Review
. 2017 Feb; 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
  • PMID: 28187283
  •     131 References
  •     67 citations

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.

Presence on a human melanoma of multiple antigens recognized by autologous CTL.
B Van den Eynde, P Hainaut, +6 authors, T Boon.
Int J Cancer, 1989 Oct 15; 44(4). PMID: 2529220
Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients.
Roy S Herbst, Jean-Charles Soria, +19 authors, F Stephen Hodi.
Nature, 2014 Nov 28; 515(7528). PMID: 25428504    Free PMC article.
Highly Cited.
Margin-infiltrating CD20(+) B cells display an atypical memory phenotype and correlate with favorable prognosis in hepatocellular carcinoma.
Jie-Yi Shi, Qiang Gao, +11 authors, Jia Fan.
Clin Cancer Res, 2013 Sep 24; 19(21). PMID: 24056784
Comparison of insertion/deletion calling algorithms on human next-generation sequencing data.
Dalia H Ghoneim, Jason R Myers, Emily Tuttle, Alex R Paciorkowski.
BMC Res Notes, 2014 Dec 02; 7. PMID: 25435282    Free PMC article.
Eradication of B-lineage cells and regression of lymphoma in a patient treated with autologous T cells genetically engineered to recognize CD19.
James N Kochenderfer, Wyndham H Wilson, +9 authors, Steven A Rosenberg.
Blood, 2010 Jul 30; 116(20). PMID: 20668228    Free PMC article.
Highly Cited.
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
Claus Lundegaard, Kasper Lamberth, +3 authors, Morten Nielsen.
Nucleic Acids Res, 2008 May 09; 36(Web Server issue). PMID: 18463140    Free PMC article.
Highly Cited.
Landscape of tumor-infiltrating T cell repertoire of human cancers.
Bo Li, Taiwen Li, +12 authors, X Shirley Liu.
Nat Genet, 2016 May 31; 48(7). PMID: 27240091    Free PMC article.
Highly Cited.
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer.
Lisle E Mose, Sara R Selitsky, +6 authors, Joel S Parker.
Bioinformatics, 2016 Aug 26; 32(24). PMID: 27559159    Free PMC article.
OptiType: precision HLA typing from next-generation sequencing data.
András Szolek, Benjamin Schubert, +3 authors, Oliver Kohlbacher.
Bioinformatics, 2014 Aug 22; 30(23). PMID: 25143287    Free PMC article.
Highly Cited.
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.
Eltaf Alamyar, Patrice Duroux, Marie-Paule Lefranc, Véronique Giudicelli.
Methods Mol Biol, 2012 Jun 06; 882. PMID: 22665256
Highly Cited.
Mutant MHC class II epitopes drive therapeutic immune responses to cancer.
Sebastian Kreiter, Mathias Vormehr, +12 authors, Ugur Sahin.
Nature, 2015 Apr 23; 520(7549). PMID: 25901682    Free PMC article.
Highly Cited.
Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes.
Evan W Newell, Natalia Sigal, +2 authors, Mark M Davis.
Immunity, 2012 Jan 24; 36(1). PMID: 22265676    Free PMC article.
Highly Cited.
Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing.
Emily Hodges, Michelle Rooks, +5 authors, Gregory J Hannon.
Nat Protoc, 2009 May 30; 4(6). PMID: 19478811    Free PMC article.
Generation of cytotoxic T lymphocytes in vitro. I. Response of normal and immune mouse spleen cells in mixed leukocyte cultures.
J C Cerottini, H D Engers, H R Macdonald, T Brunner.
J Exp Med, 1974 Sep 01; 140(3). PMID: 4278108    Free PMC article.
Highly Cited.
MiXCR: software for comprehensive adaptive immunity profiling.
Dmitriy A Bolotin, Stanislav Poslavsky, +4 authors, Dmitriy M Chudakov.
Nat Methods, 2015 Apr 30; 12(5). PMID: 25924071
Highly Cited.
Cancer regression in patients after transfer of genetically engineered lymphocytes.
Richard A Morgan, Mark E Dudley, +13 authors, Steven A Rosenberg.
Science, 2006 Sep 02; 314(5796). PMID: 16946036    Free PMC article.
Highly Cited.
T cell repertoire following autologous stem cell transplantation for multiple sclerosis.
Paolo A Muraro, Harlan Robins, +8 authors, Laurence A Turka.
J Clin Invest, 2014 Feb 18; 124(3). PMID: 24531550    Free PMC article.
Highly Cited.
T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer.
Eric Tran, Paul F Robbins, +9 authors, Steven A Rosenberg.
N Engl J Med, 2016 Dec 14; 375(23). PMID: 27959684    Free PMC article.
Highly Cited.
DNA sequencing technologies: 2006-2016.
Elaine R Mardis.
Nat Protoc, 2017 Jan 06; 12(2). PMID: 28055035
Highly Cited. Review.
The role of B cells for in vivo T cell responses to a Friend virus-induced leukemia.
K R Schultz, J P Klarnet, +2 authors, P D Greenberg.
Science, 1990 Aug 24; 249(4971). PMID: 2118273
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
Yang Li, Jeremy Chien, David I Smith, Jian Ma.
Bioinformatics, 2011 May 07; 27(12). PMID: 21546395
A gene encoding an antigen recognized by cytolytic T lymphocytes on a human melanoma.
P van der Bruggen, C Traversari, +5 authors, T Boon.
Science, 1991 Dec 13; 254(5038). PMID: 1840703
Highly Cited.
Chimeric receptors with 4-1BB signaling capacity provoke potent cytotoxicity against acute lymphoblastic leukemia.
C Imai, K Mihara, +4 authors, D Campana.
Leukemia, 2004 Feb 13; 18(4). PMID: 14961035
Highly Cited.
PD-1 blockade induces responses by inhibiting adaptive immune resistance.
Paul C Tumeh, Christina L Harview, +23 authors, Antoni Ribas.
