Table 2. Tumor-specific polymorphisms... | Rockefeller University Press

Table 2.

Tumor-specific polymorphisms and epitopes for human melanomas

Sample	Somatic mutations^a						NetMHC predicted epitopes^b
	Synonymous/nonsynonymous in UCSC annotation		Subset of nonsynonymous mutations within CCDS coding regions				Total	A0101	A0201	A0301
	Synonymous	Nonsynonymous	Total	Nonsynonymous	Missense	Non-sense	Total	A0101	A0201	A0301
01T	160	304	292	291	272	12	473	26	262	185
05T	56	115	106	106	100	6	175	12	116	47
09T	39	83	81	80	76	4	131	5	77	49
12T	427	741	706	705	656	49	1193	50	657	486
18T	91	190	179	179	168	11	286	15	144	127
22T	69	126	116	115	108	7	181	20	94	67
24T	163	397	381	379	358	21	625	26	263	336
35T	13	34	32	32	31	1	68	1	44	23
43T	68	94	91	91	86	5	175	4	90	81
51T	51	136	126	126	117	9	229	7	148	74
60T	67	129	121	120	112	8	209	14	91	104
91T	99	215	209	209	196	13	329	18	176	135
93T	54	130	125	124	116	8	184	6	105	73
96T	68	118	112	112	103	9	192	10	101	81

Sample	Somatic mutations^a						NetMHC predicted epitopes^b
	Synonymous/nonsynonymous in UCSC annotation		Subset of nonsynonymous mutations within CCDS coding regions				Total	A0101	A0201	A0301
	Synonymous	Nonsynonymous	Total	Nonsynonymous	Missense	Non-sense	Total	A0101	A0201	A0301
01T	160	304	292	291	272	12	473	26	262	185
05T	56	115	106	106	100	6	175	12	116	47
09T	39	83	81	80	76	4	131	5	77	49
12T	427	741	706	705	656	49	1193	50	657	486
18T	91	190	179	179	168	11	286	15	144	127
22T	69	126	116	115	108	7	181	20	94	67
24T	163	397	381	379	358	21	625	26	263	336
35T	13	34	32	32	31	1	68	1	44	23
43T	68	94	91	91	86	5	175	4	90	81
51T	51	136	126	126	117	9	229	7	148	74
60T	67	129	121	120	112	8	209	14	91	104
91T	99	215	209	209	196	13	329	18	176	135
93T	54	130	125	124	116	8	184	6	105	73
96T	68	118	112	112	103	9	192	10	101	81

Calculated from mutation data published by Wei et al. (2011), and using the epitope prediction step of the Epi-Seq pipeline to call the epitopes based on the mutation data.

Most common HLA alleles were chosen according to the published frequencies of such alleles (Cao et al., 2001).

[ViewLarge]