Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	TTotCov	TVarCov	NTotCov	NVarCov	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	8422892	8422892	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	92	29	120	0	0	0	0	0	0
UQCRHL	0	ucsc.edu	37	1	16133912	16133912	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	270	1	274	0	0	0	0	0	0
SPEN	23013	broad.mit.edu	37	1	16203085	16203085	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	95	4	86	0	18	18	0	0	0
MST1P2	11209	bcgsc.ca	37	1	16973159	16973159	+	RNA	SNP	A	A	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	114	9	143	6	5	5	0	0	0
MST1P2	11209	broad.mit.edu	37	1	16974585	16974585	+	RNA	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	117	7	142	0	58	58	0	0	0
MAST2	23139	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	46290209	46290209	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	265	88	282	0	6	3	3	0	0
WDR3	10885	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	118502024	118502024	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	66	24	50	0	46	20	26	0	0
PDZK1	5174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	145761288	145761288	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	184	69	176	0	693	345	348	0	0
ASH1L	55870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	155491175	155491175	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	495	164	518	0	33	10	23	0	0
TOR1AIP2	163590	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	179834038	179834038	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	184	61	151	1	28	12	16	0	0
SLC41A1	254428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	205770146	205770146	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	133	39	151	0	46	25	21	0	0
PIGR	5284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	207109097	207109097	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	43	17	41	0	5529	2506	2996	8	19
IRF6	3664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	209974723	209974723	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	151	46	161	0	30	23	7	0	0
LEFTY2	7044	hgsc.bcm.edu;broad.mit.edu	37	1	226127230	226127230	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	54	16	60	0	4	4	0	0	0
EXOC8	149371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	231472205	231472205	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	86	18	95	0	13	10	3	0	0
IRF2BP2	359948	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	234744251	234744251	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	39	15	36	0	57	30	26	0	1
MASTL	84930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	27459483	27459483	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	132	46	122	0	5	3	2	0	0
UNC5B	219699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	73055666	73055666	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	116	46	116	0	2	2	0	0	0
FUT11	170384	hgsc.bcm.edu	37	10	75532345	75532345	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	16	4	10	1	1	1	0	0	0
SEMA4G	57715	broad.mit.edu	37	10	102732887	102732887	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	58	3	72	0	0	0	0	0	0
INS	3630	ucsc.edu	37	11	2181208	2181208	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	11	4	16	0	3	3	0	0	0
PIK3C2A	5286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	17124313	17124313	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	103	37	110	0	32	14	18	0	0
HNRNPKP3	399881	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	A	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	7	3	8	0	0	0	0	0	0
PLAC1L	219990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	59811100	59811100	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	64	26	53	1	0	0	0	0	0
ENDOD1	23052	hgsc.bcm.edu;broad.mit.edu	37	11	94823276	94823276	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	17	7	15	0	11	6	5	0	0
MMP8	4317	hgsc.bcm.edu	37	11	102589165	102589165	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	33	2	27	0	1	1	0	0	0
ATM	472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	108155202	108155202	+	Splice_Site	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	96	34	107	0	0	0	0	0	0
VWF	7450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	6138619	6138619	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	126	76	108	0	35	34	1	0	0
LRRC23	10233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	7014840	7014840	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	148	43	120	0	94	62	32	0	0
C12orf39	80763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	21679409	21679409	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	43	13	49	0	0	0	0	0	0
CMAS	55907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	22218064	22218064	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	258	126	155	1	0	0	0	0	0
COL2A1	1280	ucsc.edu	37	12	48375152	48375152	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	41	4	44	0	0	0	0	0	0
MLL2	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	49416134	49416134	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	26	14	21	0	0	0	0	0	0
ULK1	8408	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	132405713	132405713	+	Silent	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	96	53	89	0	42	21	21	0	0
MIR548F5	100302239	bcgsc.ca	37	13	36382493	36382493	+	RNA	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	77	28	55	0	0	0	0	0	0
DHRS12	79758	ucsc.edu	37	13	52343425	52343425	+	Silent	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	23	4	15	0	1	1	0	0	0
SSTR1	6751	hgsc.bcm.edu	37	14	38678657	38678657	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	13	2	28	0	1	1	0	0	0
EXOC5	10640	broad.mit.edu	37	14	57702498	57702498	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	6	2	13	0	0	0	0	0	0
ARID4A	5926	hgsc.bcm.edu	37	14	58827678	58827678	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	97	13	105	0	10	10	0	0	0
ARID4A	5926	hgsc.bcm.edu	37	14	58827680	58827680	+	Missense_Mutation	SNP	G	G	C	rs145426502	alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	99	14	105	0	15	15	0	0	0
ARHGAP11A	9824	hgsc.bcm.edu;bcgsc.ca	37	15	32916475	32916475	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	142	31	157	0	2	0	2	0	0
CDAN1	146059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	43023981	43023981	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	103	35	102	0	4	4	0	0	0
