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
PGBD2	267002	broad.mit.edu	37	1	249211207	249211207	+	Missense_Mutation	SNP	G	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr1:249211207G>T	uc001ifh.2	+	3	571	c.424G>T	c.(424-426)GTG>TTG	p.V142L	PGBD2_uc001ifg.2_Intron|PGBD2_uc009xhd.2_Missense_Mutation_p.V139L	NM_170725	NP_733843	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	142										ovary(1)	1	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GCTGAGTCCCGTGGGCCTTTT	0.398000													13	35	---	---	---	---	1.99824e-07	2.47401e-07	0.004990	1	0
C10orf18	54906	broad.mit.edu	37	10	5781833	5781833	+	Missense_Mutation	SNP	A	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr10:5781833A>C	uc001iij.2	+	13	2325	c.1700A>C	c.(1699-1701)GAT>GCT	p.D567A	C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	567										ovary(1)|central_nervous_system(1)	2						CCACAAAATGATGTTTTGCTC	0.378000													21	43	---	---	---	---	0	0	0.005443	0	0
TACC2	10579	broad.mit.edu	37	10	123842613	123842613	+	Missense_Mutation	SNP	A	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr10:123842613A>G	uc001lfv.2	+	4	958	c.598A>G	c.(598-600)ATG>GTG	p.M200V	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.M200V|TACC2_uc010qtv.1_Missense_Mutation_p.M200V	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	200						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GTCACCTGGAATGTCGCCAGT	0.582000													17	33	---	---	---	---	0	0	0.001523	0	0
LOC653544	653544	broad.mit.edu	37	10	135491135	135491135	+	Missense_Mutation	SNP	C	T	T	rs139450175	by1000genomes	TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr10:135491135C>T	uc010qvi.1	+	1	857	c.746C>T	c.(745-747)ACG>ATG	p.T249M		NM_001127389	NP_001120861	F5GZ66	F5GZ66_HUMAN	double homeobox, 4-like	249						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GCGTGGGGAACGGGGCTTCCC	0.786000													5	23	---	---	---	---	0	0	0.000978	0	0
CD3D	915	broad.mit.edu	37	11	118209888	118209888	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr11:118209888G>A	uc001pss.1	-	5	642	c.505C>T	c.(505-507)CGG>TGG	p.R169W	CD3D_uc001pst.1_Missense_Mutation_p.R125W	NM_000732	NP_000723	P04234	CD3D_HUMAN	CD3 antigen, delta subunit isoform A precursor	169	Cytoplasmic (Potential).				positive thymic T cell selection|T cell costimulation|T cell receptor signaling pathway	cytoplasm|integral to membrane	protein heterodimerization activity			ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		CACTTGTTCCGAGCCCAGTTT	0.502000													31	112	---	---	---	---	0	0	0.004289	0	0
C15orf63	25764	broad.mit.edu	37	15	44093364	44093364	+	Missense_Mutation	SNP	A	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr15:44093364A>G	uc001ztf.2	+	2	397	c.221A>G	c.(220-222)GAG>GGG	p.E74G	ELL3_uc001zsx.1_5'Flank|C15orf63_uc001ztb.2_Missense_Mutation_p.E120G|SERINC4_uc001ztc.1_5'Flank|SERINC4_uc001ztd.1_5'Flank|SERINC4_uc010bds.1_5'Flank|SERINC4_uc001zte.1_5'Flank|C15orf63_uc001ztg.1_Intron	NM_016400	NP_057484	Q9NX55	HYPK_HUMAN	chromosome 15 open reading frame 63	74	Potential.										0						AGGTCCCGGGAGCAGAAAGCC	0.488000													16	83	---	---	---	---	0	0	0.002299	0	0
CDH11	1009	broad.mit.edu	37	16	64984728	64984728	+	Silent	SNP	G	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr16:64984728G>A	uc002eoi.2	-	12	2270	c.1836C>T	c.(1834-1836)AAC>AAT	p.N612N	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_Silent_p.N612N|CDH11_uc010vin.1_Silent_p.N486N	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	612	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TCAGGCCGGCGTTCAGAATGT	0.632000			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			27	61	---	---	---	---	0	0	0.002445	0	0
