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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
RTN3	10313	broad.mit.edu	37	11	63487681	63487681	+	Silent	SNP	T	C	C			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr11:63487681T>C	uc001nxq.2	+	3	1894	c.1707T>C	c.(1705-1707)CCT>CCC	p.P569P	RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Silent_p.P550P|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Silent_p.P457P|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b	569					apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1						AAGATCAGCCTGATATTCTTG	0.413													3	47					0	0	0.004672	0	0
LOC653113	653113	broad.mit.edu	37	12	8384525	8384525	+	RNA	SNP	G	T	T			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr12:8384525G>T	uc010sgk.1	-	5		c.1263C>A				NR_024254				Homo sapiens family with sequence similarity 86, member A pseudogene (LOC653113), non-coding RNA.												0						AAGCTGTGGTGGGCCCTGATT	0.562													3	6					6.4e-05	0.0001472	0.004672	1	0
Unknown	0	broad.mit.edu	37	16	15457701	15457701	+	Missense_Mutation	SNP	G	A	A			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr16:15457701G>A	uc010bvf.1	-	9	812	c.812C>T	c.(811-813)GCT>GTT	p.A271V						RecName: Full=NPIP-like protein 1;																		AGGGGAGTGAGCAGACACTCG	0.562													5	113					0	0	0.001168	0	0
FLJ36000	284124	broad.mit.edu	37	17	21904125	21904125	+	RNA	SNP	G	A	A			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr17:21904125G>A	uc002gza.2	+	1		c.64G>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ggagtcgcaaggggccgagca	0													3	43					0	0	0.004672	0	0
TOP2A	7153	broad.mit.edu	37	17	38552660	38552660	+	Missense_Mutation	SNP	T	C	C			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr17:38552660T>C	uc002huq.2	-	28	3721	c.3595A>G	c.(3595-3597)AAG>GAG	p.K1199E		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	1199					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCCTTGGCCTTCCCCCCTTTC	0.428													3	60					0	0	0.004672	0	0
C3orf15	89876	broad.mit.edu	37	3	119428733	119428733	+	Missense_Mutation	SNP	C	T	T			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr3:119428733C>T	uc010hqx.1	+	5	568	c.491C>T	c.(490-492)GCC>GTC	p.A164V	C3orf15_uc003edc.2_Missense_Mutation_p.A164V|C3orf15_uc010hqy.1_Missense_Mutation_p.A164V|C3orf15_uc003ede.3_Missense_Mutation_p.A164V|C3orf15_uc010hqz.2_Missense_Mutation_p.A102V|C3orf15_uc011bjd.1_Missense_Mutation_p.A38V|C3orf15_uc011bje.1_Missense_Mutation_p.A144V|C3orf15_uc010hra.1_5'UTR			Q7Z4T9	AAT1_HUMAN	RecName: Full=AMY-1-associating protein expressed in testis 1;          Short=AAT-1;	164						mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)		GTTGTTTATGCCGTATCCAAG	0.254													3	49					0	0	0.000248	0	0
SDHAP2	727956	broad.mit.edu	37	3	195410640	195410640	+	Silent	SNP	T	C	C	rs6583273	by1000genomes	TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr3:195410640T>C	uc003fuw.2	+	13	1731	c.537T>C	c.(535-537)TAT>TAC	p.Y179Y	SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						TTGATGAGTATGATCACTCCA	0.468													2	6					0	0	0.004672	0	0
UNC5A	90249	broad.mit.edu	37	5	176304656	176304656	+	Missense_Mutation	SNP	C	G	G			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr5:176304656C>G	uc003mey.2	+	10	1779	c.1587C>G	c.(1585-1587)GAC>GAG	p.D529E		NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor	529	ZU5.|Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCAGCCCTGACAGCTGGAGCC	0.647													3	35					0	0	0.000248	0	0
TRERF1	55809	broad.mit.edu	37	6	42236552	42236552	+	Silent	SNP	C	T	T			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr6:42236552C>T	uc003osd.2	-	5	1340	c.777G>A	c.(775-777)CAG>CAA	p.Q259Q	TRERF1_uc011duq.1_Silent_p.Q259Q|TRERF1_uc003osb.2_Silent_p.Q98Q|TRERF1_uc003osc.2_Silent_p.Q98Q|TRERF1_uc003ose.2_Silent_p.Q259Q	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	259	Gln-rich.				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GTTGCATGTGCTGTGACAGCA	0.582													3	52					0	0	0.004672	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				5	26					0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	11	18894523	18894524	+	IGR	INS	-	T	T			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr11:18894523_18894524insT								PTPN5 (81134 upstream) : MRGPRX1 (60837 downstream)																							TTTATTCCCAGTTTTTTTTTAG	0.401													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	13	19532389	19532389	+	IGR	DEL	T	-	-			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr13:19532389delT								LOC284232 (86280 upstream) : LOC348021 (50010 downstream)																							TTTGGGAGCCTTTTTTTTTTG	0.542													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	22691260	22691260	+	IGR	DEL	T	-	-			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr15:22691260delT								MIR1268 (177980 upstream) : GOLGA8DP (11025 downstream)																							GGTTGCTTCATCTAGGAGAAG	0.473													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	20397388	20397399	+	IGR	DEL	GCCGCCCCCGAT	-	-	rs71728273		TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr17:20397388_20397399delGCCGCCCCCGAT								LGALS9B (26540 upstream) : CCDC144NL (369311 downstream)																							TGCGGCTGGAgccgcccccgatgccgcccccg	0.580													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	18	57429217	57429218	+	IGR	DEL	AG	-	-	rs141641247	by1000genomes	TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr18:57429217_57429218delAG								CCBE1 (64573 upstream) : PMAIP1 (137974 downstream)																							AAAAAAAAAAAGAGGAAGACAG	0.243													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	20	18763091	18763091	+	IGR	DEL	G	-	-			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chr20:18763091delG								DTD1 (18533 upstream) : HSPC072 (5524 downstream)																							TGAGATTTCTGGGCAGACTTG	0.468													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	52858063	52858064	+	IGR	INS	-	A	A			TCGA-GE-A2C6-01A-11D-A17V-08	TCGA-GE-A2C6-10A-01D-A16O-08									Somatic	Phase_I	Capture				Illumina GAIIx	51f6ca4f-fc2a-4c99-830c-e9e09c255e80	394411ff-b0f2-4e4a-b5a3-843a397d00dc	g.chrX:52858063_52858064insA								XAGE5 (10741 upstream) : XAGE3 (33496 downstream)																							actccgtctccaaaaaaaaCAC	0.193													2	4	---	---	---	---					