GNB5	10681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	52446239	52446239	+	Silent	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	57	17	80	0	52	27	25	0	0
HERC1	8925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	64021464	64021464	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	25	4	40	0	8	7	1	0	0
SYNM	23336	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	99672333	99672333	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	93	33	78	0	2	0	2	0	0
AXIN1	8312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	396884	396884	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	70	39	59	0	28	11	17	0	0
HAGH	3029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	1869997	1869997	+	Silent	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	135	26	122	0	157	107	50	0	0
CREBBP	1387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3807907	3807907	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	147	39	111	0	12	11	1	0	0
GLYR1	84656	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	4895118	4895118	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	241	118	235	0	102	34	68	0	0
PDXDC1	23042	hgsc.bcm.edu;broad.mit.edu	37	16	15122744	15122744	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	102	6	85	0	0	0	0	0	0
PALB2	79728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	23646368	23646368	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	242	64	194	0	13	8	5	0	0
FBXL8	55336	hgsc.bcm.edu	37	16	67197640	67197640	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	40	2	40	0	6	6	0	0	0
CENPT	80152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67863889	67863889	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	314	79	290	0	44	34	10	0	0
KDM6B	23135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7755333	7755333	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	71	14	86	0	48	30	18	0	0
KRT33A	3883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	39505660	39505660	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	74	32	70	0	0	0	0	0	0
SCRN2	90507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	45916322	45916322	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	177	57	219	0	82	42	40	0	0
AATK	9625	broad.mit.edu	37	17	79094413	79094413	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	13	3	24	0	0	0	0	0	0
NARF	26502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	80443450	80443450	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	142	18	156	0	84	70	14	0	0
EPB41L3	23136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	5394764	5394764	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	125	46	133	0	25	19	6	0	0
MEP1B	4225	broad.mit.edu;bcgsc.ca	37	18	29787415	29787415	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	24	8	41	0	0	0	0	0	0
STK11	6794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	1223168	1223168	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	23	10	26	0	0	0	0	0	0
ZNF433	163059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12126384	12126384	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	118	34	128	0	9	4	5	0	0
KIAA1683	80726	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	18368726	18368726	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	127	41	121	0	0	0	0	0	0
ZNF492	57615	bcgsc.ca	37	19	22817278	22817278	+	Splice_Site	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	92	6	123	1	0	0	0	0	0
ZNF681	148213	hgsc.bcm.edu	37	19	23927139	23927139	+	Missense_Mutation	SNP	T	T	G	rs76432318	alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	75	4	72	1	9	1	8	0	0
PSG10P	653492	ucsc.edu;bcgsc.ca	37	19	43358239	43358239	+	RNA	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	561	198	593	0	0	0	0	0	0
U2AF2	11338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	56180114	56180114	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	91	30	148	0	163	72	91	0	0
GPR113	165082	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	26533773	26533773	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	39	18	36	0	0	0	0	0	0
OTOF	9381	ucsc.edu;bcgsc.ca	37	2	26700635	26700635	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	35	15	42	0	0	0	0	0	0
OTOF	9381	hgsc.bcm.edu	37	2	26702405	26702405	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	19	2	25	0	0	0	0	0	0
C2orf73	129852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	54587528	54587528	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	31	8	19	0	1	1	0	0	0
ZAP70	7535	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	98341626	98341626	+	Missense_Mutation	SNP	C	C	A	rs56404668	byfrequency;alternate_allele	TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	75	36	82	0	0	0	0	0	0
UGT1A8	54576	broad.mit.edu	37	2	234526363	234526363	+	Missense_Mutation	SNP	A	A	G	rs150485330		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	88	3	72	1	0	0	0	0	0
TBC1D20	128637	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	419913	419913	+	Silent	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	81	48	82	0	51	22	29	0	0
FRG1B	284802	bcgsc.ca	37	20	29623164	29623164	+	RNA	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	1352	65	1044	21	284	284	0	0	0
FRG1B	284802	bcgsc.ca	37	20	29623179	29623179	+	RNA	SNP	A	A	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	1523	70	1204	27	385	385	0	0	0
FRG1B	284802	bcgsc.ca	37	20	29623219	29623219	+	RNA	SNP	A	A	G	rs34726194		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	1339	48	1162	15	282	282	0	0	0
NCOA6	23054	hgsc.bcm.edu;broad.mit.edu	37	20	33345756	33345756	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	95	5	59	0	21	20	1	0	0
FAM65C	140876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	49219116	49219116	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	115	24	90	0	16	16	0	0	0
CYP24A1	1591	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	52773943	52773943	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	85	42	74	0	143	45	98	0	0
LIME1	54923	broad.mit.edu	37	20	62369217	62369217	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	29	4	21	0	36	36	0	0	0
ANKRD30BP2	149992	bcgsc.ca	37	21	14414844	14414844	+	RNA	SNP	T	T	C	rs71203526		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	88	7	78	2	0	0	0	0	0
