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	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	filter
MTHFR	4524	broad.mit.edu	37	1	11863600	11863600	+	Intron	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11863600G>T	uc001atc.1	-						MTHFR_uc001atb.1_5'Flank|MTHFR_uc001atd.1_RNA|MTHFR_uc009vnd.1_Intron|CLCN6_uc009vne.1_5'Flank|CLCN6_uc009vnf.1_5'Flank|CLCN6_uc009vng.1_5'Flank|CLCN6_uc009vnh.1_5'Flank|CLCN6_uc001ate.3_5'Flank|CLCN6_uc010oat.1_5'Flank|CLCN6_uc010oau.1_5'Flank	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase						blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	AGAGTGCGTGGGGAGGGAACA	0.642													3	14	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918653C>T	uc009vos.1	-	6	853	c.-35_splice	c.e6+1		NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418													5	80	---	---	---	---	PASS
C8A	731	broad.mit.edu	37	1	57351710	57351710	+	Silent	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57351710A>T	uc001cyo.2	+	7	1098	c.966A>T	c.(964-966)CCA>CCT	p.P322P		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	322	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3						TGGAGCTTCCAGATCAGTACA	0.413													12	89	---	---	---	---	PASS
CTH	1491	broad.mit.edu	37	1	70896063	70896063	+	Missense_Mutation	SNP	G	A	A	rs147044875		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70896063G>A	uc001dfd.2	+	7	854	c.710G>A	c.(709-711)CGT>CAT	p.R237H	CTH_uc009wbl.1_RNA|CTH_uc001dfe.2_Missense_Mutation_p.R193H|CTH_uc010oqq.1_Missense_Mutation_p.R205H	NM_001902	NP_001893	P32929	CGL_HUMAN	cystathionase isoform 1	237					cysteine biosynthetic process|hydrogen sulfide biosynthetic process|protein homotetramerization|protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	cytoplasm|nucleus	cystathionine gamma-lyase activity|L-cysteine desulfhydrase activity|pyridoxal phosphate binding			lung(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)	AATAGACTTCGTTTCTTGCAA	0.318													11	51	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	145074882	145074882	+	3'UTR	SNP	G	T	T	rs3845334		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145074882G>T	uc001emk.2	-	2					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q5VU43	MYOME_HUMAN	SubName: Full=Phosphodiesterase 4D interacting protein;						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TAAAAAGCCTGCAGCACAATC	0.303			T	PDGFRB	MPD								8	25	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155452083	155452083	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155452083G>T	uc009wqq.2	-	3	1058	c.578C>A	c.(577-579)CCA>CAA	p.P193Q	ASH1L_uc001fkt.2_Missense_Mutation_p.P193Q|ASH1L_uc009wqr.1_Missense_Mutation_p.P193Q	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	193					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AAGAGTAGATGGCGTTGCATT	0.423													6	228	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171556219	171556219	+	Silent	SNP	T	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171556219T>A	uc010pmg.1	+	31	8087	c.7821T>A	c.(7819-7821)CCT>CCA	p.P2607P	BAT2L2_uc010pmh.1_Silent_p.P1519P|BAT2L2_uc010pmi.1_Silent_p.P444P|BAT2L2_uc010pmj.1_Silent_p.P139P	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	2607	Gln-rich.						protein C-terminus binding				0						TTGCTTTGCCTCAGACTCTTC	0.463													6	16	---	---	---	---	PASS
IVNS1ABP	10625	broad.mit.edu	37	1	185268681	185268681	+	Intron	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185268681A>T	uc001grl.2	-						IVNS1ABP_uc001gri.2_Intron|IVNS1ABP_uc001grj.2_Intron|IVNS1ABP_uc009wyj.2_Intron|IVNS1ABP_uc009wyk.2_Intron|IVNS1ABP_uc001grm.2_3'UTR	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein						interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						TAGAAAATATATTTCTAAAGG	0.249													6	17	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208391298	208391298	+	5'UTR	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208391298C>T	uc001hgz.2	-	2					PLXNA2_uc001hha.3_Silent_p.R44R	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGAGACGGCTCCTGTGTGTGC	0.617													7	19	---	---	---	---	PASS
C1orf31	388753	broad.mit.edu	37	1	234509989	234509989	+	Nonsense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234509989G>T	uc001hwc.2	+	2	172	c.136G>T	c.(136-138)GGA>TGA	p.G46*	C1orf31_uc001hwb.2_Translation_Start_Site	NM_001012985	NP_001013003	Q5JTJ3	CA031_HUMAN	hypothetical protein LOC388753	46						mitochondrion	cytochrome-c oxidase activity				0	Ovarian(103;0.0339)	all_cancers(173;0.241)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			CATCGCAGTAGGAATGGCAGC	0.438													25	76	---	---	---	---	PASS
ITGB1BP1	9270	broad.mit.edu	37	2	9552282	9552282	+	Intron	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9552282C>T	uc002qzj.2	-						ITGB1BP1_uc002qzk.2_Intron|ITGB1BP1_uc002qzl.2_RNA|ITGB1BP1_uc002qzm.2_Intron|ITGB1BP1_uc010yiy.1_Intron|ITGB1BP1_uc002qzn.1_Intron	NM_004763	NP_004754	O14713	ITBP1_HUMAN	integrin cytoplasmic domain-associated protein 1						cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)		GGACTTCAGTCGAGAGCAAGC	0.557													3	14	---	---	---	---	PASS
SPRED2	200734	broad.mit.edu	37	2	65540551	65540551	+	3'UTR	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65540551A>G	uc002sdr.3	-	6					SPRED2_uc010fcw.2_3'UTR	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2						inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3						CTTGGAGTGGAAGGGAGCGGG	0.632													10	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89987066	89987066	+	Intron	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89987066G>T	uc010fhm.2	+						uc002stn.1_RNA					Parts of antibodies, mostly variable regions.																		TGCATGCAAAGTATACAGCTT	0.537													7	108	---	---	---	---	PASS
MAP4K4	9448	broad.mit.edu	37	2	102486844	102486844	+	Silent	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102486844C>G	uc002tbg.2	+	21	2539	c.2484C>G	c.(2482-2484)ACC>ACG	p.T828T	MAP4K4_uc002tbc.2_Silent_p.T909T|MAP4K4_uc002tbd.2_Silent_p.T801T|MAP4K4_uc002tbe.2_Silent_p.T747T|MAP4K4_uc002tbf.2_Silent_p.T798T|MAP4K4_uc010yvy.1_Silent_p.T824T|MAP4K4_uc002tbh.2_Silent_p.T746T|MAP4K4_uc002tbi.2_Silent_p.T631T|MAP4K4_uc010yvz.1_Silent_p.T804T|MAP4K4_uc002tbk.2_Silent_p.T283T|MAP4K4_uc002tbl.2_Silent_p.T14T	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase	828					intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						CGGCCATGACCCCATCCAAGG	0.483													4	35	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145157472	145157472	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145157472C>G	uc002tvu.2	-	8	1762	c.1282G>C	c.(1282-1284)GTT>CTT	p.V428L	ZEB2_uc002tvv.2_Missense_Mutation_p.V422L|ZEB2_uc010zbm.1_Missense_Mutation_p.V399L|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Missense_Mutation_p.V457L	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	428						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		GATGGATGAACTCCTAAAGGG	0.458													28	72	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179422748	179422748	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179422748G>C	uc010zfg.1	-	277	79853	c.79629C>G	c.(79627-79629)GAC>GAG	p.D26543E	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.D20238E|TTN_uc010zfi.1_Missense_Mutation_p.D20171E|TTN_uc010zfj.1_Missense_Mutation_p.D20046E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27470							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)			ATCTCCCAGCGTCAGCTGTAA	0.458													52	163	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179439235	179439235	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179439235G>T	uc010zfg.1	-	275	64144	c.63920C>A	c.(63919-63921)ACT>AAT	p.T21307N	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T15002N|TTN_uc010zfi.1_Missense_Mutation_p.T14935N|TTN_uc010zfj.1_Missense_Mutation_p.T14810N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22234							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)			TTTGCTCACAGTCTGCCAGAG	0.423													84	254	---	---	---	---	PASS
ANKAR	150709	broad.mit.edu	37	2	190608058	190608058	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190608058C>T	uc002uqw.1	+	20	3655	c.3655C>T	c.(3655-3657)CGC>TGC	p.R1219C	ANKAR_uc002uqu.2_RNA|ANKAR_uc002uqx.1_RNA|ANKAR_uc002uqy.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	1290						integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			AAATGCTTTCCGCATCCTATT	0.358													4	74	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225342980	225342980	+	Silent	SNP	T	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225342980T>C	uc002vny.2	-	15	2496	c.2112A>G	c.(2110-2112)GAA>GAG	p.E704E	CUL3_uc010zls.1_Silent_p.E638E|CUL3_uc010fwy.1_Silent_p.E710E	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	704					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CTATAGCAGCTTCTATCTCAT	0.403													17	92	---	---	---	---	PASS
