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Basic science

1380 - Systematic identification of (Personalized) Tumor-specific neoantigens through whole genome & whole transcriptomic analyses of 158 Asian Colorectal Cancers. (550O)


17 Nov 2017


Basic science


Pathology/Molecular Biology;  Colon and Rectal Cancer


Si-Lin Koo


Annals of Oncology (2017) 28 (suppl_10): x173-x176. 10.1093/annonc/mdx679


S. Koo1, C. Chua1, A. Nguyen2, S. Benz2, W.S. Tan3, C.L. Tang3, M.H. Chew4, B. Goh5, C.Y. Chan5, A. Gan6, W.L. Tan6, X.Q. Koh1, A. Lezhava6, S. Yan6, S. Rabizadeh2, A. Skanderup6, I.B. Tan1

Author affiliations

  • 1 Medical Oncology, National Cancer Centre Singapore, 169610 - Singapore/SG
  • 2 Nantomics, NantOmics LLC, Culver City/US
  • 3 Colorectal Surgery, Singapore General Hospital, 169608 - Singapore/SG
  • 4 Colorectal Surgery, Sengkang General Hospital, 545047 - Singapore/SG
  • 5 Hepatopancreatobiliary And Transplant Surgery, Singapore General Hospital, 169608 - Singapore/SG
  • 6 Genome Institute Of Singapore, Genome Institute of Singapore, 138672 - Singapore/SG


Abstract 1380


Somatic mutations are attractive therapeutic targets for “individuvalized neoantigen vaccines” because of lack of host central tolerance and reduced risk of autoimmunity. Here, we perform large-scale –omic analyses to assess the neoantigen landscape of colorectal cancer, a cancer largely refractory to immune-checkpoint inhibition.


We performed whole genome sequencing (WGS) (60x tumor, 30x normal) and deep whole transcriptomic sequencing (RNA-Seq) (∼200x10e6 reads per tumor) on 158 Colorectal cancers including 32 patients with microsatellite instability (MSI), 126 microsatellite stable (MSS). Whole Exome Sequencing (200x tumor,100x normal) was also performed on 120 tumours. HLA typing, somatic mutations, gene expression & neoepitope predictions were computationally evaluated. Inferred HLA-A alleles were orthogonally validated with Pacbio long-read sequencing.


The most common HLAs were, by allele count: A*11:01: 56; A*33:03: 38; B*58:01: 33; B*46:01: 29; B*40:01: 26; C*01:02: 41; C*07:02: 33. Inferred HLA-A alleles from WGS data was largely concordant with Pacbio long-read sequencing. There were a median of 2,850 (1229-6909) [MSI] & 213 (27-13,835) [MSS] coding variants, from which 10,487 (4,307-27,365) [MSI] & 726.5 (50-59,096) [MSS] possible neoepitopes were derived, after accounting for epitope processing, the normal proteome and general population variome based on dbSNP, Of these, 5,707 (2,608-15,218) [MSI] & 320 (14-25,243) [MSS] neoepitopes are expressed (based on RNA-Seq). Epitope prediction algorithms revealed a median of 423 (17-1,056) [MSI] & 26 (0-1,102) [MSS] bound & expressed neoepitopes. 5 MSS tumors did not have any predicted bound nor expressed neoepitopes, 112 of 126 (89%) of MSS tumors had at least 5 predicted bound, expressed neoepitopes.


There is substantial variability in the neoantigen landscape amongst MSI & MSS Colorectal cancers. MSI contains multiple-fold higher neo-antigens. Amongst MSS tumors, 89% of patients have at least 5 predicted bound and expressed neo-epitopes that could be targeted in neoantigen-based vaccines for personalized immunotherapy.

Clinical trial identification

Legal entity responsible for the study

National Cancer Centre Singapore


NMRC Clinician Scientist Award (Iain Tan), A*STAR Core Funding, NantOmics LLC


A. Nguyen, S. Benz, S. Rabizadeh: Employee of NantOmics LLC

All other authors have declared no conflicts of interest.

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