Nature, 2014 Nov 28; 515(7528). PMID: 25428505    Free PMC article.
Highly Cited.
CD20+ B cells: the other tumor-infiltrating lymphocytes.
Brad H Nelson.
J Immunol, 2010 Oct 22; 185(9). PMID: 20962266
Highly Cited. Review.
Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.
Naiyer A Rizvi, Matthew D Hellmann, +21 authors, Timothy A Chan.
Science, 2015 Mar 15; 348(6230). PMID: 25765070    Free PMC article.
Highly Cited.
Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer.
Eric Tran, Simon Turcotte, +10 authors, Steven A Rosenberg.
Science, 2014 May 09; 344(6184). PMID: 24812403    Free PMC article.
Highly Cited.
Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.
J Douglas Freeman, René L Warren, +2 authors, Robert A Holt.
Genome Res, 2009 Jun 23; 19(10). PMID: 19541912    Free PMC article.
Highly Cited.
A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data.
Bo Li, Jun Z Li.
Genome Biol, 2014 Sep 26; 15(9). PMID: 25253082    Free PMC article.
Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, +12 authors, Roel G W Verhaak.
Nat Commun, 2013 Oct 12; 4. PMID: 24113773    Free PMC article.
Highly Cited.
Long term culture of tumour-specific cytotoxic T cells.
S Gillis, K A Smith.
Nature, 1977 Jul 14; 268(5616). PMID: 145543
Highly Cited.
Characterizing immune repertoires by high throughput sequencing: strategies and applications.
Jorg J A Calis, Brad R Rosenberg.
Trends Immunol, 2014 Oct 13; 35(12). PMID: 25306219    Free PMC article.
Highly Cited. Review.
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Andreas Gnirke, Alexandre Melnikov, +11 authors, Chad Nusbaum.
Nat Biotechnol, 2009 Feb 03; 27(2). PMID: 19182786    Free PMC article.
Highly Cited.
B cells inhibit induction of T cell-dependent tumor immunity.
Z Qin, G Richter, +3 authors, T Blankenstein.
Nat Med, 1998 May 19; 4(5). PMID: 9585241
Highly Cited.
Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.
Michal Bassani-Sternberg, Eva Bräunlein, +16 authors, Angela M Krackhardt.
Nat Commun, 2016 Nov 22; 7. PMID: 27869121    Free PMC article.
Highly Cited.
Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
Anne Bruun Krøigård, Mads Thomassen, +2 authors, Martin Jakob Larsen.
PLoS One, 2016 Mar 24; 11(3). PMID: 27002637    Free PMC article.
Highly Cited.
Current status and recent advances of next generation sequencing techniques in immunological repertoire.
X-L Hou, L Wang, +2 authors, H-Y Diao.
Genes Immun, 2016 Mar 11; 17(3). PMID: 26963138
Review.
A vaccine targeting mutant IDH1 induces antitumour immunity.
Theresa Schumacher, Lukas Bunse, +24 authors, Michael Platten.
Nature, 2014 Jul 22; 512(7514). PMID: 25043048
Highly Cited.
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Yasin Şenbabaoğlu, Ron S Gejman, +26 authors, A Ari Hakimi.
Genome Biol, 2016 Nov 20; 17(1). PMID: 27855702    Free PMC article.
Highly Cited.
IMGT/HLA Database--a sequence database for the human major histocompatibility complex.
J Robinson, M J Waller, +2 authors, S G Marsh.
Nucleic Acids Res, 2000 Jan 11; 29(1). PMID: 11125094    Free PMC article.
Mutanome Engineered RNA Immunotherapy: Towards Patient-Centered Tumor Vaccination.
Mathias Vormehr, Barbara Schrörs, +3 authors, Ugur Sahin.
J Immunol Res, 2016 Feb 05; 2015. PMID: 26844233    Free PMC article.
Review.
Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.
Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T Reddy.
Trends Immunol, 2015 Oct 29; 36(11). PMID: 26508293
Highly Cited. Review.
Predicting tumor purity from methylation microarray data.
Naiqian Zhang, Hua-Jun Wu, +3 authors, Xiaoqi Zheng.
Bioinformatics, 2015 Jun 27; 31(21). PMID: 26112293
A population biological approach to understanding the maintenance and loss of the T-cell repertoire during aging.
Philip L F Johnson, Jörg J Goronzy, Rustom Antia.
Immunology, 2014 Jan 11; 142(2). PMID: 24405293    Free PMC article.
Review.
Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells.
Beatriz M Carreno, Vincent Magrini, +8 authors, Gerald P Linette.
Science, 2015 Apr 04; 348(6236). PMID: 25837513    Free PMC article.
Highly Cited.
Identification of indels in next-generation sequencing data.
Aakrosh Ratan, Thomas L Olson, Thomas P Loughran, Webb Miller.
BMC Bioinformatics, 2015 Apr 17; 16. PMID: 25879703    Free PMC article.
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.
Bjoern Peters, Alessandro Sette.
BMC Bioinformatics, 2005 Jun 02; 6. PMID: 15927070    Free PMC article.
Highly Cited.
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
Timothy J Ley, Elaine R Mardis, +45 authors, Richard K Wilson.
Nature, 2008 Nov 07; 456(7218). PMID: 18987736    Free PMC article.
Highly Cited.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Jin Zhang, Elaine R Mardis, Christopher A Maher.
Bioinformatics, 2016 Nov 01; 33(4). PMID: 27797777    Free PMC article.
Derivation of HLA types from shotgun sequence datasets.
René L Warren, Gina Choe, +4 authors, Robert A Holt.
Genome Med, 2012 Dec 12; 4(12). PMID: 23228053    Free PMC article.
IMMUNOLOGY OF EXPERIMENTAL TUMORS.
L J OLD, E A BOYSE.
Annu Rev Med, 1964 Jan 01; 15. PMID: 14139934
Highly Cited. Review.
Whole exome capture in solution with 3 Gbp of data.
Matthew N Bainbridge, Min Wang, +11 authors, Richard A Gibbs.