ANO7	50636	broad.mit.edu	37	2	242127987	242127987	+	5'UTR	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242127987C>A	uc002wax.2	+	1					ANO7_uc002waw.2_5'UTR	NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long							cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3						GGGCACCTCCCCTGCCTGCTT	0.647													3	26	---	---	---	---	PASS
OXSM	54995	broad.mit.edu	37	3	25833097	25833097	+	Missense_Mutation	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25833097T>G	uc003cdn.2	+	2	693	c.586T>G	c.(586-588)TAT>GAT	p.Y196D	NGLY1_uc011awo.1_5'Flank|OXSM_uc011awp.1_Intron|OXSM_uc010hfh.2_Missense_Mutation_p.Y196D	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	196					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2						CAGCATTCGATATAAACTCAA	0.433													3	84	---	---	---	---	PASS
OXSM	54995	broad.mit.edu	37	3	25835880	25835880	+	Silent	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25835880T>G	uc003cdn.2	+	3	1382	c.1275T>G	c.(1273-1275)GTT>GTG	p.V425V	OXSM_uc011awp.1_Silent_p.V150V|OXSM_uc010hfh.2_Silent_p.V342V	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	425					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2						TCAACTATGTTCCACTAAAGG	0.393													46	60	---	---	---	---	PASS
CTNNB1	1499	broad.mit.edu	37	3	41268761	41268761	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41268761C>A	uc010hia.1	+	8	1155	c.999C>A	c.(997-999)TAC>TAA	p.Y333*	CTNNB1_uc003ckp.2_Nonsense_Mutation_p.Y333*|CTNNB1_uc003ckq.2_Nonsense_Mutation_p.Y333*|CTNNB1_uc003ckr.2_Nonsense_Mutation_p.Y333*|CTNNB1_uc011azf.1_Nonsense_Mutation_p.Y326*|CTNNB1_uc011azg.1_Nonsense_Mutation_p.Y261*|uc010hib.1_5'Flank	NM_001904	NP_001895	P35222	CTNB1_HUMAN	beta-catenin	333	ARM 5.				adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding		CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)	CCTATACTTACGAAAAACTAC	0.383		15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				3	93	---	---	---	---	PASS
USP4	7375	broad.mit.edu	37	3	49337921	49337921	+	Silent	SNP	G	A	A	rs142071789		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49337921G>A	uc003cwq.2	-	11	1570	c.1491C>T	c.(1489-1491)GAC>GAT	p.D497D	USP4_uc003cwo.2_Silent_p.D209D|USP4_uc003cwp.2_Silent_p.D227D|USP4_uc003cwr.2_Silent_p.D450D	NM_003363	NP_003354	Q13107	UBP4_HUMAN	ubiquitin specific protease 4 isoform a	497					negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		TGCAGTGAGGGTCAGCAGGAA	0.522													12	30	---	---	---	---	PASS
MST1	4485	broad.mit.edu	37	3	49724902	49724902	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49724902C>A	uc003cxg.2	-	4	437	c.365G>T	c.(364-366)CGG>CTG	p.R122L	MST1_uc011bcs.1_Missense_Mutation_p.R122L|MST1_uc010hkx.2_Missense_Mutation_p.R43L|MST1_uc011bct.1_Missense_Mutation_p.R122L|MST1_uc011bcu.1_Intron|RNF123_uc003cxh.2_5'Flank	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	108					proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GATGCAGGTCCGTACGTAGTC	0.597													3	82	---	---	---	---	PASS
DUSP7	1849	broad.mit.edu	37	3	52084943	52084943	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52084943C>T	uc003dct.2	-	3	1227	c.1148G>A	c.(1147-1149)CGG>CAG	p.R383Q		NM_001947	NP_001938	Q16829	DUS7_HUMAN	dual specificity phosphatase 7	383					inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein binding|protein tyrosine phosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCCCAGCGTCCGCTCAAAGTC	0.552													3	51	---	---	---	---	PASS
FLNB	2317	broad.mit.edu	37	3	58128391	58128391	+	Silent	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58128391C>A	uc003djj.2	+	31	5361	c.5196C>A	c.(5194-5196)GCC>GCA	p.A1732A	FLNB_uc010hne.2_Silent_p.A1763A|FLNB_uc003djk.2_Silent_p.A1721A|FLNB_uc010hnf.2_Silent_p.A1708A|FLNB_uc003djl.2_Silent_p.A1552A|FLNB_uc003djm.2_Silent_p.A1539A	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1732	Filamin 16.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		CCGAAGAGGCCTATGTCCCAG	0.512													3	46	---	---	---	---	PASS
FILIP1L	11259	broad.mit.edu	37	3	99568696	99568696	+	Silent	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99568696A>G	uc003dtm.2	-	5	2287	c.1824T>C	c.(1822-1824)AAT>AAC	p.N608N	C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Silent_p.N608N|FILIP1L_uc010hpf.2_Silent_p.N184N|FILIP1L_uc010hpg.2_Silent_p.N368N|FILIP1L_uc003dtn.2_Silent_p.N368N|FILIP1L_uc003dtp.1_Silent_p.N368N	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1	608	Potential.					cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						CAGAGTCTTGATTTAATTTGT	0.343													39	158	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121208546	121208546	+	Missense_Mutation	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121208546A>T	uc003eee.3	-	16	3361	c.3232T>A	c.(3232-3234)TGT>AGT	p.C1078S	POLQ_uc003eed.2_Missense_Mutation_p.C250S	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1078					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		GGGTCTTCACAAAGACTAGGA	0.398								DNA_polymerases_(catalytic_subunits)					26	116	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179501956	179501956	+	3'UTR	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179501956G>A	uc003fkh.2	+	21						NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TTGGCGAAAAGAAGCCATACG	0.358													10	92	---	---	---	---	PASS
GABRG1	2565	broad.mit.edu	37	4	46043110	46043110	+	Silent	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46043110C>T	uc003gxb.2	-	9	1445	c.1293G>A	c.(1291-1293)AGG>AGA	p.R431R		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	431	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)		GTATGTGTATCCTTCCTTCCC	0.413													21	87	---	---	---	---	PASS
TEC	7006	broad.mit.edu	37	4	48170607	48170607	+	Missense_Mutation	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48170607T>G	uc003gxz.2	-	6	582	c.491A>C	c.(490-492)AAG>ACG	p.K164T		NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase	164					intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						ACCTACCTTCTTTGTTTCTGG	0.323													22	78	---	---	---	---	PASS
SPINK2	6691	broad.mit.edu	37	4	57677912	57677912	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57677912G>C	uc003hcg.1	-	3	213	c.148C>G	c.(148-150)CCT>GCT	p.P50A		NM_021114	NP_066937	P20155	ISK2_HUMAN	serine protease inhibitor, Kazal type 2	50	Kazal-like.					extracellular region	serine-type endopeptidase inhibitor activity				0	Glioma(25;0.08)|all_neural(26;0.181)					CCACACACAGGGTTAAAGTGT	0.403													26	106	---	---	---	---	PASS
SDHA	6389	broad.mit.edu	37	5	256592	256592	+	3'UTR	SNP	T	C	C	rs113703363		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:256592T>C	uc003jao.3	+	15					SDHA_uc011clw.1_3'UTR|SDHA_uc003jap.3_3'UTR|SDHA_uc003jaq.3_3'UTR|SDHA_uc003jar.3_3'UTR	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	TAATAGCTCATGCATGTGTCC	0.488									Familial_Paragangliomas				5	37	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33637849	33637849	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33637849G>C	uc003jia.1	-	12	1884	c.1721C>G	c.(1720-1722)CCA>CGA	p.P574R	ADAMTS12_uc010iuq.1_Missense_Mutation_p.P574R	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	574	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TCCAAACTTTGGCCTGCAAAT	0.463										HNSCC(64;0.19)			17	45	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65350483	65350483	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65350483G>A	uc003juk.1	+	21	3645	c.3337G>A	c.(3337-3339)GCG>ACG	p.A1113T	ERBB2IP_uc003jui.1_Missense_Mutation_p.A1113T|ERBB2IP_uc003juj.1_Missense_Mutation_p.A1113T|ERBB2IP_uc011cqx.1_Missense_Mutation_p.A1113T|ERBB2IP_uc011cqy.1_Missense_Mutation_p.A1113T|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Missense_Mutation_p.A1109T|ERBB2IP_uc003jul.1_Missense_Mutation_p.A1109T	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	1113					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GTTCCACTCAGCGGGAAGAAC	0.493													14	49	---	---	---	---	PASS
SERINC5	256987	broad.mit.edu	37	5	79473191	79473191	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79473191C>G	uc003kgj.2	-	4	532	c.403G>C	c.(403-405)GGG>CGG	p.G135R	SERINC5_uc003kgk.2_Missense_Mutation_p.G135R|SERINC5_uc003kgl.2_RNA|SERINC5_uc003kgm.2_Missense_Mutation_p.G135R|SERINC5_uc011ctj.1_Missense_Mutation_p.G135R	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1	135	Helical; (Potential).				phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		CACATGGCCCCCAACAGCAGA	0.403													19	56	---	---	---	---	PASS
