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	patient	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context
DNAJC11	55735	broad.mit.edu	36	1	6619976	6619976	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	6619976	6619976	DNAJC11	1	C	C	T	19
ALPL	249	broad.mit.edu	36	1	21762289	21762289	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	21762289	21762289	ALPL	1	G	G	A	34
CCDC28B	79140	broad.mit.edu	36	1	32440214	32440214	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	32440214	32440214	CCDC28B	1	A	A	C	14
FAM183A	440585	broad.mit.edu	36	1	43394541	43394541	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	43394541	43394541	FAM183A	1	G	G	A	40
RCOR3	55758	broad.mit.edu	36	1	209552736	209552736	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	209552736	209552736	RCOR3	1	A	A	G	2
USH2A	7399	broad.mit.edu	36	1	213874577	213874577	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	213874577	213874577	USH2A	1	C	C	T	31
MYO3A	53904	broad.mit.edu	36	10	26355327	26355327	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			T	G	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	26355327	26355327	MYO3A	10	T	T	G	52
UNC5B	219699	broad.mit.edu	36	10	72716536	72716536	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	72716536	72716536	UNC5B	10	C	C	T	23
HABP2	3026	broad.mit.edu	36	10	115327852	115327852	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	115327852	115327852	HABP2	10	T	T	G	55
OR51Q1	390061	broad.mit.edu	36	11	5400269	5400269	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	5400269	5400269	OR51Q1	11	G	G	T	47
FSHB	2488	broad.mit.edu	36	11	30210097	30210097	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	30210097	30210097	FSHB	11	C	C	A	21
QSER1	79832	broad.mit.edu	36	11	32912214	32912214	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	32912214	32912214	QSER1	11	G	G	A	36
OR8K1	390157	broad.mit.edu	36	11	55870397	55870397	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	55870397	55870397	OR8K1	11	T	T	C	57
DPF2	5977	broad.mit.edu	36	11	64865046	64865046	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	64865046	64865046	DPF2	11	C	C	A	26
PUS3	83480	broad.mit.edu	36	11	125270366	125270366	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	125270366	125270366	PUS3	11	G	G	T	34
CCNT1	904	broad.mit.edu	36	12	47374193	47374193	+	Silent	SNP	A	A	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	47374193	47374193	CCNT1	12	A	A	C	13
DIP2B	57609	broad.mit.edu	36	12	49378405	49378405	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	49378405	49378405	DIP2B	12	A	A	G	7
PAWR	5074	broad.mit.edu	36	12	78607731	78607731	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	78607731	78607731	PAWR	12	G	G	T	43
LATS2	26524	broad.mit.edu	36	13	20447312	20447312	+	Silent	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	20447312	20447312	LATS2	13	G	G	T	35
FRY	10129	broad.mit.edu	36	13	31550987	31550987	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Silent	SNP	31550987	31550987	FRY	13	C	C	T	19
C14orf43	91748	broad.mit.edu	36	14	73276041	73276041	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	73276041	73276041	C14orf43	14	A	A	C	15
NTRK3	4916	broad.mit.edu	36	15	86284908	86284908	+	Nonsense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Nonsense_Mutation	SNP	86284908	86284908	NTRK3	15	C	C	A	31
CDH8	1006	broad.mit.edu	36	16	60245476	60245476	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	60245476	60245476	CDH8	16	C	C	T	23
ZFHX3	463	broad.mit.edu	36	16	71380038	71380038	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	71380038	71380038	ZFHX3	16	G	G	T	39
ANKRD11	29123	broad.mit.edu	36	16	87879044	87879044	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	87879044	87879044	ANKRD11	16	G	G	A	37
TP53	7157	broad.mit.edu	36	17	7518223	7518223	+	Splice_Site_SNP	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Splice_Site_SNP	SNP	7518223	7518223	TP53	17	C	C	A	18
ZNF560	147741	broad.mit.edu	36	19	9442977	9442977	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Nonsense_Mutation	SNP	9442977	9442977	ZNF560	19	G	G	A	48
ZNF257	113835	broad.mit.edu	36	19	22062936	22062936	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	22062936	22062936	ZNF257	19	T	T	C	52
FAM83E	54854	broad.mit.edu	36	19	53808235	53808235	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	53808235	53808235	FAM83E	19	C	C	T	23
ZSWIM2	151112	broad.mit.edu	36	2	187421961	187421961	+	Nonsense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Nonsense_Mutation	SNP	187421961	187421961	ZSWIM2	2	C	C	A	30
