Extended Data Fig. 9. Neoantigen-specific T cell responses for patients with differential ctDNA and pathological responses.

Patients CGES3 (a) and CGES5 (b) both had undetectable ctDNA throughout the study, attained a complete pathological response and did not have disease recurrence within the study interval. For patient CGES3 (a), 3 neoantigen-specific TCR clone expansions were noted (CATSAPGHPNEAFF, CASRTRDRRNYGGYTF and CASSSSYNEQFF); similarly, for patient CGES5 (b), one neoantigen-specific TCR clone expansion (CASSHGRTQPQHF) was noted. (c) Two neoantigen-specific TCR clone expansions (CASSSSNQPQHF and CASSLGTGVEQYF) were noted for patient CGES12, who had detectable ctDNA until the time of surgery reflective of 90% residual tumor at the time of resection, and later experienced disease recurrence. (d) No neoantigen-specific TCR clonal expansions were noted for patient CGES27, with undetectable ctDNA throughout the study and 80% residual tumor at the time of resection.