Supplementary Materials

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

Nicholas McGranahan, Andrew J. S. Furness, Rachel Rosenthal, Sofie Ramskov, Rikke Lyngaa, Sunil Kumar Saini, Mariam Jamal-Hanjani, Gareth A. Wilson, Nicolai J. Birkbak, Crispin T. Hiley, Thomas B. K. Watkins, Seema Shafi, Nirupa Murugaesu, Richard Mitter, Ayse U. Akarca, Joseph Linares, Teresa Marafioti, Jake Y. Henry, Eliezer M. Van Allen, Diana Miao, Bastian Schilling, Dirk Schadendorf, Levi A. Garraway, Vladimir Makarov, Naiyer A. Rizvi, Alexandra Snyder, Matthew D. Hellmann, Taha Merghoub, Jedd D. Wolchok, Sachet A. Shukla, Catherine J. Wu, Karl S. Peggs, Timothy A. Chan, Sine R. Hadrup, Sergio A. Quezada, Charles Swanton

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S7
  • Tables S1 to S5
  • Full Reference List
Table S3
A) Differentially expressed immune genes between LUAD and LUSC tumor samples B) Expression of HLA genes between LUAD and LUSC tumor samples by neoantigen quartile C) Differentially expressed immune genes between LUSC normal and tumor samples
Table S4
A) Differentially expressed immune genes between tumors with a high neoantigen burden and low neoantigen ITH and remaining tumors B) Differentially expressed immune genes between tumors with a high clonal neoantigen burden (>upper quartile clonal neoantigens) and low clonal neoantigen burden (<lower quartile clonal neoantigens).
Table S5
Detailed clinical characteristics of patients from (2)