Identification of Individual Cancer-Specific Somatic Mutations for Neoantigen-Based Immunotherapy of Lung Cancer Takahiro Karasaki, MD, Kazuhiro Nagayama,

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Identification of Individual Cancer-Specific Somatic Mutations for Neoantigen-Based Immunotherapy of Lung Cancer Takahiro Karasaki, MD, Kazuhiro Nagayama, MD, PhD, Mitsuaki Kawashima, MD, Noriko Hiyama, MD, Tomonori Murayama, MD, Hideki Kuwano, MD, PhD, Jun-ichi Nitadori, MD, PhD, Masaki Anraku, MD, MSc, Masaaki Sato, MD, PhD, Manami Miyai, MSc, Akihiro Hosoi, PhD, Hirokazu Matsushita, MD, PhD, Shingo Kikugawa, PhD, Ryo Matoba, PhD, Osamu Ohara, PhD, Kazuhiro Kakimi, MD, PhD, Jun Nakajima, MD, PhD Journal of Thoracic Oncology Volume 11, Issue 3, Pages 324-333 (March 2016) DOI: 10.1016/j.jtho.2015.11.006 Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Figure 1 Pipelines to output potential neoantigens. (A) Off-the-shelf pipeline using a shared missense mutation panel curated from established online databases. Peripheral blood is a required sample to be collected from the patient. (B) Personalized pipeline using data from whole-exome sequencing. Samples of the patient’s tumor and normal tissue for control (e.g., adjacent normal lung tissue or peripheral blood) are needed. In both pipelines, mutant peptides are filtered using epitope binding prediction tools to select the potential neoantigens.21–23 COSMIC, Catalogue of Somatic Mutations in Cancer; HLA, human leucocyte antigen. Journal of Thoracic Oncology 2016 11, 324-333DOI: (10.1016/j.jtho.2015.11.006) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions

Supplemental Figure 1 Venn diagram showing the number of potential neoantigens detectable by whole-exome sequencing and targeted sequencing. A total of 1875 potential neoantigens were detected by whole-exome sequencing in 15 patients with lung cancer. If the currently available targeted sequencing assay for detection of a driver mutation were used, 32 potential neoantigens (including four off-the-shelf potential neoantigens) at most might be identified. Journal of Thoracic Oncology 2016 11, 324-333DOI: (10.1016/j.jtho.2015.11.006) Copyright © 2015 International Association for the Study of Lung Cancer Terms and Conditions