CSNK1A1	1452	broad.mit.edu	37	5	148904678	148904678	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148904678C>A	uc003lqx.1	-	3	767	c.287G>T	c.(286-288)AGC>ATC	p.S96I	CSNK1A1_uc011dcc.1_Missense_Mutation_p.S7I|CSNK1A1_uc003lqv.1_Missense_Mutation_p.S7I|CSNK1A1_uc003lqw.1_Missense_Mutation_p.S96I|CSNK1A1_uc003lqy.1_Missense_Mutation_p.S96I|CSNK1A1_uc010jha.1_Missense_Mutation_p.S96I	NM_001892	NP_001883	P48729	KC1A_HUMAN	casein kinase 1, alpha 1 isoform 2	96	Protein kinase.				cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GTCTTCGAGGCTAGGTCCCAG	0.363													12	36	---	---	---	---	PASS
SLC36A1	206358	broad.mit.edu	37	5	150856274	150856274	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150856274G>A	uc003luc.2	+	9	1163	c.946G>A	c.(946-948)GCT>ACT	p.A316T	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.A316T|SLC36A1_uc010jhw.1_Missense_Mutation_p.A316T	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	316	Extracellular (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	GCAATTTGGAGCTAATATCCA	0.512													18	70	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150922954	150922954	+	Missense_Mutation	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150922954T>G	uc003lue.3	-	9	7747	c.7734A>C	c.(7732-7734)GAA>GAC	p.E2578D	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2578	Extracellular (Potential).|Cadherin 22.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTTGTCATTTTCATCTGTGA	0.463													7	291	---	---	---	---	PASS
ADAMTS2	9509	broad.mit.edu	37	5	178557016	178557016	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178557016C>T	uc003mjw.2	-	16	2374	c.2374G>A	c.(2374-2376)GGC>AGC	p.G792S		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	792	Spacer.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		CACTCCACGCCCATGGCAATG	0.572													40	54	---	---	---	---	PASS
GFOD1	54438	broad.mit.edu	37	6	13365468	13365468	+	Missense_Mutation	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13365468A>G	uc003nat.1	-	2	1345	c.680T>C	c.(679-681)CTG>CCG	p.L227P	GFOD1_uc003nas.1_Missense_Mutation_p.L124P	NM_018988	NP_061861	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain	227						extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			CCCGCCCTCCAGCACCATCTG	0.617													12	59	---	---	---	---	PASS
CDC40	51362	broad.mit.edu	37	6	110501714	110501714	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110501714G>A	uc003pua.2	+	1	91	c.67G>A	c.(67-69)GAC>AAC	p.D23N	WASF1_uc003ptv.1_5'Flank|WASF1_uc003ptw.1_5'Flank|WASF1_uc003ptx.1_5'Flank|WASF1_uc003pty.1_5'Flank|WASF1_uc003ptz.1_5'Flank	NM_015891	NP_056975	O60508	PRP17_HUMAN	cell division cycle 40 homolog	23					mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		ATCGGACTCGGACAGTGAGAG	0.592													16	48	---	---	---	---	PASS
AKAP12	9590	broad.mit.edu	37	6	151671390	151671390	+	Missense_Mutation	SNP	C	A	A	rs143476871		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151671390C>A	uc011eep.1	+	4	2104	c.1864C>A	c.(1864-1866)CGT>AGT	p.R622S	AKAP12_uc003qoe.2_Missense_Mutation_p.R622S|AKAP12_uc003qof.2_Missense_Mutation_p.R524S|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Missense_Mutation_p.R517S	NM_005100	NP_005091	Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12 isoform 1	622	AKAP 1.				G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GCCCAAGAAGCGTGTTAGACG	0.498													12	44	---	---	---	---	PASS
SYTL3	94120	broad.mit.edu	37	6	159183159	159183159	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159183159C>A	uc003qrp.2	+	15	1710	c.1466C>A	c.(1465-1467)GCC>GAC	p.A489D	SYTL3_uc011efp.1_Missense_Mutation_p.A489D|SYTL3_uc003qro.2_Missense_Mutation_p.A421D|SYTL3_uc003qrq.2_Missense_Mutation_p.A421D|SYTL3_uc003qrr.2_Missense_Mutation_p.A489D|SYTL3_uc003qrs.2_Missense_Mutation_p.A421D|SYTL3_uc011efq.1_Missense_Mutation_p.A215D	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	489	C2 2.				intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		GTGCTAGGAGCCAAGAATTTA	0.423													5	81	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1523722	1523722	+	Missense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1523722C>A	uc003skn.2	-	25	3447	c.3346G>T	c.(3346-3348)GTG>TTG	p.V1116L	INTS1_uc003skp.1_Missense_Mutation_p.V463L	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	1116					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCGCTCAGCACGGCGTCCGAC	0.657													8	62	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57187759	57187759	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57187759G>T	uc010kzo.2	-	5	1634	c.1363C>A	c.(1363-1365)CAC>AAC	p.H455N		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	455	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			ATTCTCTTGTGGTCAGTGAGG	0.433													8	145	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65425748	65425748	+	3'UTR	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65425748C>T	uc003tun.2	-	12					GUSB_uc011kdt.1_3'UTR	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						GTGTTCCCTGCTAGAATAGAT	0.453													12	28	---	---	---	---	PASS
SERPINE1	5054	broad.mit.edu	37	7	100780229	100780229	+	Intron	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100780229T>G	uc003uxt.2	+						SERPINE1_uc011kkj.1_Intron|SERPINE1_uc003uxu.1_3'UTR	NM_000602	NP_000593	P05121	PAI1_HUMAN	plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)	GGGGTGGGGGTGGTGCCAGTG	0.348													10	17	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106522568	106522568	+	Nonsense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106522568C>T	uc003vdv.3	+	7	2630	c.2545C>T	c.(2545-2547)CGA>TGA	p.R849*	PIK3CG_uc003vdu.2_Nonsense_Mutation_p.R849*|PIK3CG_uc003vdw.2_Nonsense_Mutation_p.R849*	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	849	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						CCAGATTCTACGAATCATGGA	0.323													5	67	---	---	---	---	PASS
GPR85	54329	broad.mit.edu	37	7	112724827	112724827	+	Translation_Start_Site	SNP	T	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112724827T>C	uc010ljv.2	-	2	467	c.-50A>G	c.(-52--48)ATATC>ATGTC		GPR85_uc003vgp.1_Translation_Start_Site|GPR85_uc003vgq.2_Translation_Start_Site|GPR85_uc010ljw.1_Translation_Start_Site	NM_001146266	NP_001139738	P60893	GPR85_HUMAN	G protein-coupled receptor 85							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)	2						ATGATCTAGATATAAGAACAA	0.393													5	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142028321	142028321	+	Intron	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142028321G>C	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc003vxl.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		TGCAGGTCCAGTGAATGCTGG	0.527													18	116	---	---	---	---	PASS
UBQLN1	29979	broad.mit.edu	37	9	86279973	86279973	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86279973C>T	uc004amv.2	-	9	1994	c.1420G>A	c.(1420-1422)GCA>ACA	p.A474T	UBQLN1_uc004amw.2_Missense_Mutation_p.A446T	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1	474					apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						GCTTCCGTTGCTAATGTCTGT	0.423													24	71	---	---	---	---	PASS
NOL8	55035	broad.mit.edu	37	9	95062258	95062258	+	Silent	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95062258G>C	uc004arv.2	-	14	3553	c.3216C>G	c.(3214-3216)GTC>GTG	p.V1072V	NOL8_uc010mqw.2_RNA|NOL8_uc004arw.2_Silent_p.V304V|NOL8_uc011ltw.1_Silent_p.V1004V	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	nucleolar protein 8	1072					DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1						CTTCCTGCCAGACAATCTTTC	0.408													54	216	---	---	---	---	PASS
BAAT	570	broad.mit.edu	37	9	104130484	104130484	+	Missense_Mutation	SNP	T	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104130484T>A	uc010mtd.2	-	3	696	c.587A>T	c.(586-588)TAT>TTT	p.Y196F	BAAT_uc004bbd.3_Missense_Mutation_p.Y196F	NM_001127610	NP_001121082	Q14032	BAAT_HUMAN	bile acid Coenzyme A: amino acid	196					acyl-CoA metabolic process|bile acid and bile salt transport|bile acid biosynthetic process|digestion|fatty acid metabolic process|glycine metabolic process	cytosol|peroxisomal matrix	carboxylesterase activity|glycine N-choloyltransferase activity|N-acyltransferase activity|palmitoyl-CoA hydrolase activity			ovary(1)|lung(1)|skin(1)	3		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	CAGGTCTTCATAGTTATGGTA	0.473													27	73	---	---	---	---	PASS
