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
KIAA0090	23065	broad.mit.edu	37	1	19545706	19545706	+	3'UTR	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19545706C>T	uc001bbo.2	-	23					KIAA0090_uc001bbn.2_RNA|KIAA0090_uc001bbp.2_3'UTR|KIAA0090_uc001bbq.2_3'UTR|KIAA0090_uc001bbr.2_3'UTR	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor							integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)		GACACACACACATACTCCACC	0.483													3	27	---	---	---	---	PASS
GJB3	2707	broad.mit.edu	37	1	35250612	35250612	+	Silent	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35250612C>T	uc001bxx.2	+	2	864	c.249C>T	c.(247-249)TTC>TTT	p.F83F	GJB3_uc001bxy.2_Silent_p.F83F|GJB3_uc001bxz.3_Silent_p.F83F|uc010ohs.1_RNA	NM_024009	NP_076872	O75712	CXB3_HUMAN	connexin 31	83	Helical; (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AGCTCATCTTCGTCACATGCC	0.627													46	66	---	---	---	---	PASS
COL9A2	1298	broad.mit.edu	37	1	40777353	40777353	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40777353G>A	uc001cfh.1	-	9	522	c.452C>T	c.(451-453)CCA>CTA	p.P151L	COL9A2_uc001cfi.1_5'UTR	NM_001852	NP_001843	Q14055	CO9A2_HUMAN	alpha 2 type IX collagen precursor	151	Triple-helical region 4 (COL4).				axon guidance|skeletal system development	collagen type IX				ovary(2)	2	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			AGGGGGTCCTGGGGGCCCCGA	0.612													19	26	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144922040	144922040	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144922040T>C	uc001elw.3	-	9	1280	c.989A>G	c.(988-990)GAG>GGG	p.E330G	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.E396G|PDE4DIP_uc001emc.1_Missense_Mutation_p.E330G|PDE4DIP_uc001emd.1_Missense_Mutation_p.E330G|PDE4DIP_uc001emb.1_Missense_Mutation_p.E493G|PDE4DIP_uc001eme.1_5'UTR|PDE4DIP_uc001emf.1_Missense_Mutation_p.E117G	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	330					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)		AGAAGTACCCTCTGAGCTCTG	0.453			T	PDGFRB	MPD								16	102	---	---	---	---	PASS
DCST1	149095	broad.mit.edu	37	1	155006934	155006934	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155006934G>T	uc001fgn.1	+	3	181	c.85G>T	c.(85-87)GGG>TGG	p.G29W	DCST2_uc001fgm.2_5'Flank|DCST2_uc009wpb.2_5'Flank|DCST1_uc010per.1_Missense_Mutation_p.G54W|DCST1_uc010pes.1_Missense_Mutation_p.G29W	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	29	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CCTGACCTGGGGGCTGCCAGT	0.652													8	21	---	---	---	---	PASS
C1orf186	440712	broad.mit.edu	37	1	206239454	206239454	+	Silent	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206239454T>C	uc001hdt.1	-	6	1083	c.444A>G	c.(442-444)AGA>AGG	p.R148R		NM_001007544	NP_001007545	Q6ZWK4	CA186_HUMAN	hypothetical protein LOC440712	148						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.0754)			TGGGCTTGTGTCTTTCTGGAT	0.423													5	210	---	---	---	---	PASS
EHBP1	23301	broad.mit.edu	37	2	62934347	62934347	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62934347A>G	uc002sby.2	+	2	503	c.21A>G	c.(19-21)AGA>AGG	p.R7R	EHBP1_uc010fcp.2_Silent_p.R7R|EHBP1_uc010fcq.1_Silent_p.R7R|EHBP1_uc002sbx.2_Silent_p.R7R|EHBP1_uc002sbz.2_Silent_p.R7R|EHBP1_uc002scb.2_Silent_p.R7R|EHBP1_uc002sca.2_Silent_p.R7R	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	7						cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TTTGGAAGAGACTGCAGCGTG	0.473									Hereditary_Prostate_Cancer				33	86	---	---	---	---	PASS
DYNC1LI1	51143	broad.mit.edu	37	3	32586462	32586462	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32586462A>G	uc003cfb.3	-	4	562	c.474T>C	c.(472-474)GCT>GCC	p.A158A	DYNC1LI1_uc011axh.1_Intron	NM_016141	NP_057225	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain	158					cell division|interspecies interaction between organisms|mitosis|positive regulation of mitotic cell cycle spindle assembly checkpoint|transport	centrosome|condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|plasma membrane|spindle pole	ATP binding|motor activity			ovary(1)	1						AAGAATCCAAAGCAGTCCAAG	0.388													4	72	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47164498	47164498	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47164498G>T	uc003cqs.2	-	3	1681	c.1628C>A	c.(1627-1629)TCA>TAA	p.S543*	SETD2_uc003cqv.2_Nonsense_Mutation_p.S532*	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	543					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AGAATATGATGACCCTCGTCG	0.348			N|F|S|Mis		clear cell renal carcinoma								53	49	---	---	---	---	PASS
