Table 1. Single nucleotide variants and... | Rockefeller University Press

Table 1.

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

Mouse strain	BALB/c
Tumor type	Meth A	CMS5
RNA-Seq reads (million)	105.8	23.4
Genome mapped	75%	54%
Transcriptome mapped	83%	59%
HardMerge mapped	65%	48%
After PCR amplification filter	18%	22%
HardMerge and filtered mapped bases (Gb)	1.15	0.24
High-quality heterozygous SNVs in CCDS exons^a	1,528	208
Tumor specific	1,504	191
Non-synonymous	77.1%	78.5%
Missense	1,096	146
Nonsense	63	4
No-stop	1	-
NetMHC predicted epitopes^b	823	112
H2 K^d-restricted	203	15
H2 D^d-restricted	328	58
H2 liter^d-restricted	292	39

Mouse strain	BALB/c
Tumor type	Meth A	CMS5
RNA-Seq reads (million)	105.8	23.4
Genome mapped	75%	54%
Transcriptome mapped	83%	59%
HardMerge mapped	65%	48%
After PCR amplification filter	18%	22%
HardMerge and filtered mapped bases (Gb)	1.15	0.24
High-quality heterozygous SNVs in CCDS exons^a	1,528	208
Tumor specific	1,504	191
Non-synonymous	77.1%	78.5%
Missense	1,096	146
Nonsense	63	4
No-stop	1	-
NetMHC predicted epitopes^b	823	112
H2 K^d-restricted	203	15
H2 D^d-restricted	328	58
H2 liter^d-restricted	292	39

The number of mutations identified depends on the sequencing depth.

Based on default NetMHC 3.0 PWM peptide binding score thresholds for weak binders, of 8.72, 8.08, and 8.19 for K^d, D^d, and L^d alleles, respectively.

View Large

This Feature Is Available To Subscribers Only