Molecular Analysis of a Recurrent Sarcoma Identifies a Mutation in FAF1

Table 1

DNA exome SNPs. The DNA exomes for tumor, muscle, and bone were sequenced. The results were filtered in the following order: (1) different genotype in tumor from muscle and bone, with muscle and bone being identical to each other, (2) delete mutations with low confidence (value of 20 or lower) in all 3 tissues, (3) delete unidentified genes, (4) delete mutations that are homozygous reference in the tumor, (5) delete mutations that have a MAF in dbSNP >10%, (6) delete low impact and modifier mutations. The gene names are part of the key in the left column. In this column, results on bold font represent SNPs that were confirmed on the RNA level by RNASeq. The data files have been submitted to the NCBI short read archive (SRA) under the accession number SRP052797 (biosamples SAMN03316820, SAMN03316821, SAMN03316822).

Key	Chromosome	Position	Reference	Alternate	dbSNP ID	dbSNP MAF	ESP MAF (All)	ESP MAF (EA)	ESP MAF (AA)	Consensus impact	Bone/muscle genotype	Bone overall depth	Bone allele depths	Bone quality	Muscle overall depth	Muscle allele depths	Muscle quality	Tumor genotype	Tumor overall depth	Tumor allele depths	Tumor quality
17_7479998_T_EIF4A1	17	7479998	C	T	.	—	—	—	—	Moderate	0/0	175	184,0	99	103	108,0	99	0/1	133	79,68	99
3_89259200_T_EPHA3	3	89259200	C	T	.	—	—	—	—	Moderate	0/0	43	45,0	99	117	123,0	99	0/1	72	30,48	99
1_51204545_C_FAF1	1	51204545	T	C	.	—	—	—	—	Moderate	0/0	87	91,0	99	108	113,0	99	0/1	85	66,27	99
12_30834620_A_IPO8	12	30834620	C	A	.	—	—	—	—	Moderate	0/0	68	71,2	99	120	126,0	99	0/1	80	70,18	99
11_101834425_A_KIAA1377	11	101834425	G	A	.	—	—	—	—	Moderate	0/0	36	37,1	90	67	70,0	99	0/1	86	31,63	99
4_41682102_C_LIMCH1	4	41682102	G	C	.	—	0.000077	0	0.000227	Moderate	0/0	71	74,0	99	96	101,0	99	0/1	153	120,49	99
5_36985326_G_NIPBL	5	36985326	A	G	.	—	—	—	—	Moderate	0/0	6	6,0	18	35	36,0	81	0/1	20	10,12	99
3_77623789_A_ROBO2	3	77623789	AG	A	.	—	—	—	—	High	0/0	22	NA	54	29	NA	87	0/1	37	NA	99
2_217300095_A_SMARCAL1	2	217300095	ATTGCATCAACGTCGTGG	A	.	—	—	—	—	High	0/0	95	NA	99	122	NA	99	0/1	99	NA	99
2_152236045_T_TAA_TNFAIP6	2	152236045	TA	T/TAA	rs35060021	—	—	—	—	High	0/2	19	NA	1	24	NA	57	0/1	17	NA	38
3_52020669_T_ACY1	3	52020669	G	T	.	—	—	—	—	Moderate	0/0	130	136,0	99	86	90,0	99	0/1	80	45,43	99
9_117130734_G_AKNA	9	117130734	C	G	.	—	—	—	—	Moderate	0/0	27	28,0	78	30	31,0	90	0/1	50	30,24	99
12_6030354_A_ANO2	12	6030354	C	A	.	—	—	—	—	Moderate	0/0	101	106,0	99	114	120,0	99	0/1	135	104,45	99
18_10487667_A_APCDD1	18	10487667	G	A	.	—	—	—	—	Moderate	0/0	43	45,0	99	38	40,0	99	0/1	50	38,16	99
7_34118560_C_BMPER	7	34118560	G	C	.	—	—	—	—	Moderate	0/0	69	72,0	99	101	106,0	99	0/1	71	63,14	99
15_24921273_T_C15orf2	15	24921273	G	T	.	—	—	—	—	Moderate	0/0	12	12,0	36	38	39,0	99	0/1	26	22,6	99
19_54483249_C_CACNG8	19	54483249	T	C	.	—	—	—	—	Moderate	0/0	147	154,0	99	103	108,0	99	0/1	152	136,32	99