WDR82	80335	broad.mit.edu	37	3	52304764	52304764	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52304764C>T	uc003ddl.2	-	2	505	c.223G>A	c.(223-225)GCA>ACA	p.A75T	WDR82_uc003ddk.2_5'Flank|uc011bee.1_5'Flank|MIRLET7G_hsa-let-7g|MI0000433_5'Flank	NM_025222	NP_079498	Q6UXN9	WDR82_HUMAN	WD repeat domain 82	75					histone H3-K4 methylation	chromatin|PTW/PP1 phosphatase complex|Set1C/COMPASS complex	protein binding				0				BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)		ACTGTGTTTGCTGCATGAGTG	0.368													4	201	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52649451	52649451	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52649451G>C	uc003des.2	-	15	1852	c.1840C>G	c.(1840-1842)CTG>GTG	p.L614V	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.L614V|PBRM1_uc003der.2_Missense_Mutation_p.L582V|PBRM1_uc003det.2_Missense_Mutation_p.L629V|PBRM1_uc003deu.2_Missense_Mutation_p.L629V|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.L614V|PBRM1_uc010hmk.1_Missense_Mutation_p.L614V|PBRM1_uc003dey.2_Missense_Mutation_p.L614V|PBRM1_uc003dez.1_Missense_Mutation_p.L614V|PBRM1_uc003dfb.1_Missense_Mutation_p.L527V|PBRM1_uc003dfc.2_5'UTR	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	614					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AACTTCTCCAGGATATGTGCA	0.368			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								37	38	---	---	---	---	PASS
ALDH1L1	10840	broad.mit.edu	37	3	125854457	125854457	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125854457C>G	uc003eim.1	-	12	1583	c.1393G>C	c.(1393-1395)GTG>CTG	p.V465L	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Missense_Mutation_p.V364L|ALDH1L1_uc003eio.2_Missense_Mutation_p.V167L|ALDH1L1_uc010hsf.1_Missense_Mutation_p.V491L	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	465	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	GCTGCGGCCACTGCCTTGTCG	0.592													28	46	---	---	---	---	PASS
PLXNA1	5361	broad.mit.edu	37	3	126707667	126707667	+	Silent	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126707667C>T	uc003ejg.2	+	1	166	c.162C>T	c.(160-162)AAC>AAT	p.N54N		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	77	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		TGTCGGGGAACCTGACACTGC	0.657													5	17	---	---	---	---	PASS
GPR149	344758	broad.mit.edu	37	3	154055852	154055852	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154055852A>G	uc003faa.2	-	4	1932	c.1832T>C	c.(1831-1833)GTG>GCG	p.V611A		NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	611	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ACTGGTGTCCACAAACGTGGA	0.408													4	93	---	---	---	---	PASS
NOP14	8602	broad.mit.edu	37	4	2948137	2948137	+	Splice_Site	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2948137A>G	uc003ggj.1	-	11	1707	c.1635_splice	c.e11+1	p.V545_splice	C4orf10_uc003gge.1_Intron|C4orf10_uc003ggh.2_Intron|C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Splice_Site_p.V291_splice|NOP14_uc003ggk.3_Splice_Site_p.V545_splice|NOP14_uc003ggl.2_Splice_Site_p.V545_splice	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						AACTCTGCTTACCACATCCAA	0.527													27	39	---	---	---	---	PASS
MAN2B2	23324	broad.mit.edu	37	4	6623175	6623175	+	3'UTR	SNP	T	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6623175T>A	uc003gjf.1	+	19					MAN2B2_uc003gje.1_3'UTR|MAN2B2_uc011bwf.1_3'UTR	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2						mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2						TTTTCCCTAATTTTTTTAAAC	0.473													4	4	---	---	---	---	PASS
UGT2B11	10720	broad.mit.edu	37	4	70078407	70078407	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70078407T>C	uc003heh.2	-	2	763	c.754A>G	c.(754-756)AAA>GAA	p.K252E	uc003hei.1_Intron	NM_001073	NP_001064	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family,	252					estrogen metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3						ATGTCAGCTTTTCCCATTGTC	0.373													105	224	---	---	---	---	PASS
UGT2B4	7363	broad.mit.edu	37	4	70346629	70346629	+	Intron	SNP	C	G	G	rs71599906		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70346629C>G	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Intron	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						CTCTTTATATCTAAACGATAA	0.249													16	67	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14508563	14508563	+	3'UTR	SNP	A	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14508563A>C	uc003jff.2	+	57					TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					ATTCTCTTTCACCTGCCAATC	0.408													5	9	---	---	---	---	PASS
PRDM9	56979	broad.mit.edu	37	5	23522473	23522473	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23522473C>A	uc003jgo.2	+	7	751	c.569C>A	c.(568-570)GCA>GAA	p.A190E		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	190					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						AAGGGTCATGCATACAAAGAG	0.453										HNSCC(3;0.000094)			34	91	---	---	---	---	PASS
