Neoantigens and copy number alterations (CNAs) in in-house cases and the TCGA database.

A) Concept of the study design. Comparisons of the number of single nucleotide variants (SNVs), neoantigens (NAGs), and arm-level CNAs between eight primary tumors from early colorectal cancer cases without recurrence (PCRC) and eight primary tumors from CRC cases with recurrence (CRCR) postoperatively (Fig 1). In addition, we compared SNV, CNA, and RNA seq between primary and metastatic sites (Figs 2–5). B) Comparison of the average number of non-synonymous mutations between PCRC and CRCR. C) Neopeptides with a half-maximal inhibitory concentration (IC₅₀) of less than 50 nM were classified as having strong antigenicity. Comparison of antigenicity between PCRC and CRCR. D) Comparison of arm-level copy numbers (CNs) between eight PCRCs and eight CRCRs. Log-ratios of total CNAs were compared between PCRC and CRCR (p < 2.2e-16). E) The number of mutations differed between chromosomal loci with CNs≤2 compared with those with CNs>2 at representative chromosome 7p, 7q, 20p, and 20q of all chromosome (S2 Table). F) The tumor immune response was evaluated by cytolytic activity (CYT). i) CYT levels in 180 cases of stage I and II CRC in TCGA; ii) CYT levels in all 353 cases; iii and iv) association between CYT and ploidy determined by scatter analysis. G) There were two groups: 40 cases of stage I/II CRC with postoperative recurrence from TCGA and 232 cases of stage I/II CRC without postoperative recurrence from TCGA. We demonstrated CD8A, CD3G, CD3E, CD3G expression and CYT in all cases (S3 Table).