APP	351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	27348294	27348294	+	Silent	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	96	28	94	0	5139	2245	2887	3	4
COL18A1	80781	hgsc.bcm.edu	37	21	46930115	46930115	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	12	2	12	0	162	162	0	0	0
TRIOBP	11078	hgsc.bcm.edu	37	22	38150890	38150890	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	108	7	102	1	0	0	0	0	0
SUMF1	285362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	4490972	4490972	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	260	84	235	0	81	42	39	0	0
ANO10	55129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	43618738	43618738	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	51	18	42	0	21	9	12	0	0
ARHGEF3	50650	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	56787577	56787577	+	Silent	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	93	20	137	0	47	30	17	0	0
PTPRG-AS1	100506994	bcgsc.ca	37	3	62257262	62257262	+	RNA	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	36	14	36	0	0	0	0	0	0
PTPRG-AS1	100506994	bcgsc.ca	37	3	62263361	62263361	+	RNA	SNP	A	A	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	94	37	95	0	0	0	0	0	0
TMF1	7110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	69096768	69096770	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	98	27	88	0	0	0	0	0	0
FRMD4B	23150	hgsc.bcm.edu	37	3	69336931	69336931	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	31	2	39	0	0	0	0	0	0
EAF2	55840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	121591418	121591418	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	288	154	184	0	12	5	7	0	0
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	130287032	130287032	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	297	79	184	0	0	0	0	0	0
CP	1356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	148930432	148930432	+	Missense_Mutation	SNP	T	T	C	rs141532762		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	66	29	56	0	5	3	2	0	0
CLCN2	1181	hgsc.bcm.edu;broad.mit.edu	37	3	184071155	184071155	+	Silent	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	68	31	81	0	21	6	15	0	0
HTT	3064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	3156098	3156098	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	33	9	43	0	27	17	10	0	0
TECRL	253017	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	65180367	65180367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	33	10	51	0	0	0	0	0	0
SEPT11	55752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	77941678	77941678	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	157	52	127	0	135	60	74	1	0
LARP1B	55132	hgsc.bcm.edu	37	4	128998994	128998994	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	34	2	49	0	53	53	0	0	0
SKP2	6502	hgsc.bcm.edu;bcgsc.ca	37	5	36163851	36163851	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	82	5	82	0	1	1	0	0	0
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	36984988	36984988	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	179	72	143	0	29	18	11	0	0
ARHGAP26	23092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	142416823	142416823	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	81	41	59	0	0	0	0	0	0
JAKMIP2	9832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	147000262	147000262	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	176	85	105	0	0	0	0	0	0
CREBRF	153222	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	172518026	172518026	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	96	26	91	0	21	9	12	0	0
SPDEF	25803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	34512076	34512076	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	79	18	87	0	0	0	0	0	0
SNX9	51429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	158288583	158288583	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	72	23	99	0	0	0	0	0	0
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	116417463	116417463	+	Missense_Mutation	SNP	C	C	T	rs121913244		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	276	144	199	0	825	280	545	0	0
CTTNBP2	83992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	117365303	117365303	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	326	72	192	0	0	0	0	0	0
MLL3	58508	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	151917756	151917756	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	163	71	118	0	25	15	10	0	0
RP1L1	94137	broad.mit.edu	37	8	10470573	10470573	+	Silent	SNP	C	C	T	rs73201157		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	132	5	169	1	0	0	0	0	0
FAM160B2	64760	broad.mit.edu	37	8	21953846	21953847	+	Splice_Site	DEL	AG	AG	-	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	7	5	8	0	0	0	0	0	0
IDO2	169355	hgsc.bcm.edu	37	8	39862889	39862889	+	Silent	SNP	T	T	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	38	2	49	0	0	0	0	0	0
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	95201459	95201459	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	97	76	102	0	17	1	16	0	0
BNC2	54796	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	16419221	16419221	+	Silent	SNP	A	A	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	96	29	100	0	7	5	2	0	0
MLLT3	4300	broad.mit.edu	37	9	20414373	20414373	+	Silent	SNP	G	G	A	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	72	6	49	1	33	33	0	0	0
GRIN3A	116443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	104449145	104449145	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	68	33	54	0	0	0	0	0	0
SH2D3C	10044	hgsc.bcm.edu	37	9	130501166	130501166	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	17	2	25	0	4	4	0	0	0
EXOSC2	23404	ucsc.edu	37	9	133569210	133569210	+	Missense_Mutation	SNP	G	G	C	rs202001690		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	65	4	76	8	18	15	3	0	0
ARAF	369	hgsc.bcm.edu	37	X	47426120	47426120	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	34	2	34	0	58	57	1	0	0
TRO	7216	hgsc.bcm.edu	37	X	54948719	54948719	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	22	2	21	0	3	3	0	0	0
CLIP1	6249	broad.mit.edu	37	12	122812693	122812694	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-7997-01A-11D-2201-08	TCGA-A4-7997-10A-01D-2201-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	af158dec-5dad-4b6e-ad38-057aa9b6203c	df84187c-0ad5-45ed-9df9-6402364de115	280	8	169	0	0	0	0	0	0