LOC651250	651250	broad.mit.edu	37	17	66126418	66126418	+	RNA	SNP	A	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr17:66126418A>G	uc002jgq.2	+	6		c.5541A>G			LOC651250_uc002kit.2_RNA|LOC651250_uc002jgo.1_Intron	NR_027418				Homo sapiens cDNA FLJ33831 fis, clone CTONG2003937.												0						CCTCAATGCTATTTTTAAATT	0.413000													3	178	---	---	---	---	0	0	0.004672	0	0
TXNDC2	84203	broad.mit.edu	37	18	9887095	9887095	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr18:9887095G>A	uc002koi.3	+	2	1068	c.619G>A	c.(619-621)GGT>AGT	p.G207S	TXNDC2_uc010wzq.1_Intron|TXNDC2_uc002koh.3_Missense_Mutation_p.G140S	NM_001098529	NP_001091999	Q86VQ3	TXND2_HUMAN	thioredoxin domain-containing 2 isoform 2	207	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.|7.				cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	cytoplasm	electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity			ovary(1)|pancreas(1)	2						GCCCAAAGAGGGTGACATCCC	0.567000													4	220	---	---	---	---	0	0	0.000248	0	0
LOC644669	644669	broad.mit.edu	37	18	15323276	15323276	+	RNA	SNP	A	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr18:15323276A>T	uc002ktd.1	-	3		c.183T>A				NR_027417				Homo sapiens cDNA FLJ40312 fis, clone TESTI2029880.												0						ATCAACTGCAATTGCATTTGC	0.308000													5	9	---	---	---	---	0	0	0.006214	0	0
POLR2E	5434	broad.mit.edu	37	19	1091806	1091806	+	Silent	SNP	T	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:1091806T>G	uc002lre.3	-	3	410	c.333A>C	c.(331-333)ACA>ACC	p.T111T	POLR2E_uc010xgf.1_RNA	NM_002695	NP_002686	P19388	RPAB1_HUMAN	DNA directed RNA polymerase II polypeptide E	111					interspecies interaction between organisms|mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		TGGCGGAGGGTGTCATGCCCT	0.667000													8	189	---	---	---	---	0	0	0.001523	0	0
CACNA1A	773	broad.mit.edu	37	19	13565980	13565980	+	Missense_Mutation	SNP	C	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:13565980C>T	uc010dze.2	-	2	576	c.340G>A	c.(340-342)GTC>ATC	p.V114I	CACNA1A_uc002mwy.3_Missense_Mutation_p.V114I	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	114	Helical; Name=S1 of repeat I; (Potential).|I.				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	AGTGCGAGGACGATGCAATTC	0.453000													64	185	---	---	---	---	0	0	0.003610	0	0
ITSN2	50618	broad.mit.edu	37	2	24550934	24550934	+	Silent	SNP	G	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:24550934G>T	uc002rfe.2	-	2	276	c.18C>A	c.(16-18)CCC>CCA	p.P6P	ITSN2_uc002rff.2_Silent_p.P6P|ITSN2_uc002rfg.2_Silent_p.P6P|ITSN2_uc010eyd.2_Silent_p.P6P	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	6					endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCATAGCTGTGGGAAACTGAG	0.373000													4	57	---	---	---	---	3.59834e-05	4.15808e-05	0.001168	1	0
TGOLN2	10618	broad.mit.edu	37	2	85554607	85554607	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:85554607T>C	uc010fgd.1	-	2	537	c.248A>G	c.(247-249)AAG>AGG	p.K83R	TGOLN2_uc002soz.2_Missense_Mutation_p.K83R|TGOLN2_uc002spa.2_Intron|TGOLN2_uc002spb.2_Missense_Mutation_p.K83R|TGOLN2_uc002spc.1_Missense_Mutation_p.K83R	NM_006464	NP_006455	O43493	TGON2_HUMAN	trans-golgi network protein 2	83	Extracellular (Potential).|14 X 14 AA tandem repeats.|3.					integral to membrane|nucleus|plasma membrane|trans-Golgi network|transport vesicle	protein binding				0						CGCACCCGACTTGTTGGGGGT	0.602000													6	474	---	---	---	---	0	0	0.008291	0	0
