Presence of antigen-specific somatic allelic mutations and splice variants do not predict for immunological response to genetic vaccination

Table 1 Human genes encoding common target antigens of genetic vaccines show previously detected allelic variations

Target antigen	AR	CEA	gp100	MAGE-A3	NY-ESO-1	PAP	PSA	PSMA	TYR
Gene ID	AR-001	CEACAM5-001	PMEL-001	MAGEA3-001	CTAG1B-001	ACPP-001	KLK3-201	FOLH1-001	TYR-001
Location	Xq12	19q13.1-13.2	12q13-q14	Xq28	Xq28	3q21-q23	19q13.41	11p11.2	11q14-q21
Synonymous Coding Mutations	26	28	22	16	0	13	20	19	24
Non-Synonymous Coding Mutations	71	61	46	43	1	22	39	38	95
Stop Gain/Loss	6	1	2	0	0	3	0	0	9
Frameshift	1	1	0	0	0	0	2	2	13
Coding Unknown	337	0	0	0	0	0	0	1	207
Total	441	91	70	59	1	38	61	60	348
cDNA Length (bp)	10065	2907	2757	1724	998	3125	1464	2635	2466
Protein Length (aa)	920	702	661	314	168	386	261	750	529
Mutation Quotient	0.085	0.090	0.073	0.137	0.006	0.065	0.157	0.053	0.221

Eight genes encoding genetic vaccine target antigens under investigation in human clinical trials, and one gene encoding a prostate cancer target antigen of interest (AR), are listed in this table by antigen name as well as Gene ID taken from the USEast Ensemble online database. The NCBI-Gene and USEast Ensemble online databases provided information regarding chromosomal location of antigen gene, cDNA length (bp), and protein length (aa) as well as total number of allelic variations previously detected by others. Allelic variations are categorized into synonymous, non-synonymous, stop gain/loss, frameshift, or unknown coding mutations accordingly. Mutation quotient is defined as the sum of non-synonymous coding mutations, stop gain/loss, and frameshift mutations (mutations that could affect immunologically presented epitopes) divided by protein length (aa). Coding mutation online queries were performed April 16, 2012.