle, WA, USA.
Nina BhardwajParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Fred RamsdellParker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
Robert D SchreiberParker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
Ton N SchumacherDivision of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
Pia KvistborgDivision of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
Nadine A DefranouxParker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Electronic address: ndefranoux@parkerici.org.
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4MWomen's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5MWashington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI TIMOTHY J. EBERLEIN · 2001 to 2026
$128.0MUCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9MTraining Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8MUCLA Tumor Immunology Training ProgramT32CA009120 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Steven M. Dubinett, MICHAEL A TEITELL · 1985 to 2026
$10.3MImmunogenomic analytical approaches for research and clinical applicationsR50CA211482 · NCI · DANA-FARBER CANCER INST · PI SHUKLA, SACHET ASHOK · 2016 to 2020
$1.3MDevelopment of a pipeline tool to predict immunogenicity of cancer neo-epitopesR21AI134127 · NIAID · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI PETERS, BJOERN, SETTE, ALESSANDRO · 2018 to 2019
$495kNCI NIH HHS P30 CA008748NCI NIH HHS P30 CA016042NCI NIH HHS P30 CA091842NCI NIH HHS R50 CA211482NCI NIH HHS T32 CA009120NHGRI NIH HHS T32 HG002295NIAID NIH HHS R21 AI134127NIGMS NIH HHS T32 GM008042
Abstract
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.
Indexed as
AllelesAntigen PresentationAntigens, NeoplasmCohort StudiesEpitopesHumansNeoplasmsPeptidesProgrammed Cell Death 1 ReceptorReproducibility of ResultsAntigens, NeoplasmEpitopesPeptidesProgrammed Cell Death 1 ReceptorepitopeimmunogenicityimmunogenomicsimmunotherapyneoantigenTESLA
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Registered trials
NCT07686744ClinicalTrials.gov
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.