High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556

Signatures of mutational processes in human cancer

Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660

Cancer Genome Landscapes

Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863

Tumor-reactive CD4(+) T cells develop cytotoxic activity and eradicate large established melanoma after transfer into lymphopenic hosts

Quezada, S. A., Simpson, T. R., Peggs, K. S., Merghoub, T., Vider, J., Fan, X., Blasberg, R., Yagita, H., Muranski, P., Antony, P. A., et al. (2010) · Journal of Experimental Medicine · doi:10.1084/jem.20091918 · Cited by 898

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

Le, D. T., Uram, J. N., Wang, H., Bartlett, B. R., Kemberling, H., Eyring, A. D., Skora, A. D., Luber, B. S., Azad, N. S., Laheru, D., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1500596 · Cited by 9,377

Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer

Rizvi, N. A., Hellmann, M. D., Snyder, A., Kvistborg, P., Makarov, V., Havel, J. J., Lee, W., Yuan, J., Wong, P., Ho, T. S., et al. (2015) · Science · doi:10.1126/science.aaa1348 · Cited by 7,802

Elements of cancer immunity and the cancer–immune set point

Chen, D. S., & Mellman, I. (2017) · Nature · doi:10.1038/nature21349 · Cited by 5,352

Neoantigens in cancer immunotherapy

Schumacher, T. N., & Schreiber, R. D. (2015) · Science · doi:10.1126/science.aaa4971 · Cited by 4,783

An immunogenic personal neoantigen vaccine for patients with melanoma

Ott, P. A., Hu, Z., Keskin, D. B., Shukla, S. A., Sun, J., Bozym, D. J., Zhang, W., Luoma, A., Giobbie-Hurder, A., Peter, L., et al. (2017) · Nature · doi:10.1038/nature22991 · Cited by 2,936

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

Van Allen, E. M., Miao, D., Schilling, B., Shukla, S. A., Blank, C., Zimmer, L., Sucker, A., Hillen, U., Geukes Foppen, M. H., Goldinger, S. M., et al. (2015) · Science · doi:10.1126/science.aad0095 · Cited by 2,839

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

Sahin, U., Derhovanessian, E., Miller, M., Kloke, B.-P., Simon, P., Löwer, M., Bukur, V., Tadmor, A. D., Luxemburger, U., Schrörs, B., et al. (2017) · Nature · doi:10.1038/nature23003 · Cited by 2,488

Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential

Sharma, P., & Allison, J. P. (2015) · Cell · doi:10.1016/j.cell.2015.03.030 · Cited by 2,345

Therapeutic cancer vaccines

Saxena, M., van der Burg, S. H., Melief, C. J. M., & Bhardwaj, N. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00346-0 · Cited by 1,581

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

Kreiter, S., Vormehr, M., van de Roemer, N., Diken, M., Löwer, M., Diekmann, J., Boegel, S., Schrörs, B., Vascotto, F., Castle, J. C., et al. (2015) · Nature · doi:10.1038/nature14426 · Cited by 1,243

Towards precision medicine

Ashley, E. A. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.86 · Cited by 1,116

The Where, the When, and the How of Immune Monitoring for Cancer Immunotherapies in the Era of Checkpoint Inhibition

Hegde, P. S., Karanikas, V., & Evers, S. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1507 · Cited by 1,000

Towards personalized, tumour-specific, therapeutic vaccines for cancer

Hu, Z., Ott, P. A., & Wu, C. J. (2018) · Nature Reviews Immunology · doi:10.1038/nri.2017.131 · Cited by 1,067

Advances in the development of personalized neoantigen-based therapeutic cancer vaccines

Blass, E., & Ott, P. A. (2021) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-020-00460-2 · Cited by 1,042

Neoantigens: promising targets for cancer therapy

Xie, N., Shen, G., Gao, W., Huang, Z., Huang, C., & Fu, L. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01270-x · Cited by 1,020

Clinical relevance of host immunity in breast cancer: from TILs to the clinic

Savas, P., Salgado, R., Denkert, C., Sotiriou, C., Darcy, P. K., Smyth, M. J., & Loi, S. (2016) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2015.215 · Cited by 890

MHC-II neoantigens shape tumour immunity and response to immunotherapy

Alspach, E., Lussier, D. M., Miceli, A. P., Kizhvatov, I., DuPage, M., Luoma, A. M., Meng, W., Lichti, C. F., Esaulova, E., Vomund, A. N., et al. (2019) · Nature · doi:10.1038/s41586-019-1671-8 · Cited by 846

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

Schietinger, A., Philip, M., Krisnawan, V. E., Chiu, E. Y., Delrow, J. J., Basom, R. S., Lauer, P., Brockstedt, D. G., Knoblaugh, S. E., Hämmerling, G. J., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.07.011 · Cited by 720

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

Bassani-Sternberg, M., Bräunlein, E., Klar, R., Engleitner, T., Sinitcyn, P., Audehm, S., Straub, M., Weber, J., Slotta-Huspenina, J., Specht, K., et al. (2016) · Nature Communications · doi:10.1038/ncomms13404 · Cited by 693

Oncogenic RAS Signaling Promotes Tumor Immunoresistance by Stabilizing PD-L1 mRNA