STRBP	55342	broad.mit.edu	37	9	125895225	125895225	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125895225G>T	uc004bns.2	-	17	2226	c.1796C>A	c.(1795-1797)GCT>GAT	p.A599D	STRBP_uc004bnt.2_Missense_Mutation_p.A417D|STRBP_uc004bnu.2_Missense_Mutation_p.A585D|STRBP_uc004bnv.2_Missense_Mutation_p.A599D|STRBP_uc004bnr.2_Missense_Mutation_p.A158D	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	599					multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2						TGCAGACACAGCTGTATTCAC	0.448													9	110	---	---	---	---	PASS
SCAI	286205	broad.mit.edu	37	9	127789180	127789180	+	Silent	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127789180T>G	uc004bpe.2	-	6	504	c.423A>C	c.(421-423)ACA>ACC	p.T141T	SCAI_uc004bpd.2_Silent_p.T164T|SCAI_uc010mwu.2_RNA	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2	141	Required for interaction with MKL1 (By similarity).|Necessary to inhibit MKL1-induced SRF transcriptional activity (By similarity).				negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						TGGTTTCCGATGTGCGTAAGC	0.358													26	69	---	---	---	---	PASS
UBE2D1	7321	broad.mit.edu	37	10	60124536	60124536	+	Silent	SNP	T	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60124536T>A	uc001jke.1	+	5	427	c.204T>A	c.(202-204)GCT>GCA	p.A68A		NM_003338	NP_003329	P51668	UB2D1_HUMAN	ubiquitin-conjugating enzyme E2D 1	68					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|BMP signaling pathway|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination|transforming growth factor beta receptor signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity			skin(2)	2						TTTAGATTGCTTTCACAACAA	0.323													16	54	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	61835232	61835232	+	Missense_Mutation	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61835232A>G	uc001jky.2	-	37	5599	c.5407T>C	c.(5407-5409)TCC>CCC	p.S1803P	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1803	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						GACCCAAGGGATGTATAGAGT	0.438													45	116	---	---	---	---	PASS
CYP2E1	1571	broad.mit.edu	37	10	135347393	135347393	+	Missense_Mutation	SNP	A	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135347393A>C	uc001lnj.1	+	6	992	c.959A>C	c.(958-960)GAG>GCG	p.E320A	CYP2E1_uc001lnk.1_Missense_Mutation_p.E183A|CYP2E1_uc009ybl.1_Missense_Mutation_p.E121A|CYP2E1_uc009ybm.1_Intron|CYP2E1_uc001lnl.1_Missense_Mutation_p.E121A	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	320					drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)	AAATACCCTGAGATTGAAGGT	0.542									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				20	55	---	---	---	---	PASS
NUP98	4928	broad.mit.edu	37	11	3797242	3797242	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3797242G>A	uc001lyh.2	-	5	656	c.365C>T	c.(364-366)ACC>ATC	p.T122I	NUP98_uc001lyi.2_Missense_Mutation_p.T122I|NUP98_uc001lyj.1_Missense_Mutation_p.T122I|NUP98_uc001lyk.1_Missense_Mutation_p.T122I|NUP98_uc010qxv.1_Missense_Mutation_p.T85I	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	122	Gly/Thr-rich.				carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		GCTAGTACTGGTTCCAAAATC	0.398			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								54	144	---	---	---	---	PASS
SOX6	55553	broad.mit.edu	37	11	16340173	16340173	+	Silent	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16340173G>T	uc001mme.2	-	3	336	c.303C>A	c.(301-303)TCC>TCA	p.S101S	SOX6_uc001mmd.2_Silent_p.S91S|SOX6_uc001mmf.2_Silent_p.S88S|SOX6_uc001mmg.2_Silent_p.S88S|SOX6_uc001mmh.1_RNA|SOX6_uc009ygs.2_RNA|SOX6_uc001mmi.3_Silent_p.S88S|SOX6_uc001mmj.2_Silent_p.S88S	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	88					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						AGGAATATAGGGAACATAACT	0.378													4	154	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	55062928	55062928	+	RNA	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55062928A>T	uc001nhl.1	-	3		c.707T>A								Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit20-11-30-F.																		CCCCATGGTCAGTTCGTACTA	0.428													3	38	---	---	---	---	PASS
P2RX3	5024	broad.mit.edu	37	11	57117325	57117325	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57117325G>A	uc001nju.2	+	7	734	c.658G>A	c.(658-660)GAC>AAC	p.D220N		NM_002559	NP_002550	P56373	P2RX3_HUMAN	purinergic receptor P2X3	220	Extracellular (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0						GCGGGTAGGGGACGTGGTCAA	0.612											OREG0020966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	46	---	---	---	---	PASS
ALDH3B1	221	broad.mit.edu	37	11	67789230	67789230	+	Missense_Mutation	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67789230C>G	uc010rpy.1	+	8	955	c.839C>G	c.(838-840)CCA>CGA	p.P280R	ALDH3B1_uc001omz.2_Missense_Mutation_p.P280R|ALDH3B1_uc001ona.2_Missense_Mutation_p.P243R|ALDH3B1_uc001onb.2_RNA	NM_001161473	NP_001154945	P43353	AL3B1_HUMAN	aldehyde dehydrogenase 3B1 isoform a	280					alcohol metabolic process|cellular aldehyde metabolic process|lipid metabolic process		3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase				0					NADH(DB00157)	CAGAGCTCCCCAAACCTGGGC	0.637											OREG0021141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	130	---	---	---	---	PASS
PRB3	5544	broad.mit.edu	37	12	11420500	11420500	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11420500G>T	uc001qzs.2	-	3	721	c.683C>A	c.(682-684)CCA>CAA	p.P228Q	PRB4_uc001qzf.1_Intron	NM_006249	NP_006240	Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	228	9.|10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.					extracellular region	Gram-negative bacterial cell surface binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.201)			TTGTGGGGGTGGTCCTTCTGG	0.627													8	63	---	---	---	---	PASS
PKP2	5318	broad.mit.edu	37	12	32977004	32977004	+	Missense_Mutation	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32977004A>T	uc001rlj.3	-	8	1896	c.1781T>A	c.(1780-1782)ATT>AAT	p.I594N	PKP2_uc001rlk.3_Missense_Mutation_p.I550N|PKP2_uc010skj.1_Missense_Mutation_p.I550N	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	594	ARM 4.				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GTAATCTGCAATGGTTCCTCT	0.413													5	92	---	---	---	---	PASS
TUBA1A	7846	broad.mit.edu	37	12	49579013	49579013	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49579013C>T	uc009zlf.2	-	4	1408	c.1136G>A	c.(1135-1137)AGC>AAC	p.S379N	TUBA1B_uc001rto.2_Intron|TUBA1A_uc001rtp.2_Missense_Mutation_p.S379N|TUBA1A_uc001rtq.2_Missense_Mutation_p.S226N|TUBA1A_uc001rtr.2_Missense_Mutation_p.S226N|TUBA1A_uc009zlg.2_Missense_Mutation_p.S226N	NM_006009	NP_006000	Q71U36	TBA1A_HUMAN	tubulin, alpha 1a	379					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|structural molecule activity				0						TGTGGTGTTGCTCAGCATGCA	0.582													17	60	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53685545	53685545	+	Silent	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53685545C>G	uc001sck.2	+	26	5683	c.5592C>G	c.(5590-5592)ACC>ACG	p.T1864T	ESPL1_uc001scj.2_Silent_p.T1539T	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	1864					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						TGTGCCCAACCCAGCCAGAGC	0.602													57	213	---	---	---	---	PASS
ERBB3	2065	broad.mit.edu	37	12	56492212	56492212	+	Intron	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56492212G>A	uc001sjh.2	+						ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Intron|ERBB3_uc009zok.2_Intron|ERBB3_uc001sjk.2_Intron|ERBB3_uc001sjl.2_5'UTR	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor						cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			aaaaaaaaaagaaTTTGGGAC	0.189													6	21	---	---	---	---	PASS
GPR109A	338442	broad.mit.edu	37	12	123187634	123187634	+	Missense_Mutation	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123187634A>T	uc001ucx.1	-	1	271	c.197T>A	c.(196-198)CTG>CAG	p.L66Q	GPR81_uc001ucw.1_Intron	NM_177551	NP_808219	Q8TDS4	HCAR2_HUMAN	G protein-coupled receptor 109A	66	Helical; Name=2; (Potential).				negative regulation of lipid catabolic process|neutrophil apoptosis|positive regulation of adiponectin secretion|positive regulation of neutrophil apoptosis	integral to membrane|plasma membrane	nicotinic acid receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)	CAGGTTGAACAGGAAAATCCG	0.527													17	48	---	---	---	---	PASS