SLC30A5	64924	broad.mit.edu	37	5	68411133	68411133	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68411133T>C	uc003jvh.2	+	8	883	c.682T>C	c.(682-684)TCT>CCT	p.S228P	SLC30A5_uc003jvj.2_5'Flank|SLC30A5_uc003jvk.2_5'Flank|SLC30A5_uc003jvi.2_Missense_Mutation_p.S57P	NM_022902	NP_075053	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter),	228	Cytoplasmic (Potential).				cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		CAGAAAGCTCTCTGTCGACGT	0.408													6	393	---	---	---	---	PASS
PCDHGB4	8641	broad.mit.edu	37	5	140769724	140769724	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140769724G>C	uc003lkc.1	+	1	2273	c.2273G>C	c.(2272-2274)GGA>GCA	p.G758A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc011dav.1_Missense_Mutation_p.G758A	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	758	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACATACAGGAAAGACGGAG	0.443													67	98	---	---	---	---	PASS
FAM71B	153745	broad.mit.edu	37	5	156589916	156589916	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156589916G>A	uc003lwn.2	-	2	1460	c.1360C>T	c.(1360-1362)CGC>TGC	p.R454C		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	454	Bipartite nuclear localization signal (Potential).					nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCTCTCCTGCGGTGACTTTCA	0.478													37	88	---	---	---	---	PASS
SLC17A4	10050	broad.mit.edu	37	6	25771212	25771212	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25771212A>G	uc003nfe.2	+	6	797	c.678A>G	c.(676-678)ATA>ATG	p.I226M	SLC17A4_uc011djx.1_Intron|SLC17A4_uc003nff.1_Intron|SLC17A4_uc003nfg.2_Missense_Mutation_p.I163M|SLC17A4_uc010jqa.2_5'Flank	NM_005495	NP_005486	Q9Y2C5	S17A4_HUMAN	solute carrier family 17 (sodium phosphate),	226					phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			skin(1)	1						GCCAGACCATAGGATGGCCTT	0.453													5	314	---	---	---	---	PASS
SYNGAP1	8831	broad.mit.edu	37	6	33408548	33408548	+	Silent	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33408548G>A	uc011dri.1	+	11	1914	c.1719G>A	c.(1717-1719)CGG>CGA	p.R573R	SYNGAP1_uc010juy.2_Silent_p.R558R|SYNGAP1_uc010juz.2_Silent_p.R285R	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	573	Ras-GAP.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4						CTTCGTGGCGGCTGCGCTGCG	0.552													18	5	---	---	---	---	PASS
C6orf1	221491	broad.mit.edu	37	6	34214269	34214269	+	3'UTR	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34214269G>C	uc003ojf.2	-	5					uc003oje.1_5'Flank|C6orf1_uc003ojg.2_3'UTR|C6orf1_uc003ojh.2_3'UTR|C6orf1_uc003oji.2_RNA	NM_178508	NP_848603	Q86T20	CF001_HUMAN	hypothetical protein LOC221491 precursor							extracellular region					0		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)		GGGGATTTGTGCCCAAGCCCA	0.517													7	11	---	---	---	---	PASS
SLC26A8	116369	broad.mit.edu	37	6	35922941	35922941	+	Silent	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35922941G>A	uc003olm.2	-	17	2331	c.2220C>T	c.(2218-2220)GTC>GTT	p.V740V	SLC26A8_uc010jwa.2_RNA|SLC26A8_uc003olk.2_Silent_p.V322V|SLC26A8_uc003oln.2_Silent_p.V740V|SLC26A8_uc003oll.2_Silent_p.V635V	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	740	Interaction with RACGAP1.|STAS.|Cytoplasmic (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2						GTCTTAATACGACTAACCCCC	0.512													10	12	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55198595	55198595	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55198595C>T	uc003pcm.1	+	3	255	c.169C>T	c.(169-171)CCC>TCC	p.P57S		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	57	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TCCAGGTGACCCCTGCAAGAT	0.353													4	107	---	---	---	---	PASS
KIAA0776	23376	broad.mit.edu	37	6	96985338	96985338	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96985338A>G	uc003por.2	+	9	939	c.891A>G	c.(889-891)AAA>AAG	p.K297K	KIAA0776_uc010kck.2_RNA	NM_015323	NP_056138	O94874	UFL1_HUMAN	hypothetical protein LOC23376	297					negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|protein ufmylation	endoplasmic reticulum|nucleus	protein binding|UFM1 conjugating enzyme activity			ovary(1)	1		all_cancers(76;5.83e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0604)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0934)		TGTTTTTGAAAGCAGCTTGTG	0.378													6	262	---	---	---	---	PASS
PCMT1	5110	broad.mit.edu	37	6	150094281	150094281	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150094281A>G	uc003qne.2	+	3	375	c.342A>G	c.(340-342)CAA>CAG	p.Q114Q	PCMT1_uc003qna.2_Silent_p.Q114Q|PCMT1_uc003qnb.2_Silent_p.Q114Q|PCMT1_uc011eeg.1_Silent_p.Q79Q|PCMT1_uc003qnc.2_5'UTR|PCMT1_uc003qnd.2_Silent_p.Q114Q|PCMT1_uc003qnf.2_Silent_p.Q114Q	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		CAGGTTTCCAAGCAACAATCA	0.303													90	176	---	---	---	---	PASS