LOC151009	151009	broad.mit.edu	37	2	111144370	111144370	+	5'Flank	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:111144370T>C	uc002tfr.3	-						LIMS3-LOC440895_uc002tft.1_RNA|LOC151009_uc010yxc.1_5'Flank|LOC151009_uc002tfs.3_5'Flank|LOC151009_uc010fjy.2_5'Flank					Homo sapiens cDNA FLJ31522 fis, clone NT2RI2000270.												0						GGCAGCACCATAGTGGCGGCC	0.622000													3	8	---	---	---	---	0	0	0.000248	0	0
TTN	7273	broad.mit.edu	37	2	179402314	179402314	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:179402314T>C	uc010zfg.1	-	304	92140	c.91916A>G	c.(91915-91917)TAT>TGT	p.Y30639C	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Y24334C|TTN_uc010zfi.1_Missense_Mutation_p.Y24267C|TTN_uc010zfj.1_Missense_Mutation_p.Y24142C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31566							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACAGCTCCATAATATTTCTC	0.458000													3	37	---	---	---	---	0	0	0.000248	0	0
COL4A4	1286	broad.mit.edu	37	2	227875182	227875182	+	Missense_Mutation	SNP	C	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:227875182C>G	uc010zlt.1	-	45	5023	c.4369G>C	c.(4369-4371)GGG>CGG	p.G1457R		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1457	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GGGCCAAACCCTTTGGGCCCA	0.552000													6	21	---	---	---	---	0	0	0.001984	0	0
PITX2	5308	broad.mit.edu	37	4	111539506	111539506	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:111539506A>T	uc003iad.2	-	5	1311	c.729T>A	c.(727-729)AAT>AAA	p.N243K	PITX2_uc003iac.2_Missense_Mutation_p.N250K|PITX2_uc003iae.2_Missense_Mutation_p.N197K|PITX2_uc010iml.2_Missense_Mutation_p.N114K|PITX2_uc003iaf.2_Missense_Mutation_p.N243K	NM_153426	NP_700475	Q99697	PITX2_HUMAN	paired-like homeodomain transcription factor 2	243					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		TGTTCAAGTTATTCAGGCTGT	0.582000													28	68	---	---	---	---	0	0	0.006320	0	0
SDHAP3	728609	broad.mit.edu	37	5	1574406	1574406	+	RNA	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr5:1574406T>C	uc011cmd.1	-	3		c.440A>G			SDHAP3_uc011cme.1_RNA					Homo sapiens cDNA FLJ58919 complete cds, moderately similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC1.3.5.1).												0						CTCATCAATCTGCACCTGAGG	0.478000													3	20	---	---	---	---	0	0	0.004672	0	0
IRX2	153572	broad.mit.edu	37	5	2748624	2748624	+	Missense_Mutation	SNP	C	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr5:2748624C>A	uc003jda.2	-	3	1440	c.1198G>T	c.(1198-1200)GCG>TCG	p.A400S	IRX2_uc003jdb.2_Missense_Mutation_p.A400S	NM_001134222	NP_001127694	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	400						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)		TGCAGCGCCGCGTTCAAGTTC	0.706000													40	78	---	---	---	---	5.73435e-26	7.6458e-26	0.003610	1	0
E2F3	1871	broad.mit.edu	37	6	20486987	20486987	+	Missense_Mutation	SNP	G	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:20486987G>T	uc003nda.2	+	5	1279	c.952G>T	c.(952-954)GTG>TTG	p.V318L		NM_001949	NP_001940	O00716	E2F3_HUMAN	E2F transcription factor 3	318	Dimerization (Potential).				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			TGTTATAGTTGTGAAAGCCCC	0.383000													11	39	---	---	---	---	3.27435e-08	4.25666e-08	0.002450	1	0
FAM120B	84498	broad.mit.edu	37	6	170628184	170628184	+	Missense_Mutation	SNP	C	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:170628184C>T	uc003qxp.2	+	2	1814	c.1706C>T	c.(1705-1707)ACC>ATC	p.T569I	FAM120B_uc003qxo.1_Missense_Mutation_p.T569I|FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	569					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		CAACAAGTAACCATGGTTTCA	0.388000													10	27	---	---	---	---	0	0	0.008291	0	0