Genome Biol, 2010 Jun 23; 11(6). PMID: 20565776    Free PMC article.
Highly Cited.
A mutated beta-catenin gene encodes a melanoma-specific antigen recognized by tumor infiltrating lymphocytes.
P F Robbins, M El-Gamil, +4 authors, S A Rosenberg.
J Exp Med, 1996 Mar 01; 183(3). PMID: 8642260    Free PMC article.
Highly Cited.
The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection.
Yue Jiang, Andrei L Turinsky, Michael Brudno.
Nucleic Acids Res, 2015 Jul 02; 43(15). PMID: 26130710    Free PMC article.
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, +13 authors, Steven A McCarroll.
Cell, 2015 May 23; 161(5). PMID: 26000488    Free PMC article.
Highly Cited.
Combinatorial antigen recognition with balanced signaling promotes selective tumor eradication by engineered T cells.
Christopher C Kloss, Maud Condomines, +2 authors, Michel Sadelain.
Nat Biotechnol, 2012 Dec 18; 31(1). PMID: 23242161    Free PMC article.
Highly Cited.
Binding of immunogenic peptides to Ia histocompatibility molecules.
B P Babbitt, P M Allen, +2 authors, E R Unanue.
Nature, 1985 Sep 02; 317(6035). PMID: 3876513
Highly Cited.
A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population.
Denise M McKinney, Scott Southwood, +12 authors, Alessandro Sette.
Immunogenetics, 2013 Feb 09; 65(5). PMID: 23392739    Free PMC article.
B cells are required for optimal CD4+ and CD8+ T cell tumor immunity: therapeutic B cell depletion enhances B16 melanoma growth in mice.
David J DiLillo, Koichi Yanaba, Thomas F Tedder.
J Immunol, 2010 Mar 03; 184(7). PMID: 20194720    Free PMC article.
Highly Cited.
Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes.
Sachet A Shukla, Michael S Rooney, +14 authors, Gad Getz.
Nat Biotechnol, 2015 Sep 16; 33(11). PMID: 26372948    Free PMC article.
Highly Cited.
Structure of the human class I histocompatibility antigen, HLA-A2.
P J Bjorkman, M A Saper, +3 authors, D C Wiley.
Nature, 1987 Oct 08; 329(6139). PMID: 3309677
Highly Cited.
The IMGT/HLA database.
James Robinson, Jason A Halliwell, +3 authors, Steven G E Marsh.
Nucleic Acids Res, 2012 Oct 20; 41(Database issue). PMID: 23080122    Free PMC article.
Highly Cited.
Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1.
Paul F Robbins, Richard A Morgan, +18 authors, Steven A Rosenberg.
J Clin Oncol, 2011 Feb 02; 29(7). PMID: 21282551    Free PMC article.
Highly Cited.
Classification of current anticancer immunotherapies.
Lorenzo Galluzzi, Erika Vacchelli, +85 authors, Guido Kroemer.
Oncotarget, 2014 Dec 30; 5(24). PMID: 25537519    Free PMC article.
Highly Cited. Review.
The immunodominant antigen of an ultraviolet-induced regressor tumor is generated by a somatic point mutation in the DEAD box helicase p68.
P Dubey, R C Hendrickson, +6 authors, H Schreiber.
J Exp Med, 1997 Feb 17; 185(4). PMID: 9034148    Free PMC article.
Molecular and genetic properties of tumors associated with local immune cytolytic activity.
Michael S Rooney, Sachet A Shukla, +2 authors, Nir Hacohen.
Cell, 2015 Jan 17; 160(1-2). PMID: 25594174    Free PMC article.
Highly Cited.
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity.
Fei Duan, Jorge Duitama, +10 authors, Pramod K Srivastava.
J Exp Med, 2014 Sep 24; 211(11). PMID: 25245761    Free PMC article.
Highly Cited.
Mining the mutanome: developing highly personalized Immunotherapies based on mutational analysis of tumors.
Willem W Overwijk, Ena Wang, +2 authors, Nicholas P Restifo.
J Immunother Cancer, 2013 Jan 01; 1. PMID: 24829748    Free PMC article.
Review.
Genetic basis for clinical response to CTLA-4 blockade in melanoma.
Alexandra Snyder, Vladimir Makarov, +18 authors, Timothy A Chan.
N Engl J Med, 2014 Nov 20; 371(23). PMID: 25409260    Free PMC article.
Highly Cited.
A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status.
Victor Greiff, Pooja Bhat, +3 authors, Sai T Reddy.
Genome Med, 2015 Jul 04; 7(1). PMID: 26140055    Free PMC article.
Highly Cited.
Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.
Bo Li, Eric Severson, +10 authors, X Shirley Liu.
Genome Biol, 2016 Aug 24; 17(1). PMID: 27549193    Free PMC article.
Highly Cited.
Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells.
Paul F Robbins, Yong-Chen Lu, +9 authors, Steven A Rosenberg.
Nat Med, 2013 May 07; 19(6). PMID: 23644516    Free PMC article.
Highly Cited.
T-cell-mediated cytotoxicity against autologous malignant melanoma: analysis with interleukin 2-dependent T-cell cultures.
A Knuth, B Danowski, H F Oettgen, L J Old.
Proc Natl Acad Sci U S A, 1984 Jun 01; 81(11). PMID: 6610177    Free PMC article.
Highly Cited.
Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Giuseppe Narzisi, Jason A O'Rawe, +7 authors, Michael C Schatz.
Nat Methods, 2014 Aug 19; 11(10). PMID: 25128977    Free PMC article.
Highly Cited.
Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity.
Michael Rasmussen, Emilio Fenoy, +4 authors, Søren Buus.
J Immunol, 2016 Jul 13; 197(4). PMID: 27402703    Free PMC article.
Enhanced efficacy of melanoma vaccines in the absence of B lymphocytes.
Michael A Perricone, Karen A Smith, +5 authors, Johanne M Kaplan.
