Oops, you're using an old version of your browser so some of the features on this page may not be displaying properly.

MINIMAL Requirements: Google Chrome 24+Mozilla Firefox 20+Internet Explorer 11Opera 15–18Apple Safari 7SeaMonkey 2.15-2.23

Lunch & Poster Display session

32P - A comprehensive tumour immunogenomics platform for precision immunotherapy: Enabling simultaneous characterization of tumours and the TME from a single FFPE sample

Date

12 Dec 2019

Session

Lunch & Poster Display session

Presenters

Robert Power

Citation

Annals of Oncology (2019) 30 (suppl_11): xi1-xi11. 10.1093/annonc/mdz447

Authors

R. Power1, G. Bartha2, J. Harris2, S.M. Boyle2, E. Levy2, P. Milani2, P. Tandon2, R. Li2, M. Chinnappa2, A. Haddad2, P. McNitt2, R. McClory1, M. Morra2, S. Saldivar2, M. Clark2, C. Haudenschild2, E. Newburn2, C. Johnson2, R. Chen2, J. West2

Author affiliations

  • 1 Marketing, Personalis, Inc., 94025 - Menlo Park/US
  • 2 R & D, Personalis, Inc., 94025 - Menlo Park/US
More

Resources

Abstract 32P

Background

Immunogenomic profiling of the tumour and the TME is critical for identifying biomarkers of immunotherapy response and understanding resistance. However, running many assays for each sample is impractical given limited sample quantity, processing complexity, and prohibitive cost. To address this, we developed a novel, augmented exome-/transcriptome-based tumour immunogenomics platform.

Methods

We optimized the design of our sequencing assays and analytics for improved somatic SNV, indel, CNA, and fusion detection across ∼20,000 genes, and for the evaluation of neoantigens, expression signatures, HLA typing and LOH, TCR/BCR repertoires, oncoviruses, TILs, clinically-actionable mutations, TMB, and MSI status.

Results

With 25ng of DNA per FFPE sample and co-extracted RNA, this platform completely covers between 17-40% more genes compared to a non-augmented exome; increasing sensitivity to somatic mutations and neoantigens. For neoantigen detection, we generated immunopeptidomic data from monoallelic HLA transfected cell lines and trained neural networks to predict neoepitope binding to MHC; demonstrating higher precision (0.88) across alleles than publicly-available tools (0.9 and >0.94, respectively). For TILs, we developed signatures for immune cells, demonstrating concordance with CyTOF-derived validation sets. We achieve HLA typing accuracy of 99.1% for Class I and 95% for Class II calls, and have developed a novel tool for HLA LOH evaluation. We achieve sensitive detection of oncoviruses, as well as accurate MSI and TMB assessment. For diagnostic reporting, we report high sensitivity and specificity for clinically-reportable mutations comparable with diagnostic cancer panels.

Conclusion

We have developed a novel tumour immunogenomics platform that simultaneously profiles the tumour and TME from a single sample.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

Personalis, Inc.

Funding

Personalis, Inc.

Disclosure

R. Power: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. G. Bartha: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. J. Harris: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. S.M. Boyle: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. E. Levy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. P. Milani: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. P. Tandon: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. R. Li: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. M. Chinnappa: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. A. Haddad: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. P. McNitt: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. R. McClory: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. M. Morra: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. S. Saldivar: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. M. Clark: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. C. Haudenschild: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. E. Newburn: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. C. Johnson: Shareholder / Stockholder / Stock options, Full / Part-time employment: Personalis, Inc. R. Chen: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment, Officer / Board of Directors: Personalis, In J. West: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment, Officer / Board of Directors: Personalis, Inc.

This site uses cookies. Some of these cookies are essential, while others help us improve your experience by providing insights into how the site is being used.

For more detailed information on the cookies we use, please check our Privacy Policy.

Customise settings