AGR2	10551	broad.mit.edu	37	7	16839390	16839390	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr7:16839390T>C	uc003str.2	-	5	495	c.308A>G	c.(307-309)CAG>CGG	p.Q103R		NM_006408	NP_006399	O95994	AGR2_HUMAN	anterior gradient 2 homolog precursor	103					mucus secretion	endoplasmic reticulum|extracellular region	protein binding				0	Lung NSC(10;0.0376)|all_lung(11;0.0855)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		GAGGACAAACTGCTCTGCCAA	0.308000													6	18	---	---	---	---	0	0	0.003080	0	0
C7orf47	221908	broad.mit.edu	37	7	100033362	100033362	+	Silent	SNP	G	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr7:100033362G>C	uc003uuy.1	-	3	577	c.480C>G	c.(478-480)CTC>CTG	p.L160L	C7orf47_uc003uux.1_Silent_p.L58L	NM_145030	NP_659467	Q8TAP8	CG047_HUMAN	hypothetical protein LOC221908	160										ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGTCCCGGAAGAGCCGCTTGG	0.632000													3	8	---	---	---	---	0	0	0.000602	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	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				12	38	---	---	---	---	0	0	0.001855	0	0
ECM2	1842	broad.mit.edu	37	9	95277148	95277148	+	Missense_Mutation	SNP	C	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr9:95277148C>A	uc004ash.2	-	4	884	c.819G>T	c.(817-819)GAG>GAT	p.E273D	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ECM2_uc004asf.3_Missense_Mutation_p.E251D|ECM2_uc011lty.1_Missense_Mutation_p.E273D|ECM2_uc004asg.2_Missense_Mutation_p.E251D	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor	273	Poly-Glu.				cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2						cctcctcatcctcctcctcct	0.398000													4	118	---	---	---	---	2.0095e-06	2.37486e-06	0.001984	1	0
PAPPA	5069	broad.mit.edu	37	9	119033660	119033660	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr9:119033660T>C	uc004bjn.2	+	9	3299	c.2918T>C	c.(2917-2919)CTT>CCT	p.L973P	PAPPA_uc011lxp.1_Missense_Mutation_p.L668P|PAPPA_uc011lxq.1_Missense_Mutation_p.L348P	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	973					cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding	p.L973P(1)		ovary(4)|skin(4)|pancreas(1)	9						GGCTGCTCCCTTTTCTGCCGA	0.418000													3	109	---	---	---	---	0	0	0.000602	0	0
TUBBP5	643224	broad.mit.edu	37	9	141070969	141070969	+	Silent	SNP	A	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr9:141070969A>G	uc004com.2	+	4	633	c.372A>G	c.(370-372)GCA>GCG	p.A124A	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						TAGAAAACGCAGATGAGACCT	0.517000													6	65	---	---	---	---	0	0	0.001984	0	0
Unknown	0	broad.mit.edu	37	MT	3898	3898	+	RNA	SNP	T	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chrM:3898T>C	uc004cos.3	+	2		c.2191T>C			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		ACCGAACCCCCTTCGACCTTG	0.502000													42	1	---	---	---	---	0	0	0.003610	0	0
PTCH2	8643	broad.mit.edu	37	1	45288194	45288194	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr1:45288194delG	uc010olf.1	-	22	3517	c.3505delC	c.(3505-3507)CTGfs	p.L1169fs	PTCH2_uc010olg.1_Frame_Shift_Del_p.L867fs	NM_003738	NP_003729	Q9Y6C5	PTC2_HUMAN	patched 2	1169	Cytoplasmic (Potential).				protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)					GCACCAGGCAGGGGGGGTGGG	0.657									Basal_Cell_Nevus_syndrome				7	174	---	---	---	---					