10_16893265_C_CUBN	10	16893265	G	C	.	—	—	—	—	Moderate	0/0	57	60,0	99	90	94,0	99	0/1	40	34,10	99
7_148489854_C_CUL1	7	148489854	A	C	.	—	—	—	—	Moderate	0/0	73	76,0	99	65	68,0	99	0/1	57	42,21	99
17_41566894_C_DHX8	17	41566894	G	C	.	—	—	—	—	Moderate	0/0	106	111,0	99	88	92,0	99	0/1	124	94,42	99
20_61512358_T_DIDO1	20	61512358	G	T	rs73304513	0.0417	0.045932	0.000838	0.135456	Moderate	0/0	6	0,0	18	2	0,0	6	0/1	4	0,0	21
16_23703526_A_ERN2	16	23703526	G	A	.	—	—	—	—	Moderate	0/0	81	85,0	99	98	103,0	99	0/1	91	60,41	99
3_197880164_G_FAM157A	3	197880164	GCAGCAGCAA	G	.	—	—	—	—	Moderate	0/0	21	NA	25	25	NA	1	0/1	31	NA	6
14_45644287_G_FANCM	14	45644287	A	G	.	0.0009	—	—	—	Moderate	0/0	13	13,0	33	31	32,0	87	0/1	12	10,2	14
1_89637524_C_GBP7	1	89637524	G	C	.	—	—	—	—	Moderate	0/0	171	179,0	99	201	211,0	99	0/1	206	161,67	99
7_42003933_C_GLI3	7	42003933	G	C	.	—	—	—	—	Moderate	0/0	87	91,0	99	81	85,0	99	0/1	85	61,32	99
17_4837170_T_GP1BA	17	4837170	C	T	.	—	—	—	—	Moderate	0/0	16	16,0	45	9	9,0	15	0/1	11	10,1	1
14_24635161_G_IRF9	14	24635161	T	G	.	—	—	—	—	Moderate	0/0	66	69,0	99	43	45,0	99	0/1	36	25,13	99
15_42133096_A_JMJD7-PLA2G4B	15	42133096	G	A	.	—	—	—	—	Moderate	0/0	111	116,0	99	75	78,0	99	0/1	80	74,14	92
17_40271678_A_KAT2A	17	40271678	G	A	.	—	—	—	—	Moderate	0/0	65	68,0	99	58	61,0	99	0/1	56	30,32	99
8_73848894_G_KCNB2	8	73848894	A	G	.	—	—	—	—	Moderate	0/0	15	15,0	33	24	25,0	66	0/1	30	15,17	99
19_50827053_T_KCNC3	19	50827053	C	T	.	—	—	—	—	Moderate	0/0	220	231,0	99	136	143,0	99	0/1	160	130,46	99
17_21319069_A_KCNJ12	17	21319069	G	A	rs76265595	—	—	—	—	Moderate	0/0	23	24,1	63	43	43,4	40	0/1	28	25,5	60
12_53011932_C_KRT73	12	53011932	T	C	.	—	—	—	—	Moderate	0/0	146	153,0	99	157	165,0	99	0/1	159	117,58	99
X_75004584_A_MAGEE2	X	75004584	C	A	.	—	—	—	—	Moderate	0/0	29	30,0	81	48	50,0	99	0/1	38	26,16	99
5_140182157_A_PCDHA3	5	140182157	G	A	.	—	—	—	—	Moderate	0/0	180	189,0	99	153	161,0	99	0/1	150	132,34	99
15_42133096_A_PLA2G4B	15	42133096	G	A	.	—	—	—	—	Moderate	0/0	111	116,0	99	75	78,0	99	0/1	80	74,14	92
10_96005840_C_PLCE1	10	96005840	T	C	.	—	—	—	—	Moderate	0/0	81	85,1	99	73	76,2	99	0/1	87	55,40	99
1_166816805_G_POGK	1	166816805	C	G	.	—	—	—	—	Moderate	0/0	84	88,0	99	82	86,0	99	0/1	63	49,20	99
12_111020739_T_PPTC7	12	111020739	TCGC	T	rs71083132	—	—	—	—	Moderate	0/0	18	NA	30	14	NA	18	0/1	19	NA	10
19_804293_A_PTBP1	19	804293	C	A	.	—	—	—	—	Moderate	0/0	120	126,1	99	71	74,1	99	0/1	75	53,30	99
7_156451175_C_RNF32	7	156451175	G	C	.	—	—	—	—	Moderate	0/0	55	57,0	99	67	70,0	99	0/1	59	42,23	99
3_52020669_T_RP11-155D18.11	3	52020669	G	T	.	—	—	—	—	Moderate	0/0	130	136,0	99	86	90,0	99	0/1	80	45,43	99
21_43838624_T_UBASH3A	21	43838624	G	T	.	—	—	—	—	Moderate	0/0	70	73,0	99	45	47,0	99	0/1	89	76,21	99
19_58773857_A_ZNF544	19	58773857	G	A	.	—	—	—	—	Moderate	0/0	46	48,0	99	43	45,0	99	0/1	71	51,26	99
5_16465723_C_ZNF622	5	16465723	T	C	.	—	—	—	—	Moderate	0/0	17	17,0	39	14	14,0	33	0/1	27	14,15	99