Coelho, M. A., de Carné Trécesson, S., Rana, S., Zecchin, D., Moore, C., Molina-Arcas, M., East, P., Spencer-Dene, B., Nye, E., Barnouin, K., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.11.016 · Cited by 653

Immune escape to PD-L1/PD-1 blockade: seven steps to success (or failure)

Kim, J. M., & Chen, D. S. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw217 · Cited by 648

Development of immuno-oncology drugs — from CTLA4 to PD1 to the next generations

Hoos, A. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2015.35 · Cited by 601

Cancer Neoantigens

Schumacher, T. N., Scheper, W., & Kvistborg, P. (2019) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042617-053402 · Cited by 574

Drug development in the era of precision medicine

Dugger, S. A., Platt, A., & Goldstein, D. B. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.226 · Cited by 493

'Final common pathway' of human cancer immunotherapy: targeting random somatic mutations

Tran, E., Robbins, P. F., & Rosenberg, S. A. (2017) · Nature Immunology · doi:10.1038/ni.3682 · Cited by 443

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

Strønen, E., Toebes, M., Kelderman, S., van Buuren, M. M., Yang, W., van Rooij, N., Donia, M., Böschen, M.-L., Lund-Johansen, F., Olweus, J., et al. (2016) · Science · doi:10.1126/science.aaf2288 · Cited by 445

Prospects for gene-engineered T cell immunotherapy for solid cancers

Klebanoff, C. A., Rosenberg, S. A., & Restifo, N. P. (2016) · Nature Medicine · doi:10.1038/nm.4015 · Cited by 365

Combined Blockade of IL6 and PD-1/PD-L1 Signaling Abrogates Mutual Regulation of Their Immunosuppressive Effects in the Tumor Microenvironment

Tsukamoto, H., Fujieda, K., Miyashita, A., Fukushima, S., Ikeda, T., Kubo, Y., Senju, S., Ihn, H., Nishimura, Y., & Oshiumi, H. (2018) · Cancer Research · doi:10.1158/0008-5472.can-18-0118 · Cited by 305

Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system

Lhuillier, C., Rudqvist, N.-P., Elemento, O., Formenti, S. C., & Demaria, S. (2019) · Genome Medicine · doi:10.1186/s13073-019-0653-7 · Cited by 276

Glioblastoma-targeted CD4+ CAR T cells mediate superior antitumor activity

Wang, D., Aguilar, B., Starr, R., Alizadeh, D., Brito, A., Sarkissian, A., Ostberg, J. R., Forman, S. J., & Brown, C. E. (2018) · JCI Insight · doi:10.1172/jci.insight.99048 · Cited by 233

Peptide‐based therapeutic cancer vaccine: Current trends in clinical application

Liu, W., Tang, H., Li, L., Wang, X., Yu, Z., & Li, J. (2021) · Cell Proliferation · doi:10.1111/cpr.13025 · Cited by 200

Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma

Naghavian, R., Faigle, W., Oldrati, P., Wang, J., Toussaint, N. C., Qiu, Y., Medici, G., Wacker, M., Freudenmann, L. K., Bonté, P.-E., et al. (2023) · Nature · doi:10.1038/s41586-023-06081-w · Cited by 163

Citrullinated Vimentin Presented on MHC-II in Tumor Cells Is a Target for CD4+ T-Cell–Mediated Antitumor Immunity

Brentville, V. A., Metheringham, R. L., Gunn, B., Symonds, P., Daniels, I., Gijon, M., Cook, K., Xue, W., & Durrant, L. G. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-1085 · Cited by 98

Next-generation sequencing in cancer diagnosis and treatment: clinical applications and future directions

Ghoreyshi, N., Heidari, R., Farhadi, A., Chamanara, M., Farahani, N., Vahidi, M., & Behroozi, J. (2025) · Discover Oncology · doi:10.1007/s12672-025-01816-9 · Cited by 91

Endogenous CD4+ T Cells Recognize Neoantigens in Lung Cancer Patients, Including Recurrent Oncogenic KRAS and ERBB2 ( Her2 ) Driver Mutations

Veatch, J. R., Jesernig, B. L., Kargl, J., Fitzgibbon, M., Lee, S. M., Baik, C., Martins, R., Houghton, A. M., & Riddell, S. R. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0402 · Cited by 89

Dual PD-1 and CTLA-4 checkpoint blockade promotes antitumor immune responses through CD4(+)Foxp3(-) cell-mediated modulation of CD103(+) dendritic cells

Beavis, P. A., Henderson, M. A., Giuffrida, L., Davenport, A. J., Petley, E. V., House, I. G., Lai, J., Sek, K., Milenkovski, N., John, L. B., et al. (2018) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0291 · Cited by 68

Impact of Immunotherapy on CD4 T Cell Phenotypes and Function in Cancer

Saillard, M., Cenerenti, M., Romero, P., & Jandus, C. (2021) · Vaccines · doi:10.3390/vaccines9050454 · Cited by 23

Targeting Cross-Presentation as a Route to Improve the Efficiency of Peptide-Based Cancer Vaccines

Wylie, B., Ong, F., Belhoul-Fakir, H., Priebatsch, K., Bogdawa, H., Stirnweiss, A., Watt, P., Cunningham, P., Stone, S. R., & Waithman, J. (2021) · Cancers · doi:10.3390/cancers13246189 · Cited by 16