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151 Genetic heterogeneity between paired primary and metastatic solid tumors and implications for neoantigen-based personalized cancer vaccines
  1. Timothy I Shaw1,
  2. Darwin Chang1,
  3. Alyssa Obermayer1,
  4. Jamie Teer1,
  5. Xiaoqing Yu1,
  6. Xuefeng Wang1,
  7. Dale Hedges2,
  8. Aik Choon Tan3,
  9. Abdul Rafeh Naqash4,
  10. Margaret E Gatti-Mays5,
  11. Aakrosh Ratan6,
  12. Martin D McCarter7,
  13. John Carpten8,
  14. Howard Colman3,
  15. Igor Puzanov9,
  16. Susanne M Arnold10,
  17. Michelle Churchman12,
  18. Patrick Hwu1,
  19. William Dalton11,
  20. George J Weiner12,
  21. Jose Conejo-Garcia1,
  22. Paulo C Rodriguez1 and
  23. Ahmad A Tarhini1
  1. 1H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
  2. 2M2GEN, ORIEN, Tampa, FL, USA
  3. 3Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
  4. 4Stephenson Cancer Center Oklahoma University, Greenville, NC, USA
  5. 5The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
  6. 6University of Virginia, Charlottesville, VA, USA
  7. 7University of Colorado School of Medicine, Aurora, CO, USA
  8. 8USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
  9. 9Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
  10. 10Markey Cancer Center, Lexington, KY, USA
  11. 11M2Gen, Tampa, FL, USA
  12. 12Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Neoantigen-based personalized cancer vaccines carry significant promise in treating solid malignancies. However, there are still uncertainties regarding the choice between the primary and metastatic tumor for neoantigen prediction in individual patients. Here, we conducted a thorough examination of somatic variations in 45 patients who had both primary and metastatic solid tumors

Methods Patients were enrolled in the Total Cancer Care protocol (NCT03977402) to which patients provided an IRB-approved written informed consent across the Oncology Research Information Exchange Network® (ORIEN). Whole-exome sequencing (WES) of primary and metastatic tumor pairs was performed for 45 patients. These included head and neck (n=8), renal cell carcinoma (n=7), non-small cell lung cancer (n=6), melanoma (n=5), bladder (n=3), sarcoma (n=3), ovary (n=3), esophageal (n=2), colorectal (n=2) and other singletons (n=5). The data was analyzed through the ORIEN AVATAR Molecular Analysis Pipeline for somatic mutation variant detection and variant annotation. In this analysis, we focused on somatic events that result in an in-frame alteration (such as missense, in-frame deletion, and in-frame insertion) and out-of-frame protein-altering mutations (such as frameshifts, de novo start, out-of-frame, and nonstop gain). Clonal population structure was determined based on pyclone-vi, and our TACIER(beta) pipeline was used to predict neoantigens presented by MHC-I and II.

Results For in-frame events, we noticed that bladder cancer, melanoma, and head-and-neck cancer shared close to 75% of the mutations between paired primary and metastatic cases. In contrast, esophageal, brain, and endometrial cancers had a low overlap (< 25%) of variants. For out-of-frame events, we found that these events tend to have a lower proportion of shared somatic variants between primary and metastasis than in-frame variants. Interestingly, antigens presented by MHC class II were more conserved between primary and metastasis cases when compared to antigens presented by MHC class I (paired T-test 0.02). Melanoma had a high overlap of antigens presented by MHC class I (~80.4%), and head-and-neck cancers had a high overlap of antigens presented by MHC class II (~79.5%). Finally, oncogenic drivers (such as BRAF V600E, NRAS G13R, KRAS G12A, and TP53 loss-of-function) were more likely to be presented in both paired primary and metastatic tumors.

Conclusions Our analysis demonstrates genetic variations that exist when comparing paired primary and metastatic tumors that appear to vary by histology. Variants are potentially undergoing negative selection supported by the preferential loss of out-of-frame events in metastatic tumors. Understanding the clonal structure will be key to neoantigen prediction for effective neoantigen-based vaccines.

Ethics Approval Patients were enrolled in the Total Cancer Care protocol (NCT03977402) to which patients provided an IRB-approved written informed consent across the Oncology Research Information Exchange Network® (ORIEN).

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See

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