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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov_SOL	TVarCov_SOL	TVaf_SOL	NTotCov_SOL	NVarCov_SOL	NVaf_SOL	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	Ttot_rna	Tvar_rna	Tvaf_rna	note	germline-maf-frequency	IGV
SLC1A7	6512	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	53580475	53580475	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_006671	exon3	c.G386A	p.G129E	GGCTTCCCACTCT		140	8	0.06	89	0	0				2	0	0.00			
NBPF10	100132406	broad.mit.edu	37	1	145293269	145293269	+	Splice_Site	SNP	G	G	A	rs75226570		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	NBPF10	.	.	.	.	ACAACAGTAAGTT		39	8	0.21	26	0	0		221		0	0				
PRELP	5549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	203453089	203453089	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	PRELP,caecum,carcinoma,0,1	PRELP	NM_201348	exon2	c.C777T	p.N259N	CCCTAACGGATAC		207	26	0.13	129	0	0		0	1	29	1	0.03			
ADARB2	105	mdanderson.org	37	10	1245984	1245984	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_018702	exon8	c.G1786C	p.A596P	CGCGTGCGAGGTG		27	3	0.11	24	0	0				0	0				
TAF3	83860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	10	8006560	8006560	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_031923	exon3	c.C1087T	p.Q363X	CAAATACAGACAC		109	15	0.14	90	0	0				12	2	0.17			
LRRTM3	347731	broad.mit.edu;mdanderson.org	37	10	68687000	68687000	+	Missense_Mutation	SNP	G	G	A	rs143239282		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	LRRTM3	NM_178011	exon2	c.G326A	p.R109H	GAATACGCAGACT		52	4	0.08	39	0	0		241		0	0				
IRF7	3665	mdanderson.org	37	11	615253	615253	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_004031	exon1	c.C66A	p.A22A	GCGTGGGGCTGCC		19	2	0.11	23	0	0				125	0	0.00			
.	0	bcgsc.ca	37	11	18931986	18931986	+	RNA	SNP	T	T	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	ACTGCCTGAATCT		37	4	0.11	38	0	0				0	0				
CCDC87	55231	mdanderson.org	37	11	66360040	66360040	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_018219	exon1	c.C447A	p.A149A	GAGGGTGGCTGAT		41	3	0.07	46	0	0				1	0	0.00			
LRP5	4041	mdanderson.org	37	11	68216521	68216521	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_002335	exon23	c.T4831C	p.C1611R	TCCCCCTGCACGG		22	3	0.14	27	0	0				63	0	0.00			
STT3A	3703	mdanderson.org	37	11	125482643	125482643	+	Splice_Site	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_152713	exon12	c.1365+1G>T	.	AATGAAGTGAGAA		43	3	0.07	39	1	0.0256410256				9	0	0.00			
WBP11	51729	broad.mit.edu	37	12	14947586	14947586	+	Silent	SNP	A	A	G	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	WBP11,right_lower_lobe,carcinoma,0,2	WBP11	NM_016312	exon7	c.T606C	p.P202P	AGGGGGAGGGCCA		419	8	0.02	149	3	0.0201342282		66	2	460	3	0.01			
DDX11	1663	ucsc.edu	37	12	31254052	31254052	+	Missense_Mutation	SNP	G	G	C	rs201027785	by1000genomes	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	DDX11	NM_030653	exon20	c.G2040C	p.E680D	AAGAGAGCTGCCT		171	2	0.01	109	0	0		188		209	26	0.12	rescued with RNA-seq		
MLL2	8085	mdanderson.org	37	12	49427679	49427679	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2_ENST00000301067	NM_003482	exon39	c.G10809A	p.Q3603Q	CTGCTGCTGTTGT		52	4	0.08	27	0	0		0	2	22	0	0.00			
ITGA5	3678	broad.mit.edu	37	12	54791248	54791248	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	ITGA5	NM_002205	exon29	c.C2967A	p.T989T	TGCCTTGGTCCAT		125	4	0.03	56	1	0.0178571429		99		203	0	0.00			