GPR109A	338442	broad.mit.edu	37	12	123187635	123187635	+	Silent	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123187635G>A	uc001ucx.1	-	1	270	c.196C>T	c.(196-198)CTG>TTG	p.L66L	GPR81_uc001ucw.1_Intron	NM_177551	NP_808219	Q8TDS4	HCAR2_HUMAN	G protein-coupled receptor 109A	66	Helical; Name=2; (Potential).				negative regulation of lipid catabolic process|neutrophil apoptosis|positive regulation of adiponectin secretion|positive regulation of neutrophil apoptosis	integral to membrane|plasma membrane	nicotinic acid receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)	AGGTTGAACAGGAAAATCCGG	0.532													17	49	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133354283	133354283	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133354283G>T	uc001ukz.1	-	19	4250	c.3691C>A	c.(3691-3693)CAG>AAG	p.Q1231K	GOLGA3_uc001ula.1_Missense_Mutation_p.Q1231K	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1231	Potential.|Gln-rich.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		TGCAGCTTCTGCACCAGGTGT	0.632													10	36	---	---	---	---	PASS
NFATC4	4776	broad.mit.edu	37	14	24839730	24839730	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24839730G>A	uc001wpc.2	+	2	1447	c.1126G>A	c.(1126-1128)GAC>AAC	p.D376N	NFATC4_uc010tok.1_Missense_Mutation_p.D439N|NFATC4_uc010tol.1_Missense_Mutation_p.D439N|NFATC4_uc010alr.2_Missense_Mutation_p.D439N|NFATC4_uc010als.2_Missense_Mutation_p.D389N|NFATC4_uc010tom.1_Missense_Mutation_p.D389N|NFATC4_uc010ton.1_Missense_Mutation_p.D389N|NFATC4_uc010too.1_Missense_Mutation_p.D389N|NFATC4_uc010alt.2_Missense_Mutation_p.D408N|NFATC4_uc010top.1_Missense_Mutation_p.D408N|NFATC4_uc010toq.1_Missense_Mutation_p.D408N|NFATC4_uc010alu.2_Intron|NFATC4_uc010tor.1_Missense_Mutation_p.D376N|NFATC4_uc010tos.1_Missense_Mutation_p.D306N|NFATC4_uc010tot.1_Missense_Mutation_p.D364N|NFATC4_uc010tou.1_Missense_Mutation_p.D306N|NFATC4_uc010tov.1_Missense_Mutation_p.D364N|NFATC4_uc010tow.1_Missense_Mutation_p.D306N|NFATC4_uc010alv.2_Missense_Mutation_p.D364N|NFATC4_uc010tox.1_Missense_Mutation_p.D306N|NFATC4_uc001wpd.2_5'Flank|NFATC4_uc010toy.1_5'Flank|NFATC4_uc010toz.1_5'Flank	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	376					cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)		GGCTGGCATGGACTACCTGGC	0.637													14	35	---	---	---	---	PASS
FANCM	57697	broad.mit.edu	37	14	45639810	45639810	+	Missense_Mutation	SNP	T	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45639810T>C	uc001wwd.3	+	12	2120	c.2021T>C	c.(2020-2022)CTA>CCA	p.L674P	FANCM_uc010anf.2_Missense_Mutation_p.L648P|FANCM_uc001wwe.3_Missense_Mutation_p.L210P	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	674					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						CAAAGTAGCCTAAAGAAAGAT	0.289								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				19	36	---	---	---	---	PASS
ZFYVE1	53349	broad.mit.edu	37	14	73465019	73465019	+	Missense_Mutation	SNP	G	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73465019G>T	uc001xnm.2	-	3	1128	c.488C>A	c.(487-489)ACA>AAA	p.T163K	ZFYVE1_uc010arj.2_Missense_Mutation_p.T163K	NM_021260	NP_067083	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1 isoform 1	163						endoplasmic reticulum|Golgi stack|perinuclear region of cytoplasm	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|zinc ion binding			skin(1)	1		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		TTCTTCATTTGTTACCTGCAA	0.353													6	66	---	---	---	---	PASS
PSMC1	5700	broad.mit.edu	37	14	90730154	90730154	+	Missense_Mutation	SNP	T	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90730154T>A	uc001xyf.2	+	5	476	c.428T>A	c.(427-429)CTG>CAG	p.L143Q	PSMC1_uc001xyg.2_Missense_Mutation_p.L70Q|PSMC1_uc001xyh.2_Missense_Mutation_p.L70Q|PSMC1_uc010twh.1_Missense_Mutation_p.L70Q	NM_002802	NP_002793	P62191	PRS4_HUMAN	proteasome 26S ATPase subunit 1	143					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		GACAAGGATCTGCTGGAACCT	0.473													19	48	---	---	---	---	PASS
DDX24	57062	broad.mit.edu	37	14	94528593	94528593	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94528593G>A	uc001ycj.2	-	3	1192	c.1093C>T	c.(1093-1095)CAG>TAG	p.Q365*	DDX24_uc010twq.1_Nonsense_Mutation_p.Q322*|DDX24_uc010twr.1_Nonsense_Mutation_p.Q115*	NM_020414	NP_065147	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	365	Helicase ATP-binding.				RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		TTTCCAGTCTGCTCTTTATCA	0.478													38	143	---	---	---	---	PASS
SIN3A	25942	broad.mit.edu	37	15	75705213	75705213	+	Missense_Mutation	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75705213A>G	uc002bai.2	-	5	906	c.647T>C	c.(646-648)ATC>ACC	p.I216T	SIN3A_uc002baj.2_Missense_Mutation_p.I216T|SIN3A_uc010uml.1_Missense_Mutation_p.I216T	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	216	Interaction with REST (By similarity).			I -> T (in Ref. 3; BAC04801).	blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5						ctgtggctggATGCCATGGGT	0.279													5	47	---	---	---	---	PASS
LYSMD4	145748	broad.mit.edu	37	15	100269896	100269896	+	Missense_Mutation	SNP	T	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100269896T>G	uc002bvk.2	-	3	386	c.323A>C	c.(322-324)CAA>CCA	p.Q108P	LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvl.2_Missense_Mutation_p.Q109P|LYSMD4_uc002bvm.2_3'UTR|LYSMD4_uc010bov.2_Missense_Mutation_p.Q108P			Q5XG99	LYSM4_HUMAN	SubName: Full=cDNA FLJ77040, highly similar to Homo sapiens LysM, putative peptidoglycan-binding, domain containing 4, mRNA; SubName: Full=LysM, putative peptidoglycan-binding, domain containing 4, isoform CRA_c;	108	Extracellular (Potential).|LysM.				cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			ATATAAGTCTTGTTCTCTGAT	0.403													23	74	---	---	---	---	PASS
MAZ	4150	broad.mit.edu	37	16	29821179	29821179	+	Intron	SNP	A	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29821179A>G	uc002dty.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MAZ_uc002dtv.1_Intron|MAZ_uc010vdx.1_Intron|MAZ_uc002dtw.2_Intron|MAZ_uc002dtx.2_Intron|MAZ_uc010bzg.2_Intron|MAZ_uc002dtz.1_3'UTR|MAZ_uc002dua.2_Intron|MAZ_uc010vdy.1_Intron|uc002duc.1_Intron|PRRT2_uc002dud.2_5'Flank|PRRT2_uc002due.3_5'Flank|PRRT2_uc002duf.1_5'Flank	NM_002383	NP_002374	P56270	MAZ_HUMAN	MYC-associated zinc finger protein isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription|transcription initiation from RNA polymerase II promoter	nucleus	DNA binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1						AAGGCGAGGGATGCCCATGTA	0.647													4	4	---	---	---	---	PASS
TOP3A	7156	broad.mit.edu	37	17	18196163	18196163	+	Silent	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18196163G>A	uc002gsx.1	-	11	1306	c.1077C>T	c.(1075-1077)TAC>TAT	p.Y359Y	TOP3A_uc010cpz.1_5'Flank|TOP3A_uc010vxr.1_Intron|TOP3A_uc002gsw.1_Intron|TOP3A_uc010vxs.1_Silent_p.Y257Y	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	359					DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3						GATAGCTGATGTACCTAAAAC	0.458													11	47	---	---	---	---	PASS
MYO18A	399687	broad.mit.edu	37	17	27493028	27493028	+	Missense_Mutation	SNP	G	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27493028G>C	uc002hdt.1	-	2	1089	c.931C>G	c.(931-933)CCA>GCA	p.P311A	MYO18A_uc010csa.1_Missense_Mutation_p.P311A|MYO18A_uc002hdu.1_Missense_Mutation_p.P311A	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	311	PDZ.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CTGAGCTCTGGAATGGGCTGC	0.617													25	90	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33520805	33520805	+	Silent	SNP	T	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33520805T>C	uc002hjd.2	-	1	608	c.522A>G	c.(520-522)GGA>GGG	p.G174G		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	174	DUF6 1.|Helical; (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		AGAGTCCAGGTCCCACAATGA	0.612													9	250	---	---	---	---	PASS
DUSP14	11072	broad.mit.edu	37	17	35872618	35872618	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35872618C>T	uc002hnx.2	+	3	538	c.244C>T	c.(244-246)CCG>TCG	p.P82S	DUSP14_uc002hny.2_Missense_Mutation_p.P69S|DUSP14_uc002hnz.2_Missense_Mutation_p.P69S	NM_007026	NP_008957	O95147	DUS14_HUMAN	dual specificity phosphatase 14	82							MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)				GGCTGACATGCCGCATGCCCC	0.537													4	82	---	---	---	---	PASS
ZGLP1	100125288	broad.mit.edu	37	19	10419249	10419249	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10419249C>T	uc002mnw.3	-	1	985	c.109G>A	c.(109-111)GAC>AAC	p.D37N	FDX1L_uc002mnx.1_Intron	NM_001103167	NP_001096637	P0C6A0	ZGLP1_HUMAN	GATA like protein-1	37					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						GCAGTGGGGTCACGTTTTCTT	0.622													5	17	---	---	---	---	PASS
MAP1S	55201	broad.mit.edu	37	19	17837059	17837059	+	Missense_Mutation	SNP	T	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17837059T>C	uc002nhe.1	+	5	875	c.866T>C	c.(865-867)CTG>CCG	p.L289P	MAP1S_uc010eaz.1_RNA|MAP1S_uc010eba.1_Missense_Mutation_p.L289P|MAP1S_uc002nhf.1_Intron|MAP1S_uc010xpv.1_Missense_Mutation_p.L263P	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	289	Necessary for the microtubule-organizing center localization.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1						GATGCCGTGCTGGTGACCCAC	0.672													7	9	---	---	---	---	PASS
