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
ZNF281	23528	broad.mit.edu	36	1	198643191	198643191	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	198643191	198643191	ZNF281	1	G	G	T	48
NSUN6	221078	broad.mit.edu	36	10	18977517	18977517	+	Missense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	18977517	18977517	NSUN6	10	A	A	T	10
F2	2147	broad.mit.edu	36	11	46706902	46706902	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	46706902	46706902	F2	11	C	C	T	26
SLC43A1	8501	broad.mit.edu	36	11	57025059	57025059	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Silent	SNP	57025059	57025059	SLC43A1	11	G	G	A	43
FGF3	2248	broad.mit.edu	36	11	69334464	69334464	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Silent	SNP	69334464	69334464	FGF3	11	G	G	A	42
ABCC1	4363	broad.mit.edu	36	16	16104033	16104033	+	Missense_Mutation	SNP	A	A	G	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			A	G	A	A	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	16104033	16104033	ABCC1	16	A	A	G	4
CD19	930	broad.mit.edu	36	16	28851796	28851796	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			C	A	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	28851796	28851796	CD19	16	C	C	A	30
PAPD5	64282	broad.mit.edu	36	16	48819341	48819341	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	48819341	48819341	PAPD5	16	G	G	C	41
PCSK4	54760	broad.mit.edu	36	19	1439242	1439242	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	1439242	1439242	PCSK4	19	A	A	C	6
RETN	56729	broad.mit.edu	36	19	7640747	7640747	+	Silent	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Silent	SNP	7640747	7640747	RETN	19	C	C	T	27
SLC7A9	11136	broad.mit.edu	36	19	38046869	38046869	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	38046869	38046869	SLC7A9	19	C	C	G	17
PAFAH1B3	5050	broad.mit.edu	36	19	47493264	47493264	+	Missense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	47493264	47493264	PAFAH1B3	19	G	G	A	37
USP29	57663	broad.mit.edu	36	19	62334010	62334010	+	Nonsense_Mutation	SNP	A	A	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Nonsense_Mutation	SNP	62334010	62334010	USP29	19	A	A	T	13
HOXD12	3238	broad.mit.edu	36	2	176672933	176672933	+	Missense_Mutation	SNP	C	C	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	176672933	176672933	HOXD12	2	C	C	A	26
OBSL1	23363	broad.mit.edu	36	2	220129621	220129621	+	Missense_Mutation	SNP	A	A	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	220129621	220129621	OBSL1	2	A	A	C	2
LPIN3	64900	broad.mit.edu	36	20	39410832	39410832	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	39410832	39410832	LPIN3	20	C	C	G	18
SEC61A1	29927	broad.mit.edu	36	3	129271148	129271148	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			G	T	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	129271148	129271148	SEC61A1	3	G	G	T	40
XRN1	54464	broad.mit.edu	36	3	143534594	143534594	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	143534594	143534594	XRN1	3	C	C	T	28
SKIL	6498	broad.mit.edu	36	3	171561587	171561587	+	Silent	SNP	T	T	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			T	C	T	T	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Silent	SNP	171561587	171561587	SKIL	3	T	T	C	55
ZCCHC4	29063	broad.mit.edu	36	4	24972582	24972582	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	24972582	24972582	ZCCHC4	4	G	G	C	33
LNX1	84708	broad.mit.edu	36	4	54042704	54042704	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			G	A	G	G	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Silent	SNP	54042704	54042704	LNX1	4	G	G	A	39
EXOC1	55763	broad.mit.edu	36	4	56421433	56421433	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	56421433	56421433	EXOC1	4	T	T	C	56
GFOD1	54438	broad.mit.edu	36	6	13473240	13473240	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01			C	T	C	C	Unknown	Valid	Somatic	x	x	Sequenom_PCR_WGA			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	13473240	13473240	GFOD1	6	C	C	T	28
BTN2A1	11120	broad.mit.edu	36	6	26567866	26567866	+	Missense_Mutation	SNP	G	G	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	26567866	26567866	BTN2A1	6	G	G	C	34
BMP5	653	broad.mit.edu	36	6	55767132	55767132	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	55767132	55767132	BMP5	6	C	C	T	22
TAGAP	117289	broad.mit.edu	36	6	159379141	159379141	+	Missense_Mutation	SNP	G	G	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	159379141	159379141	TAGAP	6	G	G	T	48
TSPAN13	27075	broad.mit.edu	36	7	16784011	16784011	+	Missense_Mutation	SNP	C	C	G	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	16784011	16784011	TSPAN13	7	C	C	G	32
ZFHX4	79776	broad.mit.edu	36	8	77929051	77929051	+	Nonsense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Nonsense_Mutation	SNP	77929051	77929051	ZFHX4	8	C	C	T	17
MED22	6837	broad.mit.edu	36	9	135200886	135200886	+	Missense_Mutation	SNP	C	C	T	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	135200886	135200886	MED22	9	C	C	T	30
BRD3	8019	broad.mit.edu	36	9	135907364	135907364	+	Missense_Mutation	SNP	T	T	C	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Missense_Mutation	SNP	135907364	135907364	BRD3	9	T	T	C	60
RBBP7	5931	broad.mit.edu	36	X	16780622	16780622	+	Silent	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	x	x	---			x	TCGA-10-0931-01	Broad	Silent	SNP	16780622	16780622	RBBP7	23	G	G	A	37
TP53	7157	broad.mit.edu	36	17	7519249	7519249	+	Nonsense_Mutation	SNP	G	G	A	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-10-0931-01	Broad	Nonsense_Mutation	SNP	7519249	7519249	TP53	17	G	G	A	47
KLHDC3	116138	broad.mit.edu	36	6	43093652	43093673	+	Frame_Shift_Del	DEL	ATCATGTACATTTTTGGGGGCT	-	ATCATGTACATTTTTGGGGGCT	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-10-0931-01	Broad	Frame_Shift_Del	DEL	43093652	43093673	KLHDC3	6	ATCATGTACATTTTTGGGGGCT	-	ATCATGTACATTTTTGGGGGCT	12
PYCRL	65263	broad.mit.edu	36	8	144759070	144759096	+	In_Frame_Del	DEL	GGCTGCTCGCAGCCCGCCCTGCTCCAG	-	GGCTGCTCGCAGCCCGCCCTGCTCCAG	novel	Unknown	TCGA-10-0931-01	TCGA-10-0931-01							Unknown	Unknown	Unknown	Phase_I	Capture	---			Illumina GAIIx	TCGA-10-0931-01	Broad	In_Frame_Del	DEL	144759070	144759096	PYCRL	8	GGCTGCTCGCAGCCCGCCCTGCTCCAG	-	GGCTGCTCGCAGCCCGCCCTGCTCCAG	47