COL4A3	1285	broad.mit.edu	36	2	227855409	227855409	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	227855409	227855409	COL4A3	2	C	C	T	21
SP100	6672	broad.mit.edu	36	2	231017272	231017272	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	231017272	231017272	SP100	2	G	G	A	37
KIF16B	55614	broad.mit.edu	36	20	16444271	16444271	+	Silent	SNP	T	T	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	16444271	16444271	KIF16B	20	T	T	A	51
PLXNB2	23654	broad.mit.edu	36	22	49062153	49062153	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	49062153	49062153	PLXNB2	22	C	C	T	31
PLXNB2	23654	broad.mit.edu	36	22	49066380	49066380	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Silent	SNP	49066380	49066380	PLXNB2	22	C	C	T	24
PLXNB2	23654	broad.mit.edu	36	22	49066760	49066760	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	49066760	49066760	PLXNB2	22	G	G	T	39
BSN	8927	broad.mit.edu	36	3	49655338	49655338	+	Nonsense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Nonsense_Mutation	SNP	49655338	49655338	BSN	3	G	G	T	47
MON1A	84315	broad.mit.edu	36	3	49922959	49922959	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	49922959	49922959	MON1A	3	G	G	A	39
ROPN1	54763	broad.mit.edu	36	3	125178457	125178457	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	125178457	125178457	ROPN1	3	C	C	A	27
EIF2B5	8893	broad.mit.edu	36	3	185343300	185343300	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	185343300	185343300	EIF2B5	3	G	G	C	36
ADH5	128	broad.mit.edu	36	4	100212611	100212611	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Nonsense_Mutation	SNP	100212611	100212611	ADH5	4	G	G	A	37
CXXC4	80319	broad.mit.edu	36	4	105631754	105631754	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			A	G	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	105631754	105631754	CXXC4	4	A	A	G	8
CDH6	1004	broad.mit.edu	36	5	31335411	31335411	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	31335411	31335411	CDH6	5	G	G	A	39
PRLR	5618	broad.mit.edu	36	5	35106079	35106079	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	35106079	35106079	PRLR	5	G	G	A	48
SPZ1	84654	broad.mit.edu	36	5	79652841	79652841	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	79652841	79652841	SPZ1	5	G	G	C	33
GEMIN5	25929	broad.mit.edu	36	5	154259047	154259047	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	154259047	154259047	GEMIN5	5	C	C	G	25
RNF145	153830	broad.mit.edu	36	5	158520861	158520861	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	158520861	158520861	RNF145	5	G	G	A	33
MGAT4B	11282	broad.mit.edu	36	5	179161231	179161231	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	179161231	179161231	MGAT4B	5	T	T	G	59
PGBD1	84547	broad.mit.edu	36	6	28372645	28372645	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	28372645	28372645	PGBD1	6	G	G	A	39
DDO	8528	broad.mit.edu	36	6	110836235	110836235	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Silent	SNP	110836235	110836235	DDO	6	T	T	C	49
KIAA1244	57221	broad.mit.edu	36	6	138697573	138697573	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	138697573	138697573	KIAA1244	6	G	G	A	33
PPP1R3A	5506	broad.mit.edu	36	7	113305739	113305739	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	113305739	113305739	PPP1R3A	7	G	G	T	33
ANK1	286	broad.mit.edu	36	8	41734807	41734807	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			A	T	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	41734807	41734807	ANK1	8	A	A	T	8
CSMD3	114788	broad.mit.edu	36	8	113461831	113461831	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	T	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	113461831	113461831	CSMD3	8	G	G	T	40
GPKOW	27238	broad.mit.edu	36	X	48863011	48863011	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	48863011	48863011	GPKOW	23	G	G	T	44
BRCC3	79184	broad.mit.edu	36	X	153953096	153953096	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-13-1409-01	Broad	Missense_Mutation	SNP	153953096	153953096	BRCC3	23	G	G	A	36
FAM86B2	653333	broad.mit.edu	36	8	12335964	12335966	+	In_Frame_Del	DEL	CTG	-	CTG	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-13-1409-01	Broad	In_Frame_Del	DEL	12335964	12335966	FAM86B2	8	CTG	-	CTG	32
FUT7	2529	broad.mit.edu	36	9	139045318	139045319	+	Frame_Shift_Del	DEL	GA	-	-	novel	Unknown	TCGA-13-1409-01	TCGA-13-1409-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-13-1409-01	Broad	Frame_Shift_Del	DEL	139045318	139045319	FUT7	9	GA	-	-	45
