Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2017 Feb 9;168(4):600-612.
doi: 10.1016/j.cell.2017.01.014.

Applications of Immunogenomics to Cancer

X Shirley Liu  1 , Elaine R Mardis  2
Affiliations
Review

Applications of Immunogenomics to Cancer

X Shirley Liu et al. Cell. .

Abstract

Cancer immunogenomics originally was framed by research supporting the hypothesis that cancer mutations generated novel peptides seen as "non-self" by the immune system. The search for these "neoantigens" has been facilitated by the combination of new sequencing technologies, specialized computational analyses, and HLA binding predictions that evaluate somatic alterations in a cancer genome and interpret their ability to produce an immune-stimulatory peptide. The resulting information can characterize a tumor's neoantigen load, its cadre of infiltrating immune cell types, the T or B cell receptor repertoire, and direct the design of a personalized therapeutic.

PubMed Disclaimer

Figures

Fig 1
Fig 1. An Overall Workflow for Neoantigen Discovery and Personalized Cancer Vaccine Design
Starting from next-generation sequencing of DNA exomes to compare tumor to normal DNA, and of tumor RNA to evaluate gene expression, this figure illustrates the steps outlined in the primer to identify tumor-specific mutant antigens (neoantigens) from NGS data, to evaluate the neoantigens, and to design a personalized neoantigen vaccine.
Figure 2
Figure 2. Idealized Selection of Mutant-Containing Peptides for Neoantigen Prediction
(A) The localized peptides that tile across and contain the mutated amino acid substitution are identified and parsed into the neoantigen prediction pipeline. Each peptide is considered for HLA binding strength relative to its non-mutant (wild-type) counterpart. (B) Shown is the top scoring candidate peptide that was selected across all specified k-mers and between all HLA types that were input to the neoantigen prediction pipeline.
Fig 3
Fig 3. Structure and Diversity in the T Cell Receptor
(A) The mature T cell heterodimer, consisting of α- and β-subunit chains. The α subunit chains consist of variable (V), joining (J), and constant (C) regions, whereas the β subunit includes an additional diversity (D) region. (B) V-D-J recombination and post-transcriptional processing of a TCR-β subunit chain.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Alamyar E, Duroux P, Lefranc M-P, Giudicelli V. IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol. Biol. 2012;882:569–604. - PubMed
    1. Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, Waldner MJ, Bindea G, Mlecnik B, Galon J, et al. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 2015;16:64. - PMC - PubMed
    1. Aouinti S, Malouche D, Giudicelli V, Kossida S, Lefranc M-P. IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors. PLoS One. 2015;10:e0142353. - PMC - PubMed
    1. Babbitt BP, Allen PM, Matsueda G, Haber E, Unanue ER. Binding of immunogenic peptides to Ia histocompatibility molecules. Nature. 1985;317:359–361. - PubMed
    1. Bagaev DV, Zvyagin IV, Putintseva EV, Izraelson M, Britanova OV, Chudakov DM, Shugay M. VDJviz: a versatile browser for immunogenomics data. BMC Genomics. 2016;17:453. - PMC - PubMed

Publication types