RFC3	5983	broad.mit.edu	37	13	34398073	34398073	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	RFC3	NM_002915	exon3	c.T245A	p.I82N	AAAAAATTGAAAT		479	11	0.02	256	2	0.0078125		40		36	0	0.00			
PCCA	5095	mdanderson.org	37	13	100915059	100915059	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_001178004	exon10	c.G793T	p.D265Y	TTTATTGATAATC		46	3	0.07	36	0	0				10	0	0.00			
.	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	A	G	rs374719458		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	ATAATAAAGTTCA		35	5	0.14	20	0	0				4	0	0.00			
OR10G3	26533	mdanderson.org	37	14	22038818	22038818	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_001005465	exon1	c.C58A	p.P20T	TGAGTGGATACGG		20	2	0.10	27	0	0				0	0				
LOC727924	0	broad.mit.edu	37	15	22332492	22332492	+	RNA	SNP	A	A	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	TCTCTTATTACTA		188	5	0.03	84	0	0				0	0				
.	0	broad.mit.edu	37	15	32828941	32828973	+	RNA	DEL	GCCCCAGCCGGGCCCCCTCGCGCCGCTGCGGCT	GCCCCAGCCGGGCCCCCTCGCGCCGCTGCGGCT	-	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	GCCCCAGCCGGGCCCCCTCGCGCCGCTGCGGCT	GCCCCAGCCGGGCCCCCTCGCGCCGCTGCGGCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GCTCCAGCCCCAG		16	5	0.31	13	0	0				0	0				
TYRO3	7301	hgsc.bcm.edu;bcgsc.ca	37	15	41865666	41865666	+	Splice_Site	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_006293	exon17	c.2145+1G>T	.	GACGTGGTGAGCA		121	11	0.09	95	0	0				0	0				
TMEM62	80021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	43470879	43470879	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_024956	exon12	c.G1456A	p.V486M	TATTCTGTGTTGT		142	16	0.11	75	0	0				9	0	0.00			
MEF2A	4205	hgsc.bcm.edu	37	15	100211846	100211846	+	Missense_Mutation	SNP	G	G	A	rs75705863	bycluster	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	MEF2A_ENST00000354410,NS,carcinoma,+1,1	MEF2A_ENST00000354410	NM_005587	exon5	c.G380A	p.R127Q	TGATGCGGAATCA		54	4	0.07	23	1	0.0434782609		1	1	4	0	0.00			
WASH3P	0	broad.mit.edu	37	15	102516512	102516512	+	RNA	SNP	G	G	A	rs62635297		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	WASH3P	.	.	.	.	TGGGCCGTTGCTC		132	5	0.04	127	0	0		56		127	66	0.52	rescued with RNA-seq		
C1QTNF8	390664	mdanderson.org	37	16	1143813	1143813	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_207419	exon4	c.C447T	p.F149F	CAGGTCGAAGGCG		16	2	0.13	33	0	0				0	0				
KIAA0430	9665	broad.mit.edu	37	16	15709776	15709776	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	KIAA0430	NM_014647	exon16	c.C3164A	p.T1055N	ACACAGGTAATGA		207	4	0.02	136	0	0		154		11	0	0.00			
ERI2	112479	broad.mit.edu	37	16	20809122	20809122	+	Missense_Mutation	SNP	G	G	T	rs76921366	bycluster;byfrequency	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	ERI2	NM_001142725	exon9	c.C2000A	p.T667K	TGGCTTGTTTCTG		155	15	0.10	83	4	0.0481927711		50		14	2	0.14			
PKD1L2	114780	broad.mit.edu	37	16	81146189	81146190	+	RNA	INS	-	-	A	rs59722247		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	PKD1L2	.	.	.	.	GATGAGGGGGAGG		6	2	0.33	4	0	0		361		0	0				
PKD1L2	114780	broad.mit.edu	37	16	81146190	81146191	+	RNA	INS	-	-	GA	rs72015718	alternate_allele	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	PKD1L2	.	.	.	.	ATGAGGGGGAGGA		6	2	0.33	4	0	0		361		0	0				
ALOX12B	242	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	7982769	7982769	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_001139	exon8	c.C1016T	p.P339L	CAGAGGGGGGCGC		197	34	0.17	201	0	0				0	0				
