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	dataset	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context
KIAA0467	23334	broad.mit.edu	36	1	43686214	43686214	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	43686214	43686214	KIAA0467	1	A	A	T	11
NASP	4678	broad.mit.edu	36	1	45853636	45853636	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			A	G	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	45853636	45853636	NASP	1	A	A	G	3
ZZZ3	26009	broad.mit.edu	36	1	77870155	77870155	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	77870155	77870155	ZZZ3	1	T	T	C	52
IQGAP3	128239	broad.mit.edu	36	1	154773631	154773631	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	154773631	154773631	IQGAP3	1	G	G	C	35
F11R	50848	broad.mit.edu	36	1	159257448	159257448	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	159257448	159257448	F11R	1	G	G	A	35
TNN	63923	broad.mit.edu	36	1	173315944	173315944	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	173315944	173315944	TNN	1	G	G	C	34
LHX4	89884	broad.mit.edu	36	1	178507763	178507763	+	Silent	SNP	A	A	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	178507763	178507763	LHX4	1	A	A	T	11
TTC13	79573	broad.mit.edu	36	1	229127284	229127284	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	229127284	229127284	TTC13	1	C	C	T	31
TRIM67	440730	broad.mit.edu	36	1	229417775	229417775	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	229417775	229417775	TRIM67	1	C	C	A	20
ZNF238	10472	broad.mit.edu	36	1	242284516	242284516	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	242284516	242284516	ZNF238	1	G	G	A	40
ZFYVE27	118813	broad.mit.edu	36	10	99500132	99500132	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	99500132	99500132	ZFYVE27	10	A	A	G	11
PDCD11	22984	broad.mit.edu	36	10	105168268	105168268	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	105168268	105168268	PDCD11	10	C	C	T	22
CTTN	2017	broad.mit.edu	36	11	69946724	69946724	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			G	C	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	69946724	69946724	CTTN	11	G	G	C	43
HOXC8	3224	broad.mit.edu	36	12	52691424	52691424	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	52691424	52691424	HOXC8	12	A	A	C	5
FAM109A	144717	broad.mit.edu	36	12	110285217	110285218	+	Missense_Mutation	DNP	CC	CC	AT	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	DNP	110285217	110285218	FAM109A	12	CC	CC	AT	22
ATP8A2	51761	broad.mit.edu	36	13	25484707	25484707	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	25484707	25484707	ATP8A2	13	G	G	A	39
VPS13C	54832	broad.mit.edu	36	15	59954389	59954389	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	59954389	59954389	VPS13C	15	T	T	A	62
GTF3C1	2975	broad.mit.edu	36	16	27457177	27457177	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	27457177	27457177	GTF3C1	16	A	A	C	6
SLC38A7	55238	broad.mit.edu	36	16	57271478	57271478	+	Silent	SNP	A	A	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	57271478	57271478	SLC38A7	16	A	A	G	8
TP53	7157	broad.mit.edu	36	17	7517845	7517845	+	Missense_Mutation	SNP	C	C	A	rs28934576	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	7517845	7517845	TP53	17	C	C	A	19
STAT5B	6777	broad.mit.edu	36	17	37633087	37633087	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	37633087	37633087	STAT5B	17	C	C	A	25
FAM117A	81558	broad.mit.edu	36	17	45149912	45149912	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	45149912	45149912	FAM117A	17	C	C	A	18
CHAD	1101	broad.mit.edu	36	17	45898070	45898070	+	Missense_Mutation	SNP	C	C	T	rs35218093	byCluster;byFrequency	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	45898070	45898070	CHAD	17	C	C	T	23
ZNF521	25925	broad.mit.edu	36	18	21058980	21058980	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	21058980	21058980	ZNF521	18	C	C	T	23
MUC16	94025	broad.mit.edu	36	19	8838643	8838643	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			T	C	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	8838643	8838643	MUC16	19	T	T	C	60
PKN1	5585	broad.mit.edu	36	19	14423650	14423650	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	14423650	14423650	PKN1	19	A	A	G	11
FBL	2091	broad.mit.edu	36	19	45023138	45023138	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	45023138	45023138	FBL	19	C	C	A	30
SPTBN4	57731	broad.mit.edu	36	19	45764084	45764084	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	45764084	45764084	SPTBN4	19	C	C	T	28
AXL	558	broad.mit.edu	36	19	46417207	46417207	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	46417207	46417207	AXL	19	T	T	G	59
ARHGEF1	9138	broad.mit.edu	36	19	47080381	47080381	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	47080381	47080381	ARHGEF1	19	T	T	A	62
SCN3A	6328	broad.mit.edu	36	2	165656048	165656048	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Nonsense_Mutation	SNP	165656048	165656048	SCN3A	2	G	G	A	39