PBXIP1	57326	broad.mit.edu	37	1	154917508	154917510	+	In_Frame_Del	DEL	GGT	-	-	rs143592003		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr1:154917508_154917510delGGT	uc001ffr.2	-	11	2245_2247	c.2186_2188delACC	c.(2185-2190)CACCGG>CGG	p.H729del	PBXIP1_uc001ffs.2_In_Frame_Del_p.H700del|PBXIP1_uc010pep.1_In_Frame_Del_p.H574del	NM_020524	NP_065385	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein	729	His-rich.				cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGTCAGCCCCGGTGGTGGTGGTG	0.640													8	201	---	---	---	---					
PRB2	653247	broad.mit.edu	37	12	11546506	11546508	+	In_Frame_Del	DEL	TTG	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr12:11546506_11546508delTTG	uc010shk.1	-	3	539_541	c.504_506delCAA	c.(502-507)AACAAG>AAG	p.N168del		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACTTCGGGACTTGTTGTCTCCTT	0.596													13	672	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	78029816	78029817	+	IGR	DEL	AG	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr15:78029816_78029817delAG								LINGO1 (41341 upstream) : LOC645752 (176742 downstream)																							agggagaggaagagagagagag	0.040													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	79777769	79777791	+	IGR	DEL	TCCCCTCCCCCTCCTCACCCCAA	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr17:79777769_79777791delTCCCCTCCCCCTCCTCACCCCAA								GCGR (5880 upstream) : FAM195B (2502 downstream)																							ctctcccgcgtcccctccccctcctcaccccaatcccctcccc	0.448													6	9	---	---	---	---					
ECSIT	51295	broad.mit.edu	37	19	11618821	11618821	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:11618821delG	uc002msb.2	-	5	915	c.781delC	c.(781-783)CAGfs	p.Q261fs	ZNF653_uc002mrz.1_5'Flank|ECSIT_uc002msa.1_RNA|ECSIT_uc010dyc.1_Frame_Shift_Del_p.Q261fs|ECSIT_uc010dyd.2_Frame_Shift_Del_p.Q261fs|ECSIT_uc010xma.1_Frame_Shift_Del_p.Q47fs	NM_016581	NP_057665	Q9BQ95	ECSIT_HUMAN	evolutionarily conserved signaling intermediate	261					innate immune response|regulation of oxidoreductase activity	mitochondrion	oxidoreductase activity, acting on NADH or NADPH|protein binding			ovary(1)	1						ATGTGGGGCTGGGGGGGATCT	0.582													7	244	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	17565888	17565888	+	IGR	DEL	C	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:17565888delC								FAM125A (29748 upstream) : NXNL1 (348 downstream)																							GCCTTGGCAACCCCCCCCCAA	0.682													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	23075583	23075584	+	IGR	INS	-	TCC	TCC	rs143938164	by1000genomes	TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:23075583_23075584insTCC								ZNF99 (122799 upstream) : ZNF91 (445835 downstream)																							cctcctcctcttcctcctcctc	0.015													3	4	---	---	---	---					
KCNN4	3783	broad.mit.edu	37	19	44284861	44284861	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:44284861delC	uc002oxl.2	-	1	549	c.153delG	c.(151-153)GGGfs	p.G51fs	KCNN4_uc010eja.1_RNA	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated	51					defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)	TCACCGAGCACCCCCCGAACC	0.383													8	273	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	47511830	47511831	+	IGR	INS	-	TATTGTCCCCTCCTCCTCC	TATTGTCCCCTCCTCCTCC	rs141573875	by1000genomes	TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr19:47511830_47511831insTATTGTCCCCTCCTCCTCC								GRLF1 (3507 upstream) : NPAS1 (11270 downstream)																							gcattttgcagtattgtcccct	0.074													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	26901038	26901038	+	IGR	DEL	T	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:26901038delT								CIB4 (36827 upstream) : KCNK3 (14543 downstream)																							AGGATTCTTCTTTTTTTTTTA	0.284													10	39	---	---	---	---					