PLD6	201164	broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	17109307	17109307	+	Silent	SNP	C	C	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	PLD6	NM_178836	exon1	c.G294T	p.L98L	GGCGAACAGGCAG		31	6	0.19	48	1	0.0208333333		9		1	0	0.00			
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346594	39346594	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	KRTAP9-1_ENST00000398470,colon,carcinoma,+2,2	KRTAP9-1_ENST00000398470	NM_001190460	exon1	c.C456T	p.T152T	GCCCACCTGCTGT		80	4	0.05	51	0	0		2	2	0	0				
FZR1	51343	broad.mit.edu	37	19	3531983	3531983	+	Missense_Mutation	SNP	A	A	C	rs200584048		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	FZR1	NM_001136198	exon9	c.A898C	p.T300P	ATCCGCACCCCGC		31	13	0.42	30	9	0.3		42		74	12	0.16			
HMG20B	10362	mdanderson.org	37	19	3573771	3573771	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_006339	exon3	c.G120T	p.A40A	ACGCGCGGGCGAG		49	3	0.06	40	0	0				40	0	0.00			
TIMM44	10469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	7998431	7998431	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_006351	exon7	c.C708T	p.H236H	GTCCTTGTGCAGC		169	29	0.17	163	0	0				188	59	0.31			
RAD23A	5886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	13058807	13058807	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	RAD23A,NS,carcinoma,+1,1	RAD23A	NM_005053	exon2	c.T218A	p.V73D	TTGTGGTCGTCAT		58	8	0.14	62	0	0		1	1	295	87	0.29			
BRD4	23476	broad.mit.edu	37	19	15350233	15350233	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	BRD4	NM_058243	exon17	c.G3546A	p.Q1182Q	CGGCTCCTGTTTC		166	4	0.02	161	0	0		172		128	2	0.02			
LYPD3	27076	mdanderson.org	37	19	43967282	43967282	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_014400	exon4	c.G540A	p.T180T	ACCTGCCGTCAAG		37	3	0.08	53	0	0				6	0	0.00			
ANKRD20A8P	0	broad.mit.edu	37	2	95518674	95518674	+	RNA	DEL	G	G	-	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	AAAAAAGAATAAC		6	2	0.33	8	0	0				0	0				
AVP	551	mdanderson.org	37	20	3063730	3063730	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_000490	exon2	c.C215T	p.A72V	CGCAGCGCCTCAG		10	3	0.30	13	0	0				11	0	0.00			
RRBP1	6238	bcgsc.ca	37	20	17639834	17639834	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	RRBP1	.	.	.	.	GCCTTCTTGCCCT		257	17	0.07	242	4	0.0165289256		157		837	59	0.07			
NINL	22981	mdanderson.org	37	20	25439019	25439019	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_025176	exon22	c.G3843A	p.R1281R	ACTTACCCGCTGT		20	3	0.15	36	0	0				39	0	0.00			
FRG1B	0	broad.mit.edu	37	20	29632635	29632635	+	Missense_Mutation	SNP	C	C	G	rs375238322		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	FRG1B	.	.	.	.	CCAAGACCACAAA		650	7	0.01	352	0	0		181		104	10	0.10	rescued with RNA-seq		
.	0	broad.mit.edu	37	20	52557949	52557950	+	RNA	INS	-	-	TT	rs72548465	bycluster;by1000genomes	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GTGTGTGTGTGTG		65	11	0.17	16	0	0				0	0				
C20orf195	79025	mdanderson.org	37	20	62187284	62187284	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_024059	exon2	c.C268A	p.Q90K	GGCGACCAGAACC		21	3	0.14	16	0	0				5	0	0.00			
BAGE	85319	broad.mit.edu	37	21	11096512	11096516	+	RNA	DEL	GTTTT	GTTTT	-	rs139100150	alternate_allele	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	GTTTT	GTTTT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	TTTTAAGTTTTGT		6	2	0.33	6	0	0				0	0				
HIC2	23119	broad.mit.edu;mdanderson.org	37	22	21799538	21799538	+	Silent	SNP	C	C	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	HIC2	NM_015094	exon3	c.C354A	p.T118T	CAGCACCCTCCTC		75	6	0.08	58	0	0		42		20	10	0.50			