TMEM198	130612	broad.mit.edu	36	2	220120642	220120642	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	220120642	220120642	TMEM198	2	G	G	T	36
SIRPA	140885	broad.mit.edu	36	20	1851108	1851108	+	Missense_Mutation	SNP	G	G	A	rs2422666	byCluster;byFrequency;byHapMap	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	1851108	1851108	SIRPA	20	G	G	A	40
PCSK2	5126	broad.mit.edu	36	20	17382587	17382587	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	G	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	17382587	17382587	PCSK2	20	C	C	G	18
DIDO1	11083	broad.mit.edu	36	20	60982318	60982318	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	60982318	60982318	DIDO1	20	G	G	A	37
DIDO1	11083	broad.mit.edu	36	20	61011659	61011659	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	61011659	61011659	DIDO1	20	G	G	A	46
UMODL1	89766	broad.mit.edu	36	21	42383593	42383593	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	42383593	42383593	UMODL1	21	C	C	T	19
NUP210	23225	broad.mit.edu	36	3	13353308	13353308	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	13353308	13353308	NUP210	3	G	G	A	44
TM4SF18	116441	broad.mit.edu	36	3	150525433	150525433	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	150525433	150525433	TM4SF18	3	C	C	T	25
PIK3CA	5290	broad.mit.edu	36	3	180425287	180425287	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	180425287	180425287	PIK3CA	3	C	C	A	32
TACC3	10460	broad.mit.edu	36	4	1699370	1699370	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	1699370	1699370	TACC3	4	C	C	T	26
SFRP2	6423	broad.mit.edu	36	4	154922125	154922125	+	Silent	SNP	C	C	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	G	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	154922125	154922125	SFRP2	4	C	C	G	23
CEP120	153241	broad.mit.edu	36	5	122752141	122752141	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	122752141	122752141	CEP120	5	T	T	C	56
SEPT8	23176	broad.mit.edu	36	5	132124565	132124565	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	132124565	132124565	SEPT8	5	G	G	T	46
CCDC69	26112	broad.mit.edu	36	5	150565218	150565218	+	Missense_Mutation	SNP	T	T	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	150565218	150565218	CCDC69	5	T	T	A	60
HERV-FRD	405754	broad.mit.edu	36	6	11213451	11213451	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	11213451	11213451	HERV-FRD	6	T	T	C	64
TRIM26	7726	broad.mit.edu	36	6	30272364	30272364	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	30272364	30272364	TRIM26	6	T	T	G	63
RUNX2	860	broad.mit.edu	36	6	45588070	45588070	+	Silent	SNP	C	C	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Silent	SNP	45588070	45588070	RUNX2	6	C	C	A	21
THSD7A	221981	broad.mit.edu	36	7	11642734	11642734	+	Silent	SNP	A	A	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	11642734	11642734	THSD7A	7	A	A	C	3
NT5C3	51251	broad.mit.edu	36	7	33023709	33023709	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			A	T	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	33023709	33023709	NT5C3	7	A	A	T	11
PEX1	5189	broad.mit.edu	36	7	91985096	91985096	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	91985096	91985096	PEX1	7	C	C	T	21
CCDC132	55610	broad.mit.edu	36	7	92764000	92764000	+	Missense_Mutation	SNP	T	T	G	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	92764000	92764000	CCDC132	7	T	T	G	53
SCARA3	51435	broad.mit.edu	36	8	27584534	27584534	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	27584534	27584534	SCARA3	8	G	G	C	42
BAG4	9530	broad.mit.edu	36	8	38187027	38187027	+	Silent	SNP	T	T	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	38187027	38187027	BAG4	8	T	T	A	62
NAPRT1	93100	broad.mit.edu	36	8	144728546	144728546	+	Silent	SNP	G	G	C	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Silent	SNP	144728546	144728546	NAPRT1	8	G	G	C	43
C9orf41	138199	broad.mit.edu	36	9	76821115	76821115	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	76821115	76821115	C9orf41	9	G	G	A	41
COL5A1	1289	broad.mit.edu	36	9	136857473	136857473	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	Broad	Missense_Mutation	SNP	136857473	136857473	COL5A1	9	G	G	A	37
IRAK1	3654	broad.mit.edu	36	X	152931859	152931859	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	x	x	---			x	Broad	Missense_Mutation	SNP	152931859	152931859	IRAK1	23	C	C	T	30
SPRR1B	6699	broad.mit.edu	36	1	151271566	151271637	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	Broad	In_Frame_Del	DEL	151271566	151271637	SPRR1B	1	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	55
ELMO3	79767	broad.mit.edu	36	16	65792082	65792087	+	In_Frame_Del	DEL	AACCTC	-	AACCTC	novel	Unknown	TCGA-13-1512-01	TCGA-13-1512-10							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	Broad	In_Frame_Del	DEL	65792082	65792087	ELMO3	16	AACCTC	-	AACCTC	9