ABCB1	5243	broad.mit.edu	37	7	87214930	87214930	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87214930C>T	uc003uiz.1	-	5	602	c.184G>A	c.(184-186)GGG>AGG	p.G62R	ABCB1_uc011khc.1_Missense_Mutation_p.G62R	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	62	ABC transmembrane type-1 1.|Helical; (Potential).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	AGTCCAGCCCCATGGATGATG	0.393													33	80	---	---	---	---	PASS
SLC25A40	55972	broad.mit.edu	37	7	87483612	87483612	+	Silent	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87483612T>C	uc003uje.2	-	5	522	c.171A>G	c.(169-171)GTA>GTG	p.V57V		NM_018843	NP_061331	Q8TBP6	S2540_HUMAN	mitochondrial carrier family protein	57	Solcar 1.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			haematopoietic_and_lymphoid_tissue(1)	1	Esophageal squamous(14;0.00202)					CATTACTATATACAAAACATT	0.353													101	192	---	---	---	---	PASS
ALKBH4	54784	broad.mit.edu	37	7	102098340	102098340	+	Missense_Mutation	SNP	C	T	T	rs145100726	byFrequency	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102098340C>T	uc003uzl.2	-	3	415	c.410G>A	c.(409-411)CGG>CAG	p.R137Q	ALKBH4_uc003uzm.2_Missense_Mutation_p.R64Q	NM_017621	NP_060091	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4	137						cytoplasm|nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						GCCCATCCTCCGCACCACCTC	0.637													3	16	---	---	---	---	PASS
CLEC2L	154790	broad.mit.edu	37	7	139225199	139225199	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139225199C>A	uc010lnd.2	+	3	398	c.398C>A	c.(397-399)GCG>GAG	p.A133E		NM_001080511	NP_001073980	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	133	C-type lectin.					integral to membrane	sugar binding				0	Melanoma(164;0.233)					ACCCACGAGGCGGTGCTGGCT	0.607													4	13	---	---	---	---	PASS
PTK2B	2185	broad.mit.edu	37	8	27296898	27296898	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27296898G>A	uc003xfn.1	+	25	2625	c.1817G>A	c.(1816-1818)AGT>AAT	p.S606N	PTK2B_uc003xfo.1_Missense_Mutation_p.S606N|PTK2B_uc003xfp.1_Missense_Mutation_p.S606N|PTK2B_uc003xfq.1_Missense_Mutation_p.S606N|PTK2B_uc003xfr.1_Missense_Mutation_p.S352N	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	606	Protein kinase.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)		ACGACAGCCAGTGACGTCTGG	0.527													13	33	---	---	---	---	PASS
GSR	2936	broad.mit.edu	37	8	30538473	30538473	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30538473T>C	uc003xih.1	-	12	1458	c.1367A>G	c.(1366-1368)AAA>AGA	p.K456R		NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor	456					cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)	TGTTTTCCTTTTGGTAACTGC	0.363													172	301	---	---	---	---	PASS
MARCH8	220972	broad.mit.edu	37	10	45956930	45956930	+	Intron	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45956930G>C	uc001jci.1	-						MARCH8_uc001jch.2_Intron|MARCH8_uc001jcj.1_Intron|MARCH8_uc001jck.1_Intron|MARCH8_uc001jcg.1_5'UTR	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TCAGTGGCAGGTTAATCCCCC	0.433													3	14	---	---	---	---	PASS
A1CF	29974	broad.mit.edu	37	10	52601746	52601746	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52601746T>A	uc001jjj.2	-	5	429	c.241A>T	c.(241-243)AAA>TAA	p.K81*	A1CF_uc010qhn.1_Nonsense_Mutation_p.K89*|A1CF_uc001jji.2_Nonsense_Mutation_p.K81*|A1CF_uc001jjh.2_Nonsense_Mutation_p.K89*|A1CF_uc010qho.1_Nonsense_Mutation_p.K89*|A1CF_uc009xov.2_Nonsense_Mutation_p.K81*|A1CF_uc001jjk.1_Nonsense_Mutation_p.K81*	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	81	RRM 1.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1						TCATAAATTTTACCGATCTGC	0.269													74	173	---	---	---	---	PASS
LRRTM3	347731	broad.mit.edu	37	10	68857511	68857511	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68857511C>T	uc001jmz.1	+	3	2253	c.1703C>T	c.(1702-1704)ACA>ATA	p.T568I	CTNNA3_uc009xpn.1_Intron|CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron	NM_178011	NP_821079	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	568	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						AGCACAATCACAACAGCTGGC	0.458													4	121	---	---	---	---	PASS
LRIT2	340745	broad.mit.edu	37	10	85982281	85982281	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85982281G>T	uc001kcy.2	-	3	1056	c.1048C>A	c.(1048-1050)CTA>ATA	p.L350I	LRIT2_uc010qmc.1_Missense_Mutation_p.L360I	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	350						integral to membrane				ovary(2)	2						GGTGCATGTAGGGCCTGGGCA	0.542													6	69	---	---	---	---	PASS
FAM190B	54462	broad.mit.edu	37	10	86132005	86132005	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86132005G>T	uc001kdh.1	+	2	1391	c.1197G>T	c.(1195-1197)TTG>TTT	p.L399F	FAM190B_uc001kdg.1_Missense_Mutation_p.L399F|FAM190B_uc010qmd.1_Missense_Mutation_p.L399F	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14	399										ovary(3)|skin(1)	4						ACATTTCCTTGTCGTCTTTGT	0.333													4	149	---	---	---	---	PASS