POM121L1P	25812	mdanderson.org	37	22	22979724	22979724	+	RNA	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GTCCTGGCAGCAT		40	3	0.08	21	0	0				0	0				
POM121L9P	0	broad.mit.edu	37	22	24657088	24657088	+	RNA	DEL	A	A	-	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GGGAAGAGGCGGG		11	3	0.27	9	0	0				0	0				
KALRN	8997	mdanderson.org	37	3	124114183	124114183	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_003947	exon12	c.G2158T	p.E720X	CCCAGCGAGGCCA		49	3	0.06	47	0	0				4	0	0.00			
.	0	bcgsc.ca	37	4	49553037	49553037	+	RNA	SNP	A	A	T	rs58062155		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	ATAAGAAGGAACT		110	20	0.18	46	1	0.0217391304				0	0				
FRAS1	80144	mdanderson.org	37	4	79460492	79460492	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_025074	exon73	c.G11343T	p.V3781V	TGATGTGCCTTTT		86	6	0.07	43	0	0				1	0	0.00			
SLC9B1	150159	ucsc.edu	37	4	103822298	103822298	+	Silent	SNP	C	C	T	rs3175325	bycluster;byfrequency;by2hit2allele	TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_139173	exon12	c.G1524A	p.Q508Q	TGACAACTGCAGT		49	17	0.35	24	6	0.25				1	0	0.00			
VCAN	1462	broad.mit.edu	37	5	82836890	82836890	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	VCAN	NM_004385	exon8	c.G8068T	p.A2690S	CCCACGGCAACAT		115	4	0.03	64	0	0		498		130	0	0.00			
TNIP1	10318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	150436337	150436337	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_001252385	exon6	c.C617A	p.S206Y	AGAATGGAGGTGC		77	12	0.16	98	0	0				98	6	0.06			
LOC202181	0	broad.mit.edu	37	5	177059966	177059966	+	RNA	DEL	T	T	-	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GTGGGATTTTTTT		10	5	0.50	7	0	0				0	0				
.	0	bcgsc.ca	37	5	180541994	180541994	+	RNA	SNP	C	C	A	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	TACCACCGGGAAG		53	4	0.08	32	0	0				1	0	0.00			
ECI2	10455	mdanderson.org	37	6	4125592	4125592	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_206836	exon7	c.C687A	p.G229G	AAAACAGCCCACA		51	3	0.06	66	0	0				46	0	0.00			
ZNRD1-AS1	80862	hgsc.bcm.edu	37	6	30000857	30000857	+	RNA	SNP	A	A	G	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GAATCCAAACAGA		41	6	0.15	13	0	0				0	0				
GPR141	353345	broad.mit.edu	37	7	37780115	37780115	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	GPR141	NM_181791	exon1	c.C120T	p.F40F	TCTTTTCCTCCTG		170	16	0.09	100	6	0.06		79		0	0				
SCRIB	23513	mdanderson.org	37	8	144886857	144886857	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_182706	exon21	c.C2890A	p.P964T	TGGGGGGTGAGGA		36	3	0.08	27	0	0				151	0	0.00			
PGM5P2	0	broad.mit.edu	37	9	69082757	69082758	+	RNA	INS	-	-	AT	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	TTAAAACAAAGAG		10	4	0.40	7	0	0				0	0				
.	375748	ucsc.edu;mdanderson.org	37	9	98732886	98732886	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	.	.	.	.	GGATCATGACAGC		260	29	0.11	102	0	0				6	1	0.17			
RAPGEF1	2889	mdanderson.org	37	9	134503341	134503341	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	.	NM_198679	exon9	c.A1163G	p.D388G	CCACTGTCCCTGT		50	3	0.06	52	0	0				85	0	0.00			
PNPLA4	8228	broad.mit.edu	37	X	7868821	7868821	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-2G-AAFY-01A-11D-A42Y-10	TCGA-2G-AAFY-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6fcf0ebe-135e-4a5d-bce6-68fa0e4c3961	533341c5-782e-418a-8db9-996ff3f09e94	.	PNPLA4	NM_004650	exon7	c.T668C	p.L223P	GGAAAAAGGGCTT		371	5	0.01	165	0	0		24		94	0	0.00			