ZNF808	388558	broad.mit.edu	37	19	53057358	53057358	+	Nonsense_Mutation	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53057358A>T	uc010epq.1	+	5	1366	c.1189A>T	c.(1189-1191)AAA>TAA	p.K397*	ZNF808_uc002pzq.2_RNA|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	397					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		TAGTGGAGAGAAAACATACAA	0.373													29	96	---	---	---	---	PASS
NLRP5	126206	broad.mit.edu	37	19	56539568	56539568	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56539568G>A	uc002qmj.2	+	7	1969	c.1969G>A	c.(1969-1971)GTT>ATT	p.V657I	NLRP5_uc002qmi.2_Missense_Mutation_p.V638I	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	657						mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GGGCTGTCCCGTTCCCCTGGG	0.597													11	126	---	---	---	---	PASS
PIGT	51604	broad.mit.edu	37	20	44044813	44044813	+	Missense_Mutation	SNP	C	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44044813C>T	uc002xoh.1	+	1	90	c.17C>T	c.(16-18)CCG>CTG	p.P6L	PIGT_uc010ghb.1_Missense_Mutation_p.P6L|PIGT_uc010zwt.1_RNA|PIGT_uc010ghd.1_Missense_Mutation_p.P6L|PIGT_uc010ghc.1_RNA|PIGT_uc010ghe.1_Missense_Mutation_p.P6L|PIGT_uc010ghf.1_Missense_Mutation_p.P6L|PIGT_uc002xoj.1_Missense_Mutation_p.P6L|PIGT_uc002xok.1_Missense_Mutation_p.P6L|PIGT_uc010zwu.1_5'UTR|PIGT_uc002xoi.1_RNA|PIGT_uc010zwv.1_5'UTR|PIGT_uc010zww.1_Missense_Mutation_p.P6L|PIGT_uc010zwx.1_5'UTR|PIGT_uc010zwy.1_Missense_Mutation_p.P6L|PIGT_uc010zwz.1_5'UTR|PIGT_uc010zxa.1_5'UTR|PIGT_uc002xol.1_5'Flank	NM_015937	NP_057021	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	6					attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)				GCGGCTATGCCGCTTGCTCTG	0.647													3	9	---	---	---	---	PASS
ZSWIM3	140831	broad.mit.edu	37	20	44505664	44505664	+	Missense_Mutation	SNP	A	T	T			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44505664A>T	uc002xqd.2	+	2	670	c.467A>T	c.(466-468)CAA>CTA	p.Q156L	ZSWIM3_uc010zxg.1_Missense_Mutation_p.Q150L	NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	156							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)				GATAAGGTACAAGTGTCCTCA	0.498													4	64	---	---	---	---	PASS
NRIP1	8204	broad.mit.edu	37	21	16338673	16338673	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16338673G>A	uc002yjx.2	-	4	2439	c.1841C>T	c.(1840-1842)GCC>GTC	p.A614V		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	614	Repression domain 2.				androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TTCATTTTGGGCTGGTTTCTC	0.433													34	323	---	---	---	---	PASS
PI4KA	5297	broad.mit.edu	37	22	21161667	21161667	+	Missense_Mutation	SNP	G	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21161667G>A	uc002zsz.3	-	10	1208	c.977C>T	c.(976-978)ACT>ATT	p.T326I	PI4KA_uc010gsq.1_Missense_Mutation_p.T384I	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha	326					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GTAGTACAGAGTGTCACGCAG	0.537													9	45	---	---	---	---	PASS
SF3A1	10291	broad.mit.edu	37	22	30740940	30740940	+	Silent	SNP	T	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30740940T>A	uc003ahl.2	-	4	765	c.633A>T	c.(631-633)CTA>CTT	p.L211L		NM_005877	NP_005868	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa isoform 1	211					nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5						ACTGTTCCACTAGCTTCGTGA	0.552													47	142	---	---	---	---	PASS
ADSL	158	broad.mit.edu	37	22	40742592	40742592	+	Silent	SNP	C	G	G			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40742592C>G	uc003ayp.3	+	1	89	c.30C>G	c.(28-30)CCC>CCG	p.P10P	ADSL_uc003ays.3_Silent_p.P10P|ADSL_uc003ayq.3_Silent_p.P10P|ADSL_uc003ayr.3_5'UTR|ADSL_uc003ayt.3_Silent_p.P10P	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a	10					AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1						ATGGTTCGCCCGACAGCTACC	0.642													5	14	---	---	---	---	PASS
NCAPH2	29781	broad.mit.edu	37	22	50960640	50960640	+	Missense_Mutation	SNP	A	C	C			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50960640A>C	uc003blr.3	+	14	1315	c.1193A>C	c.(1192-1194)AAG>ACG	p.K398T	NCAPH2_uc003blv.2_Missense_Mutation_p.K398T|NCAPH2_uc010hbb.2_Intron|NCAPH2_uc003blu.3_RNA|NCAPH2_uc003bls.3_RNA|NCAPH2_uc003blt.3_RNA|NCAPH2_uc003blw.3_RNA|NCAPH2_uc003blx.3_Missense_Mutation_p.K398T|NCAPH2_uc003bly.3_RNA	NM_152299	NP_689512	Q6IBW4	CNDH2_HUMAN	kleisin beta isoform 2	398					chromosome condensation	chromosome|nucleus				ovary(1)|skin(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		ACACACGTGAAGGAGCAGTTG	0.612													12	66	---	---	---	---	PASS
BEND2	139105	broad.mit.edu	37	X	18213416	18213416	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18213416C>A	uc004cyj.3	-	7	1334	c.1180G>T	c.(1180-1182)GAA>TAA	p.E394*	BEND2_uc010nfb.2_Intron	NM_153346	NP_699177	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	394										ovary(3)|kidney(1)|central_nervous_system(1)	5						TCAAACTCACCAAAATTAGAA	0.353													4	61	---	---	---	---	PASS
CLCNKB	1188	broad.mit.edu	37	1	16366306	16366307	+	Intron	INS	-	GGGAC	GGGAC	rs145130478	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16366306_16366307insGGGAC	uc001axw.3	+						FAM131C_uc010obz.1_Intron	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		GCCAGTGGGCAGGGACAGGGCA	0.614													4	2	---	---	---	---	
COL16A1	1307	broad.mit.edu	37	1	32122425	32122425	+	Intron	DEL	A	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32122425delA	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TACAGGGTTTAAAAAAAAAAA	0.343													5	4	---	---	---	---	
BMP8A	353500	broad.mit.edu	37	1	39988318	39988319	+	Intron	INS	-	TTG	TTG	rs139401553	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39988318_39988319insTTG	uc001cdi.2	+						PPIEL_uc001cdj.1_Intron|PPIEL_uc001cdk.2_Intron	NM_181809	NP_861525	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8A precursor						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GAGAAAGGGTTTTGTTGTTGTT	0.356													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100288440	100288441	+	IGR	INS	-	CTA	CTA			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100288440_100288441insCTA								FRRS1 (57091 upstream) : AGL (27199 downstream)																							ctcctctacctcctctacctcc	0.094													4	2	---	---	---	---	
SLC35A3	23443	broad.mit.edu	37	1	100480734	100480734	+	Intron	DEL	G	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100480734delG	uc001dsp.1	+						SLC35A3_uc001dsq.1_Intron|SLC35A3_uc009wdy.1_Intron|SLC35A3_uc001dsr.1_Intron|SLC35A3_uc001dss.1_Intron	NM_012243	NP_036375	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 member 3A						UDP-N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	sugar:hydrogen symporter activity|UDP-N-acetylglucosamine transmembrane transporter activity				0		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		aaaaaaaaaagaaaGTAATCT	0.114													4	2	---	---	---	---	
CFHR4	10877	broad.mit.edu	37	1	196883940	196883941	+	Intron	INS	-	A	A	rs35868341		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196883940_196883941insA	uc001gto.2	+						CFHR4_uc009wyy.2_Intron|CFHR4_uc001gtp.2_Intron	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						TCTTGAGACTTAAAAAAAAAAA	0.208													5	4	---	---	---	---	
HADHB	3032	broad.mit.edu	37	2	26486167	26486167	+	Intron	DEL	A	-	-	rs139107013		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26486167delA	uc002rgz.2	+						HADHB_uc010yku.1_Intron|HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron	NM_000183	NP_000174	P55084	ECHB_HUMAN	mitochondrial trifunctional protein, beta						fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					actccatcttaaaaaaaaaaa	0.104													15	8	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87954556	87954556	+	Intron	DEL	A	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87954556delA	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						TCTTTCTGGCAAAAAAAAAAA	0.468													3	3	---	---	---	---	
MRPL30	51263	broad.mit.edu	37	2	99779655	99779655	+	Intron	DEL	C	-	-	rs68130738		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99779655delC	uc002szr.2	+						MRPL30_uc002szl.1_Intron	NM_145213	NP_660214	Q8TCC3	RM30_HUMAN	SubName: Full=HCG1989457, isoform CRA_a; SubName: Full=Putative uncharacterized protein MRPL30;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1						AAAAAAAAAACAAAACACAAC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122067665	122067666	+	IGR	DEL	GT	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122067665_122067666delGT								TFCP2L1 (24887 upstream) : CLASP1 (27688 downstream)																							CCACATGAACgtgtgtgtgtgt	0.401													4	3	---	---	---	---	