COX15	1355	broad.mit.edu	37	10	101478246	101478246	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101478246C>T	uc001kqb.3	-	7	1461	c.844G>A	c.(844-846)GCA>ACA	p.A282T	COX15_uc001kqc.3_Missense_Mutation_p.A282T|COX15_uc010qpj.1_Missense_Mutation_p.A103T	NM_078470	NP_510870	Q7KZN9	COX15_HUMAN	COX15 homolog isoform 1	282	Helical; (Potential).				heme a biosynthetic process|respiratory chain complex IV assembly|respiratory gaseous exchange	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;3.08e-10)|all cancers(201;2.43e-08)		TCTAGCCCTGCCACAAAAGCC	0.433													3	39	---	---	---	---	PASS
ADD3	120	broad.mit.edu	37	10	111860410	111860410	+	5'UTR	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111860410A>G	uc001kyt.3	+	3					ADD3_uc001kys.3_5'UTR|ADD3_uc001kyu.2_5'UTR|ADD3_uc001kyv.2_5'UTR|ADD3_uc001kyw.2_5'UTR	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		CAGACTTAAAACATGAGCTCA	0.398													4	40	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	19955242	19955242	+	Silent	SNP	C	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19955242C>A	uc010rdm.1	+	8	1882	c.1521C>A	c.(1519-1521)GGC>GGA	p.G507G	NAV2_uc001mpp.2_Silent_p.G420G|NAV2_uc001mpr.3_Silent_p.G484G	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	507	Potential.					nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						CTCTgaaaggcaatgagaaag	0.403													45	94	---	---	---	---	PASS
NAV2	89797	broad.mit.edu	37	11	19955243	19955243	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19955243A>T	uc010rdm.1	+	8	1883	c.1522A>T	c.(1522-1524)AAT>TAT	p.N508Y	NAV2_uc001mpp.2_Missense_Mutation_p.N421Y|NAV2_uc001mpr.3_Missense_Mutation_p.N485Y	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	508	Potential.					nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						TCTgaaaggcaatgagaaaga	0.398													45	95	---	---	---	---	PASS
TTC17	55761	broad.mit.edu	37	11	43418228	43418228	+	Intron	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43418228G>A	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron|TTC17_uc001mxj.2_Translation_Start_Site	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17								binding			ovary(5)	5						GTCTTGAGTCGTGTTTGTAAT	0.358													4	213	---	---	---	---	PASS
HSPA8	3312	broad.mit.edu	37	11	122930929	122930929	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122930929A>G	uc001pyo.2	-	4	537	c.459T>C	c.(457-459)TCT>TCC	p.S153S	HSPA8_uc009zbc.2_5'UTR|HSPA8_uc001pyp.2_Silent_p.S153S|HSPA8_uc010rzu.1_Silent_p.S76S|HSPA8_uc009zbd.1_Silent_p.S153S|HSPA8_uc010rzv.1_Silent_p.S153S	NM_006597	NP_006588	P11142	HSP7C_HUMAN	heat shock 70kDa protein 8 isoform 1	153					cellular membrane organization|interspecies interaction between organisms|mRNA metabolic process|negative regulation of transcription, DNA-dependent|neurotransmitter secretion|post-Golgi vesicle-mediated transport|protein folding|response to unfolded protein|transcription, DNA-dependent	cell surface|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|melanosome|plasma membrane|ribonucleoprotein complex	ATP binding|ATPase activity, coupled|protein binding			central_nervous_system(7)|lung(1)	8		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CCTGACGCTGAGAGTCATTAA	0.408													28	39	---	---	---	---	PASS
HSN2	378465	broad.mit.edu	37	12	977317	977317	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:977317G>T	uc001qiq.2	+	1	448	c.322G>T	c.(322-324)GTA>TTA	p.V108L	WNK1_uc001qio.3_Intron|WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_213655	NP_998820			hereditary sensory neuropathy, type II												0	all_cancers(10;0.0107)|all_epithelial(11;0.0151)|Ovarian(42;0.0512)|all_lung(10;0.0521)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.000967)|BRCA - Breast invasive adenocarcinoma(9;0.0178)			AGCCAGTAGAGTAACTGGAGA	0.483													3	60	---	---	---	---	PASS
PTMS	5763	broad.mit.edu	37	12	6879708	6879708	+	3'UTR	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6879708G>A	uc001qqq.2	+	5					PTMS_uc001qqr.2_RNA|LAG3_uc001qqs.2_5'Flank|LAG3_uc001qqt.3_5'Flank|LAG3_uc001qqu.2_5'Flank	NM_002824	NP_002815	P20962	PTMS_HUMAN	parathymosin						DNA replication	nucleus				liver(1)	1						CCCTGCTCTGGGCCCTGCACC	0.652													3	1	---	---	---	---	PASS
ARID2	196528	broad.mit.edu	37	12	46215243	46215243	+	Silent	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46215243A>G	uc001ros.1	+	6	678	c.678A>G	c.(676-678)AAA>AAG	p.K226K	ARID2_uc001ror.2_Silent_p.K226K	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	226					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		AAGAATGGAAAGAGAAGACTG	0.289													5	146	---	---	---	---	PASS
