Chapter 7 References
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. 1990. “Basic Local Alignment Search Tool.” Journal of Molecular Biology 215 (3): 403–10. https://doi.org/10.1016/s0022-2836(05)80360-2.
Bai, Yu, David Wang, and Wen Fury. 2018. “PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing.” In Methods in Molecular Biology, 193–201. Springer New York. https://doi.org/10.1007/978-1-4939-8546-3_13.
Brown, Scott D., Rene L. Warren, Ewan A. Gibb, Spencer D. Martin, John J. Spinelli, Brad H. Nelson, and Robert A. Holt. 2014. “Neo-Antigens Predicted by Tumor Genome Meta-Analysis Correlate with Increased Patient Survival.” Genome Research 24 (5): 743–50. https://doi.org/10.1101/gr.165985.113.
Haas, Brian J., Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet, and Aviv Regev. 2019. “Accuracy Assessment of Fusion Transcript Detection via Read-Mapping and de Novo Fusion Transcript Assembly-Based Methods.” Genome Biology 20 (1). https://doi.org/10.1186/s13059-019-1842-9.
Hilf, Norbert, Sabrina Kuttruff-Coqui, Katrin Frenzel, Valesca Bukur, Stefan Stevanović, Cécile Gouttefangeas, Michael Platten, et al. 2018. “Actively Personalized Vaccination Trial for Newly Diagnosed Glioblastoma.” Nature 565 (7738): 240–45. https://doi.org/10.1038/s41586-018-0810-y.
Hundal, Jasreet, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. 2016. “pVAC-Seq: A Genome-Guided in Silico Approach to Identifying Tumor Neoantigens.” Genome Medicine 8 (1). https://doi.org/10.1186/s13073-016-0264-5.
Hundal, Jasreet, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, et al. 2018. “Accounting for Proximal Variants Improves Neoantigen Prediction.” Nature Genetics 51 (1): 175–79. https://doi.org/10.1038/s41588-018-0283-9.
Hundal, Jasreet, Susanna Kiwala, Joshua McMichael, Christopher A. Miller, Huiming Xia, Alexander T. Wollam, Connor J. Liu, et al. 2020. “pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.” Cancer Immunology Research 8 (3): 409–20. https://doi.org/10.1158/2326-6066.cir-19-0401.
Jurtz, Vanessa, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters, and Morten Nielsen. 2017. “NetMHCpan 4.0: Improved Peptide-MHC Class i Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data,” June. https://doi.org/10.1101/149518.
Keskin, Derin B., Annabelle J. Anandappa, Jing Sun, Itay Tirosh, Nathan D. Mathewson, Shuqiang Li, Giacomo Oliveira, et al. 2018. “Neoantigen Vaccine Generates Intratumoral t Cell Responses in Phase Ib Glioblastoma Trial.” Nature 565 (7738): 234–39. https://doi.org/10.1038/s41586-018-0792-9.
McLaren, William, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, and Fiona Cunningham. 2016. “The Ensembl Variant Effect Predictor.” Genome Biology 17 (1). https://doi.org/10.1186/s13059-016-0974-4.
Murphy, Charlie, and Olivier Elemento. 2016. “AGFusion: Annotate and Visualize Gene Fusions,” October. https://doi.org/10.1101/080903.
Nielsen, Morten, Claus Lundegaard, Ole Lund, and Can Keşmir. 2005. “The Role of the Proteasome in Generating Cytotoxic t-Cell Epitopes: Insights Obtained from Improved Predictions of Proteasomal Cleavage.” Immunogenetics 57 (1-2): 33–41. https://doi.org/10.1007/s00251-005-0781-7.
ODonnell, Timothy J., Alex Rubinsteyn, Maria Bonsack, Angelika B. Riemer, Uri Laserson, and Jeff Hammerbacher. 2018. “MHCflurry: Open-Source Class i MHC Binding Affinity Prediction.” Cell Systems 7 (1): 129–132.e4. https://doi.org/10.1016/j.cels.2018.05.014.
Ott, Patrick A., Zhuting Hu, Derin B. Keskin, Sachet A. Shukla, Jing Sun, David J. Bozym, Wandi Zhang, et al. 2017. “An Immunogenic Personal Neoantigen Vaccine for Patients with Melanoma.” Nature 547 (7662): 217–21. https://doi.org/10.1038/nature22991.
Rasmussen, Michael, Emilio Fenoy, Mikkel Harndahl, Anne Bregnballe Kristensen, Ida Kallehauge Nielsen, Morten Nielsen, and Søren Buus. 2016. “Pan-Specific Prediction of PeptideMHC Class i Complex Stability, a Correlate of t Cell Immunogenicity.” The Journal of Immunology 197 (4): 1517–24. https://doi.org/10.4049/jimmunol.1600582.
Richters, Megan M., Huiming Xia, Katie M. Campbell, William E. Gillanders, Obi L. Griffith, and Malachi Griffith. 2019. “Best Practices for Bioinformatic Characterization of Neoantigens for Clinical Utility.” Genome Medicine 11 (1). https://doi.org/10.1186/s13073-019-0666-2.
Rizvi, Naiyer A., Matthew D. Hellmann, Alexandra Snyder, Pia Kvistborg, Vladimir Makarov, Jonathan J. Havel, William Lee, et al. 2015. “Mutational Landscape Determines Sensitivity to PD-1 Blockade in Nonsmall Cell Lung Cancer.” Science 348 (6230): 124–28. https://doi.org/10.1126/science.aaa1348.
Rubinsteyn, Alexander, Isaac Hodes, Julia Kodysh, and Jeffrey Hammerbacher. 2017. “Vaxrank: A Computational Tool for Designing Personalized Cancer Vaccines,” May. https://doi.org/10.1101/142919.
Schumacher, Ton N., and Robert D. Schreiber. 2015. “Neoantigens in Cancer Immunotherapy.” Science 348 (6230): 69–74. https://doi.org/10.1126/science.aaa4971.
Shao, Xiaoshan M., Rohit Bhattacharya, Justin Huang, I. K. Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, et al. 2020. “High-Throughput Prediction of MHC Class i and II Neoantigens with MHCnuggets.” Cancer Immunology Research 8 (3): 396–408. https://doi.org/10.1158/2326-6066.cir-19-0464.
Szolek, András, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, and Oliver Kohlbacher. 2014. “OptiType: Precision HLA Typing from Next-Generation Sequencing Data.” Bioinformatics 30 (23): 3310–16. https://doi.org/10.1093/bioinformatics/btu548.
Uhrig, Sebastian, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H. Toprak, et al. 2021. “Accurate and Efficient Detection of Gene Fusions from RNA Sequencing Data.” Genome Research 31 (3): 448–60. https://doi.org/10.1101/gr.257246.119.
Vita, Randi, Swapnil Mahajan, James A Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R Cantrell, Daniel K Wheeler, Alessandro Sette, and Bjoern Peters. 2018. “The Immune Epitope Database (IEDB): 2018 Update.” Nucleic Acids Research 47 (D1): D339–43. https://doi.org/10.1093/nar/gky1006.
Xia, Huiming, Joshua McMichael, Michelle Becker-Hapak, Onyinyechi C. Onyeador, Rico Buchli, Ethan McClain, Patrick Pence, et al. 2023. “Computational Prediction of MHC Anchor Locations Guides Neoantigen Identification and Prioritization.” Science Immunology 8 (82). https://doi.org/10.1126/sciimmunol.abg2200.