Identification and ranking of recurrent neo-epitopes in cancer

BMC Medical Genomics

Table 1 Overview of the 33 TCGA studies used in this analysis

Project name	Number of patients		Variants per patients		Missense variant per patient		Recurrent variants	Strong binders
	Total	With clinical data	Average	Median	Average	Median
TCGA-BLCA	412	412	326	226	157	109	22	14
TCGA-BRCA	986	986	123	62	50	25	8	10
TCGA-CESC	289	289	358	157	143	62	17	16
TCGA-COAD	399	397	666	176	288	82	41	34
TCGA-ESCA	184	184	246	187	95	73	80	72
TCGA-GBM	393	390	212	70	93	36	15	5
TCGA-HNSC	508	508	201	139	97	66	14	3
TCGA-KIRC	336	336	79	69	33	31	0	0
TCGA-KIRP	281	281	85	82	39	38	5	2
TCGA-LAML	143	143	69	15	16	6	14	7
TCGA-LGG	508	507	70	36	33	16	14	0
TCGA-LIHC	364	364	149	120	70	58	11	16
TCGA-LUAD	567	515	367	242	180	113	7	0
TCGA-LUSC	492	492	368	301	187	153	20	19
TCGA-OV	436	435	173	121	58	47	10	7
TCGA-PAAD	178	178	168	50	77	19	24	12
TCGA-PCPG	179	179	13	12	5	4	8	5
TCGA-PRAD	495	495	59	35	27	15	3	7
TCGA-READ	137	136	475	148	232	70	320	186
TCGA-SARC	237	237	119	70	45	26	2	0
TCGA-SKCM	467	467	841	472	413	229	266	220
TCGA-STAD	437	437	488	157	211	74	17	14
TCGA-TGCT	144	128	23	21	9	8	9	6
TCGA-THCA	492	492	22	12	6	5	4	3
TCGA-THYM	123	123	39	24	10	4	6	2
TCGA-UCEC	530	530	1672	149	708	54	118	109
TCGA-ACC	92	92	117	36	0	0	0	0
TCGA-CHOL	51	45	110	62	0	0	0	0
TCGA-DLBC	37	37	173	157	0	0	0	0
TCGA-KICH	66	66	44	25	0	0	0	0
TCGA-MESO	82	82	47	44	0	0	0	0
TCGA-UCS	57	57	183	67	0	0	0	0
TCGA-UVM	80	80	23	16	0	0	0	0
Total	10182	10100	Total number: 3155183		Total number: 1384531		1055	769

The 7 studies displayed at the bottom have not been used for the determination of recurrent vairants, as the number of patients is less than 100. The number of strong binders includes all occurrences of neo-epitopes candidates, so a candidate may be counted multiple times when it is predicted to be binding several HLA-1 types

ISSN: 1755-8794