J Immunother, 2004 Jul 06; 27(4). PMID: 15235388
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.
Yue Jiang, Yadong Wang, Michael Brudno.
Bioinformatics, 2012 Aug 02; 28(20). PMID: 22851530
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference.
Adam Cornish, Chittibabu Guda.
Biomed Res Int, 2015 Nov 06; 2015. PMID: 26539496    Free PMC article.
Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier-Guided Amplicon Assembly.
Charles Cole, Roger Volden, +2 authors, Christopher Vollmers.
J Immunol, 2016 Feb 10; 196(6). PMID: 26856699
Practical guidelines for B-cell receptor repertoire sequencing analysis.
Gur Yaari, Steven H Kleinstein.
Genome Med, 2015 Nov 22; 7. PMID: 26589402    Free PMC article.
Highly Cited. Review.
Interferon-gamma ELISPOT assay for the quantitative measurement of antigen-specific murine CD8+ T-cells.
Geoffrey A Cole.
Methods Mol Biol, 2005 Jun 07; 302. PMID: 15937353
Immunosequencing: applications of immune repertoire deep sequencing.
Harlan Robins.
Curr Opin Immunol, 2013 Oct 22; 25(5). PMID: 24140071
Highly Cited. Review.
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
Hao Zhang, Ole Lund, Morten Nielsen.
Bioinformatics, 2009 Mar 20; 25(10). PMID: 19297351    Free PMC article.
Tumor neoantigens: building a framework for personalized cancer immunotherapy.
Matthew M Gubin, Maxim N Artyomov, Elaine R Mardis, Robert D Schreiber.
J Clin Invest, 2015 Aug 11; 125(9). PMID: 26258412    Free PMC article.
Highly Cited. Review.
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, +6 authors, Marc W Kirschner.
Cell, 2015 May 23; 161(5). PMID: 26000487    Free PMC article.
Highly Cited.
Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer.
David R Kroeger, Katy Milne, Brad H Nelson.
Clin Cancer Res, 2016 Jan 15; 22(12). PMID: 26763251
Highly Cited.
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.
James Robinson, Matthew J Waller, +5 authors, Steven G E Marsh.
Nucleic Acids Res, 2003 Jan 10; 31(1). PMID: 12520010    Free PMC article.
Highly Cited.
Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy.
Jianjun Gao, Lewis Zhichang Shi, +13 authors, Padmanee Sharma.
Cell, 2016 Sep 27; 167(2). PMID: 27667683    Free PMC article.
Highly Cited.
CTLA4 blockade broadens the peripheral T-cell receptor repertoire.
Lidia Robert, Jennifer Tsoi, +11 authors, Antoni Ribas.
Clin Cancer Res, 2014 Mar 04; 20(9). PMID: 24583799    Free PMC article.
Highly Cited.
An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples.
Jonathan A Scolnick, Michelle Dimon, +2 authors, Douglas A Amorese.
PLoS One, 2015 Jul 02; 10(7). PMID: 26132974    Free PMC article.
PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors.
Thammakorn Saethang, Osamu Hirose, +7 authors, Kenji Satou.
J Immunol Methods, 2012 Oct 13; 387(1-2). PMID: 23058674
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.
Safa Aouinti, Dhafer Malouche, +2 authors, Marie-Paule Lefranc.
PLoS One, 2015 Nov 06; 10(11). PMID: 26540440    Free PMC article.
The present status and future prospects of peptide-based cancer vaccines.
Masatoshi Hirayama, Yasuharu Nishimura.
Int Immunol, 2016 May 29; 28(7). PMID: 27235694
Review.
Adoptive cell transfer as personalized immunotherapy for human cancer.
Steven A Rosenberg, Nicholas P Restifo.
Science, 2015 Apr 04; 348(6230). PMID: 25838374    Free PMC article.
Highly Cited. Review.
Cancer regression and autoimmunity in patients after clonal repopulation with antitumor lymphocytes.
Mark E Dudley, John R Wunderlich, +16 authors, Steven A Rosenberg.
Science, 2002 Sep 21; 298(5594). PMID: 12242449    Free PMC article.
Highly Cited.
Chimeric receptors containing CD137 signal transduction domains mediate enhanced survival of T cells and increased antileukemic efficacy in vivo.
Michael C Milone, Jonathan D Fish, +11 authors, Carl H June.
Mol Ther, 2009 Apr 23; 17(8). PMID: 19384291    Free PMC article.
Highly Cited.
Personalized cancer vaccines: Targeting the cancer mutanome.
Xiuli Zhang, Piyush K Sharma, S Peter Goedegebuure, William E Gillanders.
Vaccine, 2016 Jul 28; 35(7). PMID: 27449681    Free PMC article.
Review.
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy.
Mihaela Angelova, Pornpimol Charoentong, +8 authors, Zlatko Trajanoski.
Genome Biol, 2015 Apr 09; 16. PMID: 25853550    Free PMC article.
Highly Cited.
Identifying fusion transcripts using next generation sequencing.
Shailesh Kumar, Sundus Khalid Razzaq, +2 authors, Hui Li.
Wiley Interdiscip Rev RNA, 2016 Aug 04; 7(6). PMID: 27485475    Free PMC article.
Review.
VDJviz: a versatile browser for immunogenomics data.
Dmitriy V Bagaev, Ivan V Zvyagin, +4 authors, Mikhail Shugay.
BMC Genomics, 2016 Jun 15; 17. PMID: 27297497    Free PMC article.
Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma.
Michael A Postow, Manuarii Manuel, +9 authors, Jedd D Wolchok.
J Immunother Cancer, 2015 Jun 19; 3. PMID: 26085931    Free PMC article.
Highly Cited.
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Eliezer M Van Allen, Diana Miao, +19 authors, Levi A Garraway.
Science, 2015 Sep 12; 350(6257). PMID: 26359337    Free PMC article.
Highly Cited.
Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.
Gabriela Bindea, Bernhard Mlecnik, +14 authors, Jérôme Galon.