ZNF740	283337	broad.mit.edu	37	12	53579788	53579788	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53579788T>A	uc001scb.3	+	5	694	c.300T>A	c.(298-300)AAT>AAA	p.N100K		NM_001004304	NP_001004304	Q8NDX6	ZN740_HUMAN	zinc finger protein 740	100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|protein binding|zinc ion binding				0						TTCCCAAAAATTTTGTTTGTG	0.438													55	104	---	---	---	---	PASS
SYT1	6857	broad.mit.edu	37	12	79747321	79747321	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79747321G>A	uc001sys.2	+	10	1521	c.850G>A	c.(850-852)GTA>ATA	p.V284I	SYT1_uc001syt.2_Missense_Mutation_p.V284I|SYT1_uc001syu.2_Missense_Mutation_p.V281I|SYT1_uc001syv.2_Missense_Mutation_p.V284I	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I	284	Cytoplasmic (Potential).|Phospholipid binding (Probable).				detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						CCTTCGCTACGTACCTACTGC	0.398													82	148	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117728212	117728212	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117728212T>A	uc001twm.1	-	4	1558	c.872A>T	c.(871-873)CAG>CTG	p.Q291L		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	291					multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	TGTGGGGGACTGTTTTCCTGA	0.562													4	50	---	---	---	---	PASS
CSNK1A1L	122011	broad.mit.edu	37	13	37679428	37679428	+	5'UTR	SNP	T	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37679428T>G	uc001uwm.1	-	1						NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GGCTCAGCCCTGACCCCTCTA	0.617													13	30	---	---	---	---	PASS
TPT1	7178	broad.mit.edu	37	13	45911319	45911319	+	3'UTR	SNP	A	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45911319A>T	uc001uzy.1	-	6					TPT1_uc001uzz.1_3'UTR	NM_003295	NP_003286	P13693	TCTP_HUMAN	tumor protein, translationally-controlled 1						anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)		AAATGAGTTTAAATGCATTTT	0.328													7	4	---	---	---	---	PASS
TPT1	7178	broad.mit.edu	37	13	45911320	45911320	+	3'UTR	SNP	A	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45911320A>T	uc001uzy.1	-	6					TPT1_uc001uzz.1_3'UTR	NM_003295	NP_003286	P13693	TCTP_HUMAN	tumor protein, translationally-controlled 1						anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)		AATGAGTTTAAATGCATTTTA	0.323													7	4	---	---	---	---	PASS
DCAF11	80344	broad.mit.edu	37	14	24587733	24587733	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24587733G>C	uc001wlv.2	+	7	994	c.714G>C	c.(712-714)TGG>TGC	p.W238C	DCAF11_uc001wlw.2_Missense_Mutation_p.W238C|DCAF11_uc001wlz.2_Missense_Mutation_p.W138C|DCAF11_uc001wly.2_Missense_Mutation_p.W194C|DCAF11_uc001wme.2_Missense_Mutation_p.W198C|DCAF11_uc010tny.1_Missense_Mutation_p.W105C|DCAF11_uc001wmd.2_Missense_Mutation_p.W238C|DCAF11_uc001wmc.2_Missense_Mutation_p.W138C|DCAF11_uc001wmb.3_Missense_Mutation_p.W212C|DCAF11_uc001wma.3_Missense_Mutation_p.W238C	NM_001163484	NP_001156956	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11 isoform 1	238	WD 2.					CUL4 RING ubiquitin ligase complex	protein binding				0						ACTCTAGCTGGTCTGATTACA	0.552													19	47	---	---	---	---	PASS
ARHGAP5	394	broad.mit.edu	37	14	32563340	32563340	+	Nonsense_Mutation	SNP	T	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32563340T>G	uc001wrl.2	+	2	3704	c.3465T>G	c.(3463-3465)TAT>TAG	p.Y1155*	ARHGAP5_uc001wrm.2_Nonsense_Mutation_p.Y1155*|ARHGAP5_uc001wrn.2_Nonsense_Mutation_p.Y1155*|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	1155					cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AATACAAATATAAATCTAAAA	0.353													29	46	---	---	---	---	PASS
C14orf138	79609	broad.mit.edu	37	14	50579393	50579393	+	Silent	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50579393T>C	uc001wxo.1	-	5	642	c.615A>G	c.(613-615)AAA>AAG	p.K205K	C14orf138_uc001wxn.1_Intron|C14orf138_uc001wxp.1_Intron|C14orf138_uc001wxq.1_RNA	NM_024558	NP_078834	Q9H867	MT21D_HUMAN	hypothetical protein LOC79609 isoform a	205							methyltransferase activity				0	all_epithelial(31;0.000822)|Breast(41;0.0065)					CTTCATCATGTTTTTCCAAAG	0.254													57	118	---	---	---	---	PASS
CHP	11261	broad.mit.edu	37	15	41571706	41571706	+	3'UTR	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41571706C>T	uc001znl.2	+	7					CHP_uc010bcd.1_5'Flank	NM_007236	NP_009167	Q99653	CHP1_HUMAN	calcium binding protein P22						potassium ion transport|small GTPase mediated signal transduction		potassium channel regulator activity			ovary(1)	1		all_cancers(109;1.19e-18)|all_epithelial(112;5.87e-16)|Lung NSC(122;8.86e-12)|all_lung(180;2.47e-10)|Melanoma(134;0.0574)|Colorectal(260;0.0946)|Ovarian(310;0.143)		GBM - Glioblastoma multiforme(113;1.68e-06)|LUSC - Lung squamous cell carcinoma(244;0.008)|Lung(196;0.00802)|BRCA - Breast invasive adenocarcinoma(123;0.169)		ACTGCTGTTGCATGACAACCC	0.438													3	25	---	---	---	---	PASS