GBX2	2637	broad.mit.edu	37	2	237076427	237076435	+	In_Frame_Del	DEL	GGCGGCGGC	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237076427_237076435delGGCGGCGGC	uc002vvw.1	-	1	218_226	c.180_188delGCCGCCGCC	c.(178-189)CCGCCGCCGCCC>CCC	p.60_63PPPP>P	GBX2_uc010zng.1_In_Frame_Del_p.50_53PPPP>P	NM_001485	NP_001476	P52951	GBX2_HUMAN	gastrulation brain homeo box 2	60_63	Poly-Pro.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)		GGGCAGCGCGggcggcggcggcggcggcg	0.622													5	3	---	---	---	---	
SHQ1	55164	broad.mit.edu	37	3	72841935	72841936	+	Intron	INS	-	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72841935_72841936insA	uc003dpf.2	-						SHQ1_uc010hod.2_Intron	NM_018130	NP_060600	Q6PI26	SHQ1_HUMAN	SHQ1 homolog						ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		acctccatctcaaaaaaaaaaa	0.139													4	2	---	---	---	---	
PLSCR4	57088	broad.mit.edu	37	3	145939755	145939756	+	Intron	INS	-	A	A	rs139631809	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145939755_145939756insA	uc010huy.2	-						PLSCR4_uc010huz.2_Intron|PLSCR4_uc003evt.3_Intron|PLSCR4_uc010hva.2_Intron|PLSCR4_uc003evu.3_Intron	NM_001128305	NP_001121777	Q9NRQ2	PLS4_HUMAN	phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0						AAATGTTAAACAAAAAAAAATC	0.193													3	6	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188295546	188295549	+	Intron	DEL	TTCG	-	-	rs72048204		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188295546_188295549delTTCG	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ccttcgttccttcgttccttcctt	0.039			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
SEC31A	22872	broad.mit.edu	37	4	83748950	83748954	+	Intron	DEL	AAAGT	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83748950_83748954delAAAGT	uc003hnf.2	-						SEC31A_uc003hnd.2_Intron|SEC31A_uc003hne.2_Intron|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				taaagtaaacaaagtaaaacataaa	0.107													5	3	---	---	---	---	
CCRN4L	25819	broad.mit.edu	37	4	139964675	139964675	+	Intron	DEL	T	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139964675delT	uc003ihl.2	+						CCRN4L_uc003ihk.1_3'UTR	NM_012118	NP_036250	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like						rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)					TGGTTTTCACTTTTTTTTTTT	0.378													3	3	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98204056	98204056	+	Intron	DEL	G	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98204056delG	uc003knf.2	-						CHD1_uc010jbn.2_Intron	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	aaaaaaaaaaGACACCCTTCA	0.129													9	4	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92027037	92027038	+	Frame_Shift_Del	DEL	AT	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92027037_92027038delAT	uc003ulw.2	+	19	2772_2773	c.2396_2397delAT	c.(2395-2397)GATfs	p.D799fs	ANKIB1_uc010lew.1_Frame_Shift_Del_p.D68fs	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	799							protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTGAAACAGATATTCCAGAAG	0.441													268	121	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143508187	143508188	+	Intron	INS	-	T	T	rs150064856		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143508187_143508188insT	uc011ktn.1	+						uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_001130026	NP_001123498			hypothetical protein LOC285966 isoform B																		TGACCCCAttcttttttttttt	0.243													8	5	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69728341	69728346	+	Intron	DEL	GTGTGT	-	-	rs111246993		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69728341_69728346delGTGTGT	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TTTCCTAAGAgtgtgtgtgtgtgtgt	0.257													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76858719	76858720	+	IGR	INS	-	TTCC	TTCC	rs148513973	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76858719_76858720insTTCC								HNF4G (379660 upstream) : LOC100192378 (664395 downstream)																							tccttccttcgttccttccttc	0.069													4	3	---	---	---	---	
FAM108B1	51104	broad.mit.edu	37	9	74490146	74490147	+	Intron	INS	-	T	T	rs5898234		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74490146_74490147insT	uc004aim.1	-						FAM108B1_uc004ail.2_Intron	NM_001025780	NP_001020951	Q5VST6	F108B_HUMAN	family with sequence similarity 108, member B1							extracellular region	hydrolase activity				0						TTTTTGGCttcttttttttttt	0.139													3	4	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92286580	92286581	+	Intron	INS	-	TGA	TGA			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92286580_92286581insTGA	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						ggtgatggtggtgatggtggtg	0.000													4	2	---	---	---	---	
AKR1C4	1109	broad.mit.edu	37	10	5246177	5246178	+	Intron	INS	-	GTA	GTA	rs140536638	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5246177_5246178insGTA	uc001ihw.2	+							NM_001818	NP_001809	P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4						androgen metabolic process|bile acid biosynthetic process	cytosol	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid transmembrane transporter activity|chlordecone reductase activity|electron carrier activity			ovary(1)	1					NADH(DB00157)	ATATGCAATATGTAGCTTTCAT	0.307													5	3	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24498289	24498290	+	Intron	INS	-	A	A	rs113382859		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24498289_24498290insA	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						CCCGGCAAAGGAAAAAAAAAAA	0.446													13	7	---	---	---	---	
ABCC2	1244	broad.mit.edu	37	10	101579171	101579172	+	Intron	DEL	TG	-	-	rs5787360		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101579171_101579172delTG	uc001kqf.2	+							NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),							apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	TTCTGGGTTCTGTGTCTCTTTG	0.416													6	3	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114574898	114574899	+	Intron	INS	-	CACA	CACA	rs631578	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114574898_114574899insCACA	uc001kzz.2	+							NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		TTTCGCGCGCGcacacacacac	0.480													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	19296062	19296063	+	IGR	INS	-	A	A	rs11381338		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19296062_19296063insA								E2F8 (32895 upstream) : NAV2 (76208 downstream)																							gactctgtttcaaaaaaaaaaa	0.178													6	3	---	---	---	---	
RTN3	10313	broad.mit.edu	37	11	63523428	63523429	+	Intron	INS	-	A	A	rs112296263		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63523428_63523429insA	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831	O95197	RTN3_HUMAN	reticulon 3 isoform b						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						ggctccgtctcaaaaaaaaaaa	0.158													4	3	---	---	---	---	
CAPN1	823	broad.mit.edu	37	11	64954882	64954882	+	Intron	DEL	C	-	-	rs3832790		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64954882delC	uc009yqd.1	+						CAPN1_uc001odf.1_Intron|CAPN1_uc001odg.1_Intron|CAPN1_uc010roa.1_Intron	NM_005186	NP_005177	P07384	CAN1_HUMAN	calpain 1, large subunit						positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CCTTTCCCCTCCTGCAGCACC	0.617													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127810795	127810797	+	IGR	DEL	TTA	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127810795_127810797delTTA								KIRREL3 (937440 upstream) : ETS1 (517859 downstream)																							TTGTTATAGTTTAACATTTCTGT	0.345													40	18	---	---	---	---	
KDM5A	5927	broad.mit.edu	37	12	415910	415910	+	Intron	DEL	A	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:415910delA	uc001qif.1	-						KDM5A_uc001qie.1_Intron	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ctccatctccaaaaaaaaaaa	0.124			T 	NUP98	AML								8	5	---	---	---	---	
CACNA2D4	93589	broad.mit.edu	37	12	2016939	2016951	+	Intron	DEL	GCCTGGTGAGTAT	-	-	rs113797488		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2016939_2016951delGCCTGGTGAGTAT	uc001qjp.2	-						CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TGGTGGGCCAGCCTGGTGAGTATGCCTGGTGGG	0.662													4	2	---	---	---	---	
