Table 1.

Single nucleotide variants and predicted epitopes of tumor lines as deduced from transcriptome sequencing and bioinformatic analyses

Mouse strainBALB/c
Tumor typeMeth ACMS5
RNA-Seq reads (million)105.823.4
Genome mapped75%54%
Transcriptome mapped83%59%
HardMerge mapped65%48%
After PCR amplification filter18%22%
HardMerge and filtered mapped bases (Gb)1.150.24
High-quality heterozygous SNVs in CCDS exonsa1,528208
Tumor specific1,504191
NetMHC predicted epitopesb823112
H2 Kd-restricted20315
H2 Dd-restricted32858
H2 literd-restricted29239
  • a The number of mutations identified depends on the sequencing depth.

  • b Based on default NetMHC 3.0 PWM peptide binding score thresholds for weak binders, of 8.72, 8.08, and 8.19 for Kd, Dd, and Ld alleles, respectively.