ACSBG1	23205	broad.mit.edu	37	15	78486923	78486923	+	Silent	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78486923G>A	uc002bdh.2	-	3	434	c.378C>T	c.(376-378)CGC>CGT	p.R126R	ACSBG1_uc010umw.1_Silent_p.R126R|ACSBG1_uc010umx.1_Intron|ACSBG1_uc010umy.1_Silent_p.R19R	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	126					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						ACTTGTCCTGGCGCTTGAAGC	0.592													43	49	---	---	---	---	PASS
ALDOA	226	broad.mit.edu	37	16	30081653	30081653	+	3'UTR	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30081653C>T	uc002dvw.2	+	12					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|ALDOA_uc002dvx.2_3'UTR|ALDOA_uc002dvy.2_3'UTR|ALDOA_uc002dvz.2_3'UTR|ALDOA_uc002dwa.3_3'UTR|ALDOA_uc002dwb.1_3'UTR|ALDOA_uc002dwc.2_3'UTR|ALDOA_uc010veg.1_3'UTR|ALDOA_uc002dwd.2_3'UTR	NM_184043	NP_908932	P04075	ALDOA_HUMAN	fructose-bisphosphate aldolase A						actin filament organization|ATP biosynthetic process|fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|muscle cell homeostasis|platelet activation|platelet degranulation|protein homotetramerization|regulation of cell shape|striated muscle contraction	actin cytoskeleton|cytosol|extracellular vesicular exosome|I band|platelet alpha granule lumen	actin binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding|tubulin binding			lung(1)	1						TCCCTCGTGACAGTGGTGTGT	0.607													5	3	---	---	---	---	PASS
UBE2MP1	606551	broad.mit.edu	37	16	34404516	34404516	+	RNA	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34404516C>T	uc002edv.1	-	1		c.247G>A				NR_002837				full-length cDNA clone CS0DH003YB23 of T cells (Jurkat cell line) of Homo sapiens (human).												0						CTTCTGGATCCGCAGCTGCGC	0.557													7	16	---	---	---	---	PASS
CHD9	80205	broad.mit.edu	37	16	53269085	53269085	+	Intron	SNP	T	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53269085T>A	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002eha.1_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_5'UTR|CHD9_uc002ehd.2_Intron|CHD9_uc002ehe.1_5'UTR	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)				CATTCTTTGTTTTTCCACAAA	0.353													41	74	---	---	---	---	PASS
CCDC144C	348254	broad.mit.edu	37	17	20224931	20224931	+	RNA	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20224931T>C	uc010cqy.1	+	1		c.445T>C				NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						CACGTCTTGGTTCCTGGAGAC	0.642													4	23	---	---	---	---	PASS
NAT9	26151	broad.mit.edu	37	17	72769713	72769713	+	Splice_Site	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72769713A>G	uc002jlq.2	-	3	264	c.190_splice	c.e3+1	p.K64_splice	NAT9_uc002jlr.2_Splice_Site_p.K63_splice|TMEM104_uc010wrf.1_5'Flank|TMEM104_uc010wrg.1_5'Flank|TMEM104_uc002jls.3_5'Flank|TMEM104_uc010dfx.2_5'Flank	NM_015654	NP_056469	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9							protein complex	N-acetyltransferase activity				0						GGCACTCCTCACTGTCTGCAT	0.612													15	29	---	---	---	---	PASS
TAF4B	6875	broad.mit.edu	37	18	23845140	23845140	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23845140T>C	uc002kvu.3	+	2	839	c.350T>C	c.(349-351)GTT>GCT	p.V117A	TAF4B_uc002kvs.3_RNA|TAF4B_uc002kvt.3_Missense_Mutation_p.V117A	NM_005640	NP_005631	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding	117					transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			ATAGGAACCGTTTTGATTAAA	0.373													4	63	---	---	---	---	PASS
KIAA1468	57614	broad.mit.edu	37	18	59854885	59854885	+	Silent	SNP	T	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59854885T>G	uc002lil.2	+	1	362	c.147T>G	c.(145-147)CCT>CCG	p.P49P	PIGN_uc002lii.3_5'Flank|PIGN_uc002lij.3_5'Flank|KIAA1468_uc002lik.1_Silent_p.P49P|KIAA1468_uc010xel.1_Silent_p.P49P	NM_020854	NP_065905	Q9P260	K1468_HUMAN	hypothetical protein LOC57614	49							binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)				GCCTAGATCCTGGCTCTGCGG	0.657													17	29	---	---	---	---	PASS
VAV1	7409	broad.mit.edu	37	19	6828475	6828475	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6828475C>T	uc002mfu.1	+	11	1166	c.1069C>T	c.(1069-1071)CGG>TGG	p.R357W	VAV1_uc010xjh.1_Missense_Mutation_p.R325W|VAV1_uc010dva.1_Missense_Mutation_p.R357W|VAV1_uc002mfv.1_Missense_Mutation_p.R302W	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	357	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						GGAGAACCTGCGGCTGGCCCT	0.627													14	33	---	---	---	---	PASS
ADAMTS10	81794	broad.mit.edu	37	19	8661425	8661425	+	Splice_Site	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8661425C>T	uc002mkj.1	-	9	1358	c.1084_splice	c.e9+1	p.G362_splice	ADAMTS10_uc002mkk.1_Splice_Site	NM_030957	NP_112219	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(2)	4						GGCTCGGGTACCTAGTGTGCC	0.612													4	99	---	---	---	---	PASS