Immunity, 2013 Oct 22; 39(4). PMID: 24138885
Highly Cited.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Jin Zhang, Nicole M White, +5 authors, Christopher A Maher.
Genome Res, 2015 Nov 12; 26(1). PMID: 26556708    Free PMC article.
A unique tumor antigen produced by a single amino acid substitution.
P A Monach, S C Meredith, C T Siegel, H Schreiber.
Immunity, 1995 Jan 01; 2(1). PMID: 7600302
Immunity to methylcholanthrene-induced sarcomas.
R T PREHN, J M MAIN.
J Natl Cancer Inst, 1957 Jun 01; 18(6). PMID: 13502695
Highly Cited.
Antigenic properties of methylcholanthrene-induced tumors in mice of the strain of origin.
E J FOLEY.
Cancer Res, 1953 Dec 01; 13(12). PMID: 13116120
Highly Cited.
Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens.
Matthew M Gubin, Xiuli Zhang, +24 authors, Robert D Schreiber.
Nature, 2014 Nov 28; 515(7528). PMID: 25428507    Free PMC article.
Highly Cited.
Towards error-free profiling of immune repertoires.
Mikhail Shugay, Olga V Britanova, +13 authors, Dmitriy M Chudakov.
Nat Methods, 2014 May 06; 11(6). PMID: 24793455
Highly Cited.
Pembrolizumab for the treatment of non-small-cell lung cancer.
Edward B Garon, Naiyer A Rizvi, +25 authors, KEYNOTE-001 Investigators.
N Engl J Med, 2015 Apr 22; 372(21). PMID: 25891174
Highly Cited.
Hybrid biogeography based simultaneous feature selection and MHC class I peptide binding prediction using support vector machines and random forests.
Atulji Srivastava, Shameek Ghosh, N Anantharaman, V K Jayaraman.
J Immunol Methods, 2012 Oct 13; 387(1-2). PMID: 23058675
IMGT, the international ImMunoGeneTics database.
V Giudicelli, D Chaume, +7 authors, M P Lefranc.
Nucleic Acids Res, 1997 Jan 01; 25(1). PMID: 9016537    Free PMC article.
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
Mikhail Shugay, Dmitriy V Bagaev, +10 authors, Dmitriy M Chudakov.
PLoS Comput Biol, 2015 Nov 26; 11(11). PMID: 26606115    Free PMC article.
Highly Cited.
Absolute quantification of somatic DNA alterations in human cancer.
Scott L Carter, Kristian Cibulskis, +13 authors, Gad Getz.
Nat Biotechnol, 2012 May 01; 30(5). PMID: 22544022    Free PMC article.
Highly Cited.
Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.
Willy Hugo, Jesse M Zaretsky, +15 authors, Roger S Lo.
Cell, 2016 Mar 22; 165(1). PMID: 26997480    Free PMC article.
Highly Cited.
ABRA: improved coding indel detection via assembly-based realignment.
Lisle E Mose, Matthew D Wilkerson, +2 authors, Joel S Parker.
Bioinformatics, 2014 Jun 08; 30(19). PMID: 24907369    Free PMC article.
Colocalization of inflammatory response with B7-h1 expression in human melanocytic lesions supports an adaptive resistance mechanism of immune escape.
Janis M Taube, Robert A Anders, +8 authors, Lieping Chen.
Sci Transl Med, 2012 Mar 31; 4(127). PMID: 22461641    Free PMC article.
Highly Cited.
Peptide binding predictions for HLA DR, DP and DQ molecules.
Peng Wang, John Sidney, +4 authors, Bjoern Peters.
BMC Bioinformatics, 2010 Nov 26; 11. PMID: 21092157    Free PMC article.
Highly Cited.
PD-1 Blockade in Tumors with Mismatch-Repair Deficiency.
Dung T Le, Jennifer N Uram, +32 authors, Luis A Diaz.
N Engl J Med, 2015 Jun 02; 372(26). PMID: 26028255    Free PMC article.
Highly Cited.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, +34 authors, Levi A Garraway.
Science, 2016 Apr 29; 352(6282). PMID: 27124452    Free PMC article.
Highly Cited.
T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia.
Michael Kalos, Bruce L Levine, +4 authors, Carl H June.
Sci Transl Med, 2011 Aug 13; 3(95). PMID: 21832238    Free PMC article.
Highly Cited.
Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma.
Jesse M Zaretsky, Angel Garcia-Diaz, +26 authors, Antoni Ribas.
N Engl J Med, 2016 Jul 20; 375(9). PMID: 27433843    Free PMC article.
Highly Cited.
Distribution and significance of interstitial fibrosis and stroma-infiltrating B cells in tongue squamous cell carcinoma.
Xiao-Mei Lao, Yu-Jie Liang, +3 authors, Gui-Qing Liao.
Oncol Lett, 2016 Mar 22; 11(3). PMID: 26998116    Free PMC article.
Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, +6 authors, Ash A Alizadeh.
Nat Methods, 2015 Mar 31; 12(5). PMID: 25822800    Free PMC article.
Highly Cited.
MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.
Xiaoqi Zheng, Qian Zhao, +15 authors, Xiaole Shirley Liu.
Genome Biol, 2014 Aug 12; 15(8). PMID: 25103624    Free PMC article.
High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer.
Ryan O Emerson, Anna M Sherwood, +7 authors, Harlan S Robins.
J Pathol, 2013 Sep 13; 231(4). PMID: 24027095    Free PMC article.
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
Claus Lundegaard, Ole Lund, Morten Nielsen.
Bioinformatics, 2008 Apr 17; 24(11). PMID: 18413329
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Morten Nielsen, Claus Lundegaard, +5 authors, Ole Lund.
Protein Sci, 2003 Apr 30; 12(5). PMID: 12717023    Free PMC article.
Highly Cited.
Immunogenic (tum-) variants of mouse tumor P815: cloning of the gene of tum- antigen P91A and identification of the tum- mutation.
