Returning in April 2020


Day One

Day Two
Thursday, 25TH APRIL 2019


Chair’s Opening Remarks

Approaches to Improve Neoantigen Predication

Neoantigen Prediction: Approach & Validation

  • Jennifer Busby Senior Director of Mass Spectrometry & Proteomics, Gritstone Oncology


  • Most solid tumour patients could benefit from personalised immunotherapy against private neoantigens – discussing the critical need for neoantigen identification and product manufacturing
  • Addressing the significant challenge of neoantigen identification for cancer immunotherapy
  • Understanding how tumour immunopeptidomics combined with deep learning provides a powerful approach for neoantigen prediction
  • Evaluating Gritstone’s EDGETM prediction model which identifies therapeutically relevant neoantigens

A Non-Functional Neoepitope Specific CD8+ T-cell Response Induced by Tumour Derived Antigen Exposure In Vivo


  • High frequencies of mutation-specific T cells are rarely spontaneously induced. Hence, therapies that broaden the tumour specific T-cell response are of interest
  • We analysed neoepitope-specific CD8+ T-cell responses mounted either spontaneously or after immunotherapy regimens, which induce local tumour inflammation and cell death in mice
  • Review how all tested treatment regimens were found to induce a single significant CD8+ T-cell response which was not able to recognize and kill tumour cells
  • Evaluate the presented data which exemplifies that neo-antigen specific T cells primed by tumor-released antigen exposure might not always be functionally relevant as previously expected

An Integrated Machine-Learning Approach to Improve the Prediction of Clinically Relevant Neoantigens


  • Outlining a high-performing machine learning approach, trained on massspectrometry data, that predicts naturally processed and presented antigens
  • Demonstrating how the predictor is integrated with several immune parameters, such as HLA binding, in a deep learning layer to predict bone fide neoantigens
  • Illustrating its application to significantly improve the identification of neoantigen targets for personalised cancer immunotherapy

Speed Networking & Morning Refreshments

Enhancing the Validation of Neoantigens to Ensure Immunogenicity

Connecting Neoantigens to TCR Recognition

  • John Castle Associate Vice President, Head of Translational Medicine & Bioinformatics , Agenus


Evaluating how:

  • Not all aberrations are equal in the eyes of the immune system
  • Only some non-self aberrations are processed and presented
  • Only some presented peptides are recognised and impart effective immune response
  • TCRs have a defined specificity for recognition

Obtaining a Fuller Picture of Immunogenicity to Improve Neoantigen Selection

  • John Castle Associate Vice President, Head of Translational Medicine & Bioinformatics , Agenus
  • Lélia Delamarre Senior Scientist, Cancer Immunology Research, Genentech
  • Jennifer Busby Senior Director of Mass Spectrometry & Proteomics, Gritstone Oncology


  • Reviewing important parameters to consider for neo-epitope selection
  • Improving neoantigen prediction for MHC II peptides
  • Comparing and contrasting methods for prediction for better T cell epitope discovery
  • Balancing high throughput capabilities while selecting all presented and immunogenic MHC ligands

Lunch & Networking

Determinants of Cancer Neoantigen Immunogenicity

ImmunoID NeXT Platform: Improving Neoantigen Prediction, TME Assessment, & ctDNA Detection for Vaccine Development

  • Sean Boyle Senior Director, Bioinformatics Applications , Personalis


  • Exploring innovative genomics methods for more comprehensive assessment of neoantigens
  • Improving neoantigen to MHC binding prediction and ranking
  • Assessing TME/TCR and tumour escape mechanisms that may impact vaccine response

Afternoon Break & Poster Session

Roundtable Discussion:


Be part of practical and highly interactive breakout roundtables where attendees can crowd-source solutions and
share opinions around pre-assigned topic areas. This is a valuable chance for you to unite with your peers around
hot topics and debate best practice.

Chair’s Closing Remarks

End of Day One