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
ZW10	9183	broad.mit.edu	37	11	113644351	113644351	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr11:113644351C>T	uc001poe.2	-	1	75	c.38G>A	c.(37-39)GGG>GAG	p.G13E	ZW10_uc009yyv.2_RNA	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10	13	Interaction with RINT1.|Interaction with ZWINT.				cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TTCCAGCCTCCCGGAGTGTGC	0.642000													23	43	---	---	---	---	0	0	0.000117367	0	0
MLL	4297	broad.mit.edu	37	11	118375798	118375798	+	Missense_Mutation	SNP	A	G	G			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr11:118375798A>G	uc001pta.2	+	27	9205	c.9182A>G	c.(9181-9183)AAT>AGT	p.N3061S	MLL_uc001ptb.2_Missense_Mutation_p.N3064S	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	3061					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		CAGATTTCCAATGCAGCTGTC	0.502000			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								31	126	---	---	---	---	0	0	0.000491102	0	0
C12orf66	144577	broad.mit.edu	37	12	64615867	64615867	+	Missense_Mutation	SNP	A	G	G			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr12:64615867A>G	uc001srw.3	-	1	210	c.151T>C	c.(151-153)TGG>CGG	p.W51R	uc001srx.2_5'Flank|C12orf66_uc009zql.2_Intron	NM_152440	NP_689653	Q96MD2	CL066_HUMAN	hypothetical protein LOC144577	51										ovary(1)	1						AGCGACAGCCAGCTGCCCCCC	0.622000													3	21	---	---	---	---	0	0	6.4e-05	0	0
Unknown	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	G	G			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr14:19857036A>G	uc001vvq.1	-	5		c.494T>C								Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		CTGGATAATAAAGTTCATCTC	0.373000													5	136	---	---	---	---	0	0	1.23904e-05	0	0
LILRP2	79166	broad.mit.edu	37	19	55224692	55224692	+	RNA	SNP	T	C	C	rs17207369	by1000genomes	TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr19:55224692T>C	uc002qgs.1	+	1		c.5092T>C			LILRP2_uc002qgt.1_RNA	NR_003061				Homo sapiens leukocyte immunoglobulin-like receptor pseudogene 2 (LILRP2), non-coding RNA.												0						TGCTTTAGGATTGGCACAGCT	0.542000													2	14	---	---	---	---	0	0	6.4e-05	0	0
RXFP1	59350	broad.mit.edu	37	4	159568291	159568291	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr4:159568291C>T	uc003ipz.2	+	16	1776	c.1694C>T	c.(1693-1695)CCT>CTT	p.P565L	RXFP1_uc011cja.1_Missense_Mutation_p.P460L|RXFP1_uc010iqo.2_Missense_Mutation_p.P517L|RXFP1_uc011cjb.1_Missense_Mutation_p.P463L|RXFP1_uc010iqk.2_Missense_Mutation_p.P433L|RXFP1_uc011cjc.1_Missense_Mutation_p.P484L|RXFP1_uc011cjd.1_Missense_Mutation_p.P484L|RXFP1_uc010iql.2_Missense_Mutation_p.P409L|RXFP1_uc011cje.1_Missense_Mutation_p.P592L|RXFP1_uc010iqm.2_Missense_Mutation_p.P532L|RXFP1_uc011cjf.1_Missense_Mutation_p.P434L|RXFP1_uc010iqn.2_Missense_Mutation_p.P510L	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	565	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		GTATGCTTCCCTCTTCATTCA	0.333000													30	36	---	---	---	---	0	0	0.000147802	0	0
TBCC	6903	broad.mit.edu	37	6	42713803	42713803	+	Silent	SNP	G	A	A			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr6:42713803G>A	uc003osl.2	-	1	82	c.9C>T	c.(7-9)TCC>TCT	p.S3S		NM_003192	NP_003183	Q15814	TBCC_HUMAN	beta-tubulin cofactor C	3					'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|photoreceptor connecting cilium	chaperone binding|GTPase activity				0	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			AGCAACTGACGGACTCCATAT	0.617000													6	52	---	---	---	---	0	0	0.000157383	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	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	0.368000	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				29	38	---	---	---	---	0	0	0.000279167	0	0
FLJ10661	286042	broad.mit.edu	37	8	8094672	8094672	+	RNA	SNP	T	C	C	rs73199790	by1000genomes	TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr8:8094672T>C	uc011kwt.1	+	7		c.901T>C			FLJ10661_uc010lrq.2_RNA|FLJ10661_uc003wsf.3_RNA	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						CCAGAAGCCATTGTGTCACTG	0.602000													3	14	---	---	---	---	0	0	6.4e-05	0	0
Unknown	0	broad.mit.edu	37	1	50865016	50865017	+	IGR	INS	-	T	T			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr1:50865016_50865017insT								ELAVL4 (197476 upstream) : DMRTA2 (18212 downstream)																							TCACTGAGCACttttttttttc	0.203													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	65772734	65772734	+	IGR	DEL	A	-	-			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr17:65772734delA								NOL11 (32468 upstream) : BPTF (49046 downstream)																							actccatctcaaaaaaaaaaa	0.229													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	78950793	78950793	+	IGR	DEL	A	-	-	rs112496455		TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr17:78950793delA								RPTOR (10620 upstream) : CHMP6 (14848 downstream)																							tttgacaattaaaaaaaaaaa	0.129													3	3	---	---	---	---					
C19orf34	255193	broad.mit.edu	37	19	1953966	1953966	+	Frame_Shift_Del	DEL	C	-	-			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr19:1953966delC	uc002lum.2	-	2	526	c.69delG	c.(67-69)AGGfs	p.R23fs	CSNK1G2_uc002lul.3_Intron	NM_152771	NP_689984			chromosome 19 open reading frame 34												0		Ovarian(11;0.000137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGACGGGGCCTTCTCGTGG	0.662													7	105	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	4985367	4985367	+	IGR	DEL	T	-	-			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr8:4985367delT								CSMD1 (133039 upstream) : None (None downstream)																							ctgacgcttcttttttttttt	0.224													4	5	---	---	---	---					
HRCT1	646962	broad.mit.edu	37	9	35906584	35906586	+	In_Frame_Del	DEL	CCA	-	-			TCGA-FY-A3BL-01A-11D-A19J-08	TCGA-FY-A3BL-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	effadd42-bbb3-4ec9-bcd4-80d9e2d09a8d	a8cbca5d-503d-4484-928b-ae5d9a9726a3	g.chr9:35906584_35906586delCCA	uc003zyr.1	+	1	396_398	c.300_302delCCA	c.(298-303)CTCCAC>CTC	p.H105del	LOC158376_uc003zys.1_5'Flank	NM_001039792	NP_001034881	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	105	His-rich.					integral to membrane					0						ctcaccacctccaccaccaccac	0.374													6	12	---	---	---	---					