ANKRD36	375248	broad.mit.edu	37	2	97847365	97847368	+	Splice_Site	DEL	TAAT	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr2:97847365_97847368delTAAT	uc010yva.1	+	25	2008	c.1764_splice	c.e25+2	p.K588_splice	ANKRD36_uc010fic.2_Splice_Site_p.K307_splice|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Splice_Site|ANKRD36_uc002sxq.1_Splice_Site	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						GCTGAGAAGGTAATTAAAGTCTCA	0.314													4	8	---	---	---	---					
Unknown	0	broad.mit.edu	37	22	49153040	49153042	+	IGR	DEL	AGA	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr22:49153040_49153042delAGA								FAM19A5 (5298 upstream) : C22orf34 (655134 downstream)																							AAggaggaggagaagggaggagg	0.069													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	3	32232268	32232270	+	IGR	DEL	GAA	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr3:32232268_32232270delGAA								GPD1L (22072 upstream) : CMTM8 (47901 downstream)																							tcctacaaatgaaggagGAGGAT	0.394													6	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	3	75599221	75599223	+	IGR	DEL	CCA	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr3:75599221_75599223delCCA								FAM86D (114955 upstream) : MIR1324 (80691 downstream)																							TACCATTTTCccaccaccaccac	0.330													6	13	---	---	---	---					
Unknown	0	broad.mit.edu	37	3	97926696	97926697	+	IGR	INS	-	TATTAATCTTGTCA	TATTAATCTTGTCA	rs150244498		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr3:97926696_97926697insTATTAATCTTGTCA								OR5H15 (38213 upstream) : OR5H6 (56432 downstream)																							GTGCATCCGGCTATGTAGGTGG	0.391													8	14	---	---	---	---					
Unknown	0	broad.mit.edu	37	3	194712128	194712130	+	IGR	DEL	TCC	-	-	rs9838410		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr3:194712128_194712130delTCC								FAM43A (302364 upstream) : C3orf21 (76885 downstream)																							ctcctcctcttcctcctcctcct	0.172													5	2	---	---	---	---					
CRIPAK	285464	broad.mit.edu	37	4	1388441	1388442	+	Frame_Shift_Ins	INS	-	CG	CG	rs144787346	byFrequency	TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:1388441_1388442insCG	uc003gdf.2	+	1	3102_3103	c.142_143insCG	c.(142-144)ATGfs	p.M48fs		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	48	1.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTGCTCACACATGCCCATGTGG	0.644													12	1206	---	---	---	---					
TNIP2	79155	broad.mit.edu	37	4	2757866	2757866	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:2757866delG	uc003gfg.2	-	1	238	c.151delC	c.(151-153)CGCfs	p.R51fs	TNIP2_uc003gff.2_5'Flank|TNIP2_uc003gfh.2_Frame_Shift_Del_p.R51fs	NM_024309	NP_077285	Q8NFZ5	TNIP2_HUMAN	A20-binding inhibitor of NF-kappaB activation 2	51	Potential.					cytosol	protein binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCGGCCAGGCGGGCGCGGAGG	0.761													2	4	---	---	---	---					
GABRA2	2555	broad.mit.edu	37	4	46392073	46392073	+	5'Flank	DEL	G	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:46392073delG	uc003gxc.3	-						GABRA2_uc010igc.2_5'Flank|GABRA2_uc011bzc.1_5'Flank|GABRA2_uc003gxe.2_Intron|GABRA2_uc010igd.1_5'Flank	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2						gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	AGCTGGGGCCGGGGGGGGAAA	0.582													4	2	---	---	---	---					