ANKRD27	84079	broad.mit.edu	37	19	33110234	33110234	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33110234A>T	uc002ntn.1	-	20	2095	c.1939T>A	c.(1939-1941)TCC>ACC	p.S647T		NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	647					early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					CTGGAAGTGGAGGACTCTTGG	0.622													15	32	---	---	---	---	PASS
CYP2F1	1572	broad.mit.edu	37	19	41628763	41628763	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41628763A>G	uc002opu.1	+	7	915	c.859A>G	c.(859-861)ACC>GCC	p.T287A	CYP2F1_uc010xvw.1_Missense_Mutation_p.T73A|CYP2F1_uc010xvv.1_Missense_Mutation_p.T287A|CYP2F1_uc002opv.1_RNA	NM_000774	NP_000765	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F,	287					naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						CCACATGGATACCCTGCTGAT	0.567													4	139	---	---	---	---	PASS
FPR1	2357	broad.mit.edu	37	19	52249899	52249899	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52249899C>T	uc002pxq.2	-	2	444	c.349G>A	c.(349-351)GCC>ACC	p.A117T		NM_002029	NP_002020	P21462	FPR1_HUMAN	formyl peptide receptor 1	117	Helical; Name=3; (Potential).				activation of MAPK activity|cellular component movement|chemotaxis|G-protein signaling, coupled to cAMP nucleotide second messenger|nitric oxide mediated signal transduction	endosome|integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)|lung(1)|skin(1)	3		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	GCAATGAGGGCGATCAGGAAG	0.557													10	36	---	---	---	---	PASS
ZNF808	388558	broad.mit.edu	37	19	53056520	53056520	+	Silent	SNP	T	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53056520T>C	uc010epq.1	+	5	528	c.351T>C	c.(349-351)TGT>TGC	p.C117C	ZNF808_uc002pzq.2_RNA|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	117					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)		AGTTTCAGTGTCAAGAAGATG	0.398													5	143	---	---	---	---	PASS
FAM71E2	284418	broad.mit.edu	37	19	55873723	55873723	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55873723G>A	uc002qkr.2	-	3	640	c.454C>T	c.(454-456)CTC>TTC	p.L152F	FAM71E2_uc002qkq.2_5'UTR	NM_001145402	NP_001138874	Q8N5Q1	F71E2_HUMAN	hypothetical protein LOC284418	152											0						AGGTTGATGAGGCGGACCCAG	0.697													7	8	---	---	---	---	PASS
EYA2	2139	broad.mit.edu	37	20	45702893	45702893	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45702893C>A	uc002xsm.2	+	7	954	c.580C>A	c.(580-582)CCT>ACT	p.P194T	EYA2_uc010ghp.2_Missense_Mutation_p.P194T|EYA2_uc002xsn.2_Missense_Mutation_p.P199T|EYA2_uc002xso.2_Missense_Mutation_p.P194T|EYA2_uc002xsp.2_Missense_Mutation_p.P194T|EYA2_uc002xsq.2_Missense_Mutation_p.P194T	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a	194					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				CAGCATCTGCCCTTCGCCCCT	0.612													22	39	---	---	---	---	PASS
DDX27	55661	broad.mit.edu	37	20	47838004	47838004	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47838004G>C	uc002xuh.2	+	2	263	c.202G>C	c.(202-204)GGC>CGC	p.G68R		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	68	Asp/Glu/Lys-rich.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CATTGTGCTGGGCAGACGACA	0.458													34	70	---	---	---	---	PASS
ZNFX1	57169	broad.mit.edu	37	20	47887950	47887950	+	Silent	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47887950C>T	uc002xui.2	-	3	646	c.399G>A	c.(397-399)AAG>AAA	p.K133K		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	133							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GTTCTGTAGGCTTCTGGTGGG	0.522													12	21	---	---	---	---	PASS
GATA5	140628	broad.mit.edu	37	20	61041502	61041502	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61041502G>A	uc002ycx.1	-	4	867	c.805C>T	c.(805-807)CTC>TTC	p.L269F		NM_080473	NP_536721	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	269					blood coagulation|intestinal epithelial cell differentiation|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			TTCATGTAGAGGCCGCAGGCA	0.697													3	15	---	---	---	---	PASS
SOD1	6647	broad.mit.edu	37	21	33032038	33032038	+	5'UTR	SNP	C	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33032038C>T	uc002ypa.2	+	1					uc002yoz.1_5'Flank|SOD1_uc002ypb.2_5'UTR|SOD1_uc002ypc.2_RNA	NM_000454	NP_000445	P00441	SODC_HUMAN	superoxide dismutase 1, soluble						activation of MAPK activity|auditory receptor cell stereocilium organization|cell aging|cellular iron ion homeostasis|DNA fragmentation involved in apoptotic nuclear change|double-strand break repair|embryo implantation|glutathione metabolic process|heart contraction|hydrogen peroxide biosynthetic process|locomotory behavior