E De Plaen, C Lurquin, +6 authors, T Boon.
Proc Natl Acad Sci U S A, 1988 Apr 01; 85(7). PMID: 3127830    Free PMC article.
Highly Cited.
IgG subclass switching and clonal expansion in cutaneous melanoma and normal skin.
Louise Saul, Kristina M Ilieva, +20 authors, Sophia N Karagiannis.
Sci Rep, 2016 Jul 15; 6. PMID: 27411958    Free PMC article.
Human neoplasms elicit multiple specific immune responses in the autologous host.
U Sahin, O Türeci, +7 authors, M Pfreundschuh.
Proc Natl Acad Sci U S A, 1995 Dec 05; 92(25). PMID: 8524854    Free PMC article.
Highly Cited.
Immunology: The patterns of T-cell target recognition.
Sai T Reddy.
Nature, 2017 Jun 22; 547(7661). PMID: 28636588
Clinical implications of neoepitope landscapes for adult and pediatric cancers.
Yang-Yang Feng, Obi L Griffith, Malachi Griffith.
Genome Med, 2017 Sep 01; 9(1). PMID: 28854952    Free PMC article.
Review.
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.
Florian Rubelt, Christian E Busse, +17 authors, Steven H Kleinstein.
Nat Immunol, 2017 Nov 17; 18(12). PMID: 29144493    Free PMC article.
Precision oncology in the age of integrative genomics.
Chandan Kumar-Sinha, Arul M Chinnaiyan.
Nat Biotechnol, 2018 Jan 11; 36(1). PMID: 29319699    Free PMC article.
Precision Immuno-Oncology: Prospects of Individualized Immunotherapy for Pancreatic Cancer.
Jiajia Zhang, Christopher L Wolfgang, Lei Zheng.
Cancers (Basel), 2018 Feb 02; 10(2). PMID: 29385739    Free PMC article.
Review.
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.
Yafeng Zhu, Lukas M Orre, +6 authors, Janne Lehtiö.
Nat Commun, 2018 Mar 04; 9(1). PMID: 29500430    Free PMC article.
Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.
Enkelejda Miho, Alexander Yermanos, +3 authors, Victor Greiff.
Front Immunol, 2018 Mar 09; 9. PMID: 29515569    Free PMC article.
Highly Cited. Review.
Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma.
Hyun-Sung Lee, Hee-Jin Jang, +11 authors, Bryan M Burt.
JCI Insight, 2018 Apr 06; 3(7). PMID: 29618661    Free PMC article.
The perfect personalized cancer therapy: cancer vaccines against neoantigens.
Luigi Aurisicchio, Matteo Pallocca, Gennaro Ciliberto, Fabio Palombo.
J Exp Clin Cancer Res, 2018 Apr 22; 37(1). PMID: 29678194    Free PMC article.
Review.
Pathway perturbations in signaling networks: Linking genotype to phenotype.
Yongsheng Li, Daniel J McGrail, +3 authors, Nidhi Sahni.
Semin Cell Dev Biol, 2018 May 09; 99. PMID: 29738884    Free PMC article.
Review.
Personalized cancer neoantigen vaccines come of age.
Yanhong Chu, Qin Liu, Jia Wei, Baorui Liu.
Theranostics, 2018 Aug 22; 8(15). PMID: 30128050    Free PMC article.
Review.
Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology.
Francesca Finotello, Federica Eduati.
Front Oncol, 2018 Oct 23; 8. PMID: 30345255    Free PMC article.
Review.
Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes.
Weilong Zhao, Xinwei Sher.
PLoS Comput Biol, 2018 Nov 09; 14(11). PMID: 30408041    Free PMC article.
Landscape of B cell immunity and related immune evasion in human cancers.
Xihao Hu, Jian Zhang, +17 authors, X Shirley Liu.
Nat Genet, 2019 Feb 12; 51(3). PMID: 30742113    Free PMC article.
Highly Cited.
Genomics-Guided Immunotherapy for Precision Medicine in Cancer.
Shradha Mukherjee.
Cancer Biother Radiopharm, 2019 Jul 18; 34(8). PMID: 31314580    Free PMC article.
Review.
Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity.
Guangchuan Wang, Ryan D Chow, +12 authors, Sidi Chen.
Nat Immunol, 2019 Oct 16; 20(11). PMID: 31611701    Free PMC article.
Predictive Factors for Response to PD-1/PD-L1 Checkpoint Inhibition in the Field of Hepatocellular Carcinoma: Current Status and Challenges.
Zuzana Macek Jilkova, Caroline Aspord, Thomas Decaens.
Cancers (Basel), 2019 Oct 17; 11(10). PMID: 31615069    Free PMC article.
Review.
Immunotherapeutic Challenges for Pediatric Cancers.
Brian Hutzen, Mohammed Ghonime, +7 authors, Kevin A Cassady.
Mol Ther Oncolytics, 2019 Oct 28; 15. PMID: 31650024    Free PMC article.
Review.
The Landscape of Tumor Fusion Neoantigens: A Pan-Cancer Analysis.
Zhiting Wei, Chi Zhou, +4 authors, Qi Liu.
iScience, 2019 Nov 05; 21. PMID: 31677477    Free PMC article.
The Immunogenicity and Anti-tumor Efficacy of a Rationally Designed Neoantigen Vaccine for B16F10 Mouse Melanoma.
Yan Zhang, Zhibing Lin, +3 authors, Rongxiu Li.
Front Immunol, 2019 Nov 22; 10. PMID: 31749795    Free PMC article.
Identification and ranking of recurrent neo-epitopes in cancer.
Eric Blanc, Manuel Holtgrewe, +4 authors, Dieter Beule.
BMC Med Genomics, 2019 Nov 30; 12(1). PMID: 31775766    Free PMC article.
Characterization of 108 Genomic DNA Reference Materials for 11 Human Leukocyte Antigen Loci: A GeT-RM Collaborative Project.