LRRC23	10233	broad.mit.edu	37	12	7022359	7022360	+	Intron	INS	-	G	G	rs143984274	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7022359_7022360insG	uc001qrt.3	+						LRRC23_uc001qrp.2_Intron|LRRC23_uc001qrq.2_Intron|LRRC23_uc001qrr.2_Intron|LRRC23_uc001qrs.2_Intron|LRRC23_uc009zfh.2_Intron|ENO2_uc001qru.1_5'Flank|ENO2_uc009zfi.1_5'Flank|ENO2_uc010sfq.1_5'Flank|ENO2_uc001qrv.1_5'Flank	NM_001135217	NP_001128689	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23 isoform a											ovary(1)	1						AAGGGACCCAAGGGGCCTGGGA	0.569													6	3	---	---	---	---	
MRPS35	60488	broad.mit.edu	37	12	27872605	27872606	+	Intron	INS	-	A	A	rs34620750		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27872605_27872606insA	uc001rih.2	+						MRPS35_uc001rii.2_Intron	NM_021821	NP_068593	P82673	RT35_HUMAN	mitochondrial ribosomal protein S35 precursor						DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)					gactctgtctcaaaaaaaaaaa	0.104													6	3	---	---	---	---	
RAD9B	144715	broad.mit.edu	37	12	110950776	110950776	+	Intron	DEL	T	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110950776delT	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655	Q6WBX8	RAD9B_HUMAN	RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2						AGTCGGCACAttttttttttt	0.204													4	3	---	---	---	---	
ALDH2	217	broad.mit.edu	37	12	112222867	112222867	+	Intron	DEL	C	-	-	rs3832868		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112222867delC	uc001tst.2	+						ALDH2_uc010syi.1_Intron|ALDH2_uc009zvy.2_Intron	NM_000690	NP_000681	P05091	ALDH2_HUMAN	mitochondrial aldehyde dehydrogenase 2						carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)	GCTCATCCTGCCTGGCCCCCT	0.532			T	HMGA2	leiomyoma								4	9	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31647112	31647112	+	Intron	DEL	T	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31647112delT	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		tttttagaaattttttttttt	0.318													4	2	---	---	---	---	
CTAGE5	4253	broad.mit.edu	37	14	39783814	39783815	+	Intron	INS	-	TTT	TTT	rs55732496		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39783814_39783815insTTT	uc001wvg.3	+						CTAGE5_uc010tqe.1_Intron|CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921	O15320	CTGE5_HUMAN	CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		GAGTTCTGGAGTTTTTTTTTTT	0.257													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20104041	20104041	+	IGR	DEL	T	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20104041delT								None (None upstream) : GOLGA6L6 (633053 downstream)																							TACTTACATCTTTTTTTTTTG	0.413													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22118395	22118396	+	IGR	DEL	AC	-	-	rs139043886		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22118395_22118396delAC								CXADRP2 (101517 upstream) : LOC727924 (159636 downstream)																							ATAAATTATAACATTCTTTTTG	0.342													5	5	---	---	---	---	
ENO3	2027	broad.mit.edu	37	17	4856733	4856733	+	Intron	DEL	T	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4856733delT	uc002gab.3	+						ENO3_uc010vsr.1_Intron|ENO3_uc002gac.3_Intron|ENO3_uc010vss.1_Intron|ENO3_uc010vst.1_5'Flank	NM_053013	NP_443739	P13929	ENOB_HUMAN	enolase 3						gluconeogenesis|glycolysis	phosphopyruvate hydratase complex	magnesium ion binding|phosphopyruvate hydratase activity			ovary(1)	1						GGGTCCCCCATTTTGGGTCAC	0.393													22	16	---	---	---	---	
GRIN2C	2905	broad.mit.edu	37	17	72843840	72843841	+	Intron	DEL	TG	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72843840_72843841delTG	uc002jlt.1	-						GRIN2C_uc010wrh.1_Intron|GRIN2C_uc002jlu.1_Intron	NM_000835	NP_000826	Q14957	NMDE3_HUMAN	N-methyl-D-aspartate receptor subunit 2C						glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)	TGTGTGTTTCTGTGTGTGTGTG	0.619													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3581662	3581663	+	Intron	INS	-	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3581662_3581663insA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TTCTCACCATGaaaaaaaaaaa	0.381													3	3	---	---	---	---	
MOCOS	55034	broad.mit.edu	37	18	33784939	33784942	+	Intron	DEL	GAGT	-	-	rs71833586		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33784939_33784942delGAGT	uc002kzq.3	+							NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	ctgggtgacagagtgagtgagacc	0.103													3	6	---	---	---	---	
TXNL4A	10907	broad.mit.edu	37	18	77737811	77737815	+	Intron	DEL	TTTTG	-	-	rs71338078		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77737811_77737815delTTTTG	uc002lnp.2	-						TXNL4A_uc002lnr.2_Intron|TXNL4A_uc002lnq.2_Intron|TXNL4A_uc010drf.2_Intron|TXNL4A_uc010drg.2_Intron	NM_006701	NP_006692	P83876	TXN4A_HUMAN	thioredoxin-like 4A						cell division|mitosis|spliceosome assembly	nucleoplasm|spliceosomal complex	protein binding				0		all_cancers(4;1.15e-12)|all_epithelial(4;8.61e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0646)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;7.36e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0249)		TCAGGGCAAtttttgttttgttttt	0.137													6	6	---	---	---	---	
C3	718	broad.mit.edu	37	19	6710538	6710540	+	Intron	DEL	AGG	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6710538_6710540delAGG	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		agagagagaaaggagagagaaaa	0.079													4	2	---	---	---	---	
SMARCA4	6597	broad.mit.edu	37	19	11137174	11137174	+	Intron	DEL	T	-	-	rs35017701		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11137174delT	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc002mqg.1_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc010dxt.1_Intron|SMARCA4_uc002mqh.3_Intron|SMARCA4_uc002mqi.1_Intron	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AATACAAAtcttttttttttt	0.154			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				4	2	---	---	---	---	
CC2D1A	54862	broad.mit.edu	37	19	14030490	14030491	+	Intron	INS	-	A	A			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14030490_14030491insA	uc002mxo.2	+						CC2D1A_uc002mxn.2_Intron|CC2D1A_uc002mxp.2_Intron|CC2D1A_uc010dzh.2_Intron|CC2D1A_uc002mxq.1_Intron	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			gatcctgtctcaaaaaaaaaaa	0.173													6	3	---	---	---	---	
PODNL1	79883	broad.mit.edu	37	19	14043756	14043756	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14043756delA	uc002mxr.2	-	8	1575	c.1301delT	c.(1300-1302)CTGfs	p.L434fs	PODNL1_uc010xni.1_Frame_Shift_Del_p.L352fs|PODNL1_uc010xnj.1_Frame_Shift_Del_p.L432fs|PODNL1_uc002mxs.2_Frame_Shift_Del_p.L343fs	NM_024825	NP_079101	Q6PEZ8	PONL1_HUMAN	podocan-like 1 isoform 1	434	LRR 16.|Leu-rich.					proteinaceous extracellular matrix				central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			TTGCAGCTGCAGGGTGCGCAG	0.716													4	2	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17994332	17994332	+	Intron	DEL	G	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17994332delG	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						GCAGGAACAAGGGGGGGGGGT	0.542													8	6	---	---	---	---	
GPI	2821	broad.mit.edu	37	19	34890729	34890729	+	Intron	DEL	G	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34890729delG	uc002nvg.1	+						GPI_uc002nvf.2_Intron|GPI_uc010xrv.1_Intron|GPI_uc010xrw.1_Intron|GPI_uc010edl.1_Intron|GPI_uc002nvi.1_Intron	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase						angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)					GAATACCTTTGTGTCGGCTCA	0.537													38	21	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2056543	2056543	+	IGR	DEL	T	-	-	rs141636945	by1000genomes	TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2056543delT								PDYN (81840 upstream) : STK35 (25985 downstream)																							AAAAAAAAAATacacacacac	0.179													6	3	---	---	---	---	
CCDC117	150275	broad.mit.edu	37	22	29181913	29181913	+	Intron	DEL	A	-	-	rs35631283		TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29181913delA	uc003aeb.2	+						CCDC117_uc011aki.1_Intron|CCDC117_uc011akj.1_Intron|CCDC117_uc011akk.1_Intron	NM_173510	NP_775781	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117											breast(1)	1						cccatctcttaaaaaaaaaaa	0.139													7	5	---	---	---	---	
PCDH11Y	83259	broad.mit.edu	37	Y	5442530	5442530	+	Intron	DEL	A	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:5442530delA	uc004fqo.2	+							NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0						GTACAGAGTTAAAAAAAaaag	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13496206	13496206	+	IGR	DEL	G	-	-			TCGA-EU-5906-01A-11D-1669-08	TCGA-EU-5906-10A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13496206delG								None (None upstream) : None (None downstream)																							CTTCTGTCATGTGAAATAATT	0.318													4	3	---	---	---	---	