PCDH10	57575	broad.mit.edu	37	4	134073569	134073571	+	In_Frame_Del	DEL	CTG	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:134073569_134073571delCTG	uc003iha.2	+	1	3100_3102	c.2274_2276delCTG	c.(2272-2277)CTCTGC>CTC	p.C763del	PCDH10_uc003igz.2_In_Frame_Del_p.C763del	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	763	Cys-rich.|Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)		ATTGCTGCCTCTGCTGCTGCTGC	0.581													8	92	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	150916605	150916606	+	IGR	INS	-	G	G	rs151220190	by1000genomes	TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr4:150916605_150916606insG								None (None upstream) : DCLK2 (83474 downstream)																							ggaagggaggagggggaaggga	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	70143981	70143981	+	IGR	DEL	G	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:70143981delG								BAI3 (44579 upstream) : LMBRD1 (241770 downstream)																							gggagggggagggggagggga	0.060													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	160132772	160132789	+	IGR	DEL	CACTCACATTGCTCTGAT	-	-	rs62437331		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr6:160132772_160132789delCACTCACATTGCTCTGAT								SOD2 (18419 upstream) : WTAP (15340 downstream)																							ccacaaccaccactcacattgctctgatcaccataacc	0.000													22	651	---	---	---	---					
SFRP1	6422	broad.mit.edu	37	8	41166638	41166640	+	In_Frame_Del	DEL	GCT	-	-	rs3055861		TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr8:41166638_41166640delGCT	uc003xnt.2	-	1	341_343	c.39_41delAGC	c.(37-42)GCAGCC>GCC	p.13_14AA>A		NM_003012	NP_003003	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1 precursor	13_14				Missing (in Ref. 1 and 3).	brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CACGCCCAGGGCTGCCCCGCGGC	0.764													7	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	113146178	113146179	+	IGR	DEL	AG	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr8:113146178_113146179delAG								None (None upstream) : CSMD3 (88982 downstream)																							agagacagaaagagagagagag	0.243													5	8	---	---	---	---					
TMEM2	23670	broad.mit.edu	37	9	74383829	74383830	+	5'Flank	INS	-	G	G			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chr9:74383829_74383830insG	uc011lsa.1	-						TMEM2_uc010mos.2_5'Flank|TMEM2_uc011lsb.1_5'Flank	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ggcgggcgggcgggcggTGGAG	0.500													2	4	---	---	---	---					
PLCXD1	55344	broad.mit.edu	37	X	196983	196984	+	5'Flank	INS	-	C	C			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chrX:196983_196984insC	uc004cpc.2	+						PLCXD1_uc011mgx.1_Intron	NM_018390	NP_060860	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid metabolic process		phospholipase C activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				gcagggggaagggaggccgtgc	0.248													3	5	---	---	---	---					
USP9X	8239	broad.mit.edu	37	X	41043681	41043682	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chrX:41043681_41043682insA	uc004dfb.2	+	23	3944_3945	c.3311_3312insA	c.(3310-3312)GCAfs	p.A1104fs	USP9X_uc004dfc.2_Frame_Shift_Ins_p.A1104fs	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	1104					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						CCTGCTGGTGCACCTCTGGCTG	0.401													20	41	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	48307150	48307150	+	IGR	DEL	T	-	-			TCGA-EL-A3MY-01A-11D-A21A-08	TCGA-EL-A3MY-11A-12D-A21A-08									Somatic	Phase_I	Capture				Illumina GAIIx	a9c29edd-2ef1-46ef-93c6-796cf0332a2b	8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3	g.chrX:48307150delT								SSX4 (54365 upstream) : SLC38A5 (9778 downstream)																							ccggtcTGGATTTTTTTTTTT	0.209													6	8	---	---	---	---					