Maria P Bettinotti, Deborah Ferriola, +5 authors, Dimitri Monos.
J Mol Diagn, 2018 Jul 01; 20(5). PMID: 29959025    Free PMC article.
Lung Cancer Heterogeneity in Modulation of Th17/IL17A Responses.
Dominique Armstrong, Cheng-Yen Chang, +2 authors, Farrah Kheradmand.
Front Oncol, 2020 Jan 11; 9. PMID: 31921642    Free PMC article.
Review.
neoANT-HILL: an integrated tool for identification of potential neoantigens.
Ana Carolina M F Coelho, André L Fonseca, +3 authors, Sandro J de Souza.
BMC Med Genomics, 2020 Feb 24; 13(1). PMID: 32087727    Free PMC article.
Insights Into Lung Cancer Immune-Based Biology, Prevention, and Treatment.
Sara Saab, Hussein Zalzale, +3 authors, Humam Kadara.
Front Immunol, 2020 Mar 03; 11. PMID: 32117295    Free PMC article.
Review.
Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers.
Roozbeh Dehghannasiri, Donald E Freeman, +4 authors, Julia Salzman.
Proc Natl Acad Sci U S A, 2019 Jul 17; 116(31). PMID: 31308241    Free PMC article.
High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets.
Xiaoshan M Shao, Rohit Bhattacharya, +12 authors, Rachel Karchin.
Cancer Immunol Res, 2019 Dec 25; 8(3). PMID: 31871119    Free PMC article.
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.
Jasreet Hundal, Susanna Kiwala, +15 authors, Malachi Griffith.
Cancer Immunol Res, 2020 Jan 08; 8(3). PMID: 31907209    Free PMC article.
Hyperprogression under Immune Checkpoint Inhibitor: a potential role for germinal immunogenetics.
Sadal Refae, Jocelyn Gal, +7 authors, Esma Saada-Bouzid.
Sci Rep, 2020 Feb 29; 10(1). PMID: 32107407    Free PMC article.
Functional genomics: paving the way for more successful cancer immunotherapy.
Reham Ajina, Danielle Zamalin, Louis M Weiner.
Brief Funct Genomics, 2018 May 16; 18(2). PMID: 29762641    Free PMC article.
Review.
Accounting for proximal variants improves neoantigen prediction.
Jasreet Hundal, Susanna Kiwala, +8 authors, Malachi Griffith.
Nat Genet, 2018 Dec 05; 51(1). PMID: 30510237    Free PMC article.
Recent updates in cancer immunotherapy: a comprehensive review and perspective of the 2018 China Cancer Immunotherapy Workshop in Beijing.
Zihai Li, Wenru Song, Mark Rubinstein, Delong Liu.
J Hematol Oncol, 2018 Dec 24; 11(1). PMID: 30577797    Free PMC article.
Highly Cited. Review.
Genomic correlates of response to immune checkpoint blockade.
Tanya E Keenan, Kelly P Burke, Eliezer M Van Allen.
Nat Med, 2019 Mar 08; 25(3). PMID: 30842677    Free PMC article.
Highly Cited. Review.
Peptides identified on monocyte-derived dendritic cells: a marker for clinical immunogenicity to FVIII products.
Wojciech Jankowski, Yara Park, +8 authors, Zuben E Sauna.
Blood Adv, 2019 May 06; 3(9). PMID: 31053570    Free PMC article.
Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma.
Sehhoon Park, Je-Gun Joung, +10 authors, Jong-Mu Sun.
J Immunother Cancer, 2019 May 18; 7(1). PMID: 31097034    Free PMC article.
Patients Selection for Immunotherapy in Solid Tumors: Overcome the Naïve Vision of a Single Biomarker.
Diego Signorelli, Patrizia Giannatempo, +11 authors, Immune-Oncology YOUNG Group.
Biomed Res Int, 2019 Jun 11; 2019. PMID: 31179334    Free PMC article.
Review.
Best practices for bioinformatic characterization of neoantigens for clinical utility.
Megan M Richters, Huiming Xia, +3 authors, Malachi Griffith.
Genome Med, 2019 Aug 30; 11(1). PMID: 31462330    Free PMC article.
Highly Cited. Review.
Identification of prognostic immune-related genes in the tumor microenvironment of endometrial cancer.
Peigen Chen, Yuebo Yang, +3 authors, Jing Wan.
Aging (Albany NY), 2020 Feb 20; 12(4). PMID: 32074080    Free PMC article.
Liquid Biopsy Applications in the Clinic.
Dake Chen, Tao Xu, +4 authors, Jian Chen.
Mol Diagn Ther, 2020 Jan 11; 24(2). PMID: 31919754
Review.
Is There a Place for Immunotherapy for Metastatic Microsatellite Stable Colorectal Cancer?
François Ghiringhelli, Jean-David Fumet.
Front Immunol, 2019 Aug 27; 10. PMID: 31447840    Free PMC article.
Review.
Immune Cytolytic Activity Is Associated With Genetic and Clinical Properties of Glioma.
Zhi-Liang Wang, Zheng Wang, +4 authors, Tao Jiang.
Front Immunol, 2019 Aug 21; 10. PMID: 31428092    Free PMC article.
Editorial: Targeting MYB Oncogene Expression in Adenoid Cystic Carcinoma.
Scott A Ness.
J Natl Cancer Inst, 2017 Sep 28; 109(9). PMID: 28954283    Free PMC article.
Features and therapeutic potential of T-cell receptors in high-grade glioma.
Jie-Lin Zhang, Xiao-Song Zhong, +4 authors, Wen-Bin Li.
Chin Med J (Engl), 2019 Jun 18; 132(12). PMID: 31205101    Free PMC article.
Common, intermediate and well-documented HLA alleles in world populations: CIWD version 3.0.0.
Carolyn K Hurley, Jane Kempenich, +35 authors, Jason Dehn.
HLA, 2020 Jan 24; 95(6). PMID: 31970929    Free PMC article.
