Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

Mohini Rajasagi, Sachet A. Shukla, Edward F. Fritsch, Derin B. Keskin, David DeLuca, Ellese Carmona, Wandi Zhang, Carrie Sougnez, Kristian Cibulskis, John Sidney, Kristen Stevenson, Jerome Ritz, Donna Neuberg, Vladimir Brusic, Stacey Gabriel, Eric S. Lander, Gad Getz, Nir Hacohen, Catherine J. Wu

Research output: Journal PublicationArticlepeer-review

250 Citations (Scopus)


Genome sequencing has revealed a large number of shared and personal somatic mutations across human cancers. In principle, any genetic alteration affecting a protein-coding region has the potential to generate mutated peptides that are presented by surface HLA class I proteins that might be recognized by cytotoxic T cells. To test this possibility, we implemented a streamlined approach for the prediction and validation of such neoantigens derived from individual tumors and presented by patient-specific HLA alleles. We applied our computational pipeline to 91 chronic lymphocytic leukemias (CLLs) that underwent whole-exome sequencing (WES). We predicted ~22 mutated HLA-binding peptides per leukemia (derived from ~16 missense mutations) and experimentally confirmed HLA binding for ~55% of such peptides. Two CLL patients that achieved long-term remission following allogeneic hematopoietic stem cell transplantation were monitored for CD8+ T-cell responses against predicted or confirmed HLA-binding peptides. Long-lived cytotoxic T-cell responses were detected against peptides generated from personal tumor mutations in ALMS1, C6ORF89, and FNDC3B presented on tumor cells. Finally, we applied our computational pipeline to WES data (N = 2488 samples) across 13 different cancer types and estimated dozens to thousands of predicted neoantigens per individual tumor, suggesting that neoantigens are frequent in most tumors.

Original languageEnglish
Pages (from-to)453-462
Number of pages10
Issue number3
Publication statusPublished - 17 Jul 2014
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Immunology
  • Hematology
  • Cell Biology


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