Challenges and strategies for next-generation bispecific antibody-based antitumor therapeutics.
Heliang Li, Phei Er Saw, Erwei Song.
Cell Mol Immunol, 2020 Apr 22; 17(5). PMID: 32313210    Free PMC article.
Review.
Cancer systems immunology.
Nathan E Reticker-Flynn, Edgar G Engleman.
Elife, 2020 Jul 14; 9. PMID: 32657757    Free PMC article.
Review.
Classification of Muscle-Invasive Bladder Cancer Based on Immunogenomic Profiling.
Xianghong Zhou, Shi Qiu, +5 authors, Qiang Wei.
Front Oncol, 2020 Sep 26; 10. PMID: 32974156    Free PMC article.
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment.
Yi Zhang, Mohith Manjunath, +4 authors, Jun S Song.
Front Genet, 2019 Sep 12; 10. PMID: 31507631    Free PMC article.
Investigating the correlation between DNA methylation and immune‑associated genes of lung adenocarcinoma based on a competing endogenous RNA network.
Chun Chang, Wei Kong, Xiaoyang Mou, Shuaiqun Wang.
Mol Med Rep, 2020 Sep 19; 22(4). PMID: 32945447    Free PMC article.
Identification and Validation of an Immunological Expression-Based Prognostic Signature in Breast Cancer.
Jianying Pei, Yan Li, +6 authors, Yanping Li.
Front Genet, 2020 Nov 17; 11. PMID: 33193571    Free PMC article.
Detecting Tumor Antigen-Specific T Cells via Interaction-Dependent Fucosyl-Biotinylation.
Zilei Liu, Jie P Li, +5 authors, Peng Wu.
Cell, 2020 Oct 24; 183(4). PMID: 33096019    Free PMC article.
CRI iAtlas: an interactive portal for immuno-oncology research.
James A Eddy, Vésteinn Thorsson, +9 authors, Justin Guinney.
F1000Res, 2020 Nov 21; 9. PMID: 33214875    Free PMC article.
Emerging immunotherapies for malignant glioma: from immunogenomics to cell therapy.
Gavin P Dunn, Timothy F Cloughesy, +3 authors, Adam M Sonabend.
Neuro Oncol, 2020 Jul 03; 22(10). PMID: 32615600    Free PMC article.
Review.
Cancer research in the era of immunogenomics.
Yochai Wolf, Yardena Samuels.
ESMO Open, 2019 Jan 10; 3(7). PMID: 30622743    Free PMC article.
Review.
Cytolytic activity correlates with the mutational burden and deregulated expression of immune checkpoints in colorectal cancer.
Apostolos Zaravinos, Constantinos Roufas, +5 authors, Georgios D Ayiomamitis.
J Exp Clin Cancer Res, 2019 Aug 21; 38(1). PMID: 31429779    Free PMC article.
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.
Siwen Hu-Lieskovan, Srabani Bhaumik, +14 authors, Holden T Maecker.
J Immunother Cancer, 2020 Dec 04; 8(2). PMID: 33268350    Free PMC article.
Tumour evolution in hepatocellular carcinoma.
Amanda J Craig, Johann von Felden, +2 authors, Augusto Villanueva.
Nat Rev Gastroenterol Hepatol, 2019 Dec 04; 17(3). PMID: 31792430
Review.
Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology.
Md Aminul Islam, Sharmin Aqter Rony, +4 authors, Haruki Kitazawa.
Animals (Basel), 2020 Dec 03; 10(12). PMID: 33260762    Free PMC article.
Review.
Recent Discoveries of Macromolecule- and Cell-Based Biomarkers and Therapeutic Implications in Breast Cancer.
Hsing-Ju Wu, Pei-Yi Chu.
Int J Mol Sci, 2021 Jan 14; 22(2). PMID: 33435254    Free PMC article.
Review.
Antigen folding improves loading efficiency and antitumor efficacy of PC7A nanoparticle vaccine.
Jonathan Wilhelm, Manuel Quiñones-Pérez, +3 authors, Jinming Gao.
J Control Release, 2020 Dec 11; 329. PMID: 33301836    Free PMC article.
T Cell Receptor Beta-Chain Profiling of Tumor Tissue, Peripheral Blood and Regional Lymph Nodes From Patients With Papillary Thyroid Carcinoma.
Yizeng Wang, Yuanchao Liu, +5 authors, Xianghui He.
Front Immunol, 2021 Mar 09; 12. PMID: 33679738    Free PMC article.
Advances in immunotherapy for hepatocellular carcinoma.
Bruno Sangro, Pablo Sarobe, Sandra Hervás-Stubbs, Ignacio Melero.
Nat Rev Gastroenterol Hepatol, 2021 Apr 15;. PMID: 33850328    Free PMC article.
Review.
Personal Neoantigens From Patients With NSCLC Induce Efficient Antitumor Responses.
Wei Zhang, Qi Yin, +8 authors, Qiang Li.
Front Oncol, 2021 May 01; 11. PMID: 33928024    Free PMC article.
Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates.
Yannick Simoni, Etienne Becht, +29 authors, Evan W Newell.
Nature, 2018 May 18; 557(7706). PMID: 29769722
Highly Cited.
Neoantigen landscape in metastatic nasopharyngeal carcinoma.
Mei Lin, Xiao-Long Zhang, +20 authors, Ming-Yuan Chen.
Theranostics, 2021 May 18; 11(13). PMID: 33995666    Free PMC article.
Triple-negative breast cancer: promising prognostic biomarkers currently in development.
Jasmine Sukumar, Kelly Gast, +2 authors, Nicole Williams.
Expert Rev Anticancer Ther, 2020 Nov 18; 21(2). PMID: 33198517    Free PMC article.
A novel genomic classification system of gastric cancer via integrating multidimensional genomic characteristics.
Haiyong Wang, Yongfeng Ding, +23 authors, Lisong Teng.
Gastric Cancer, 2021 Jun 08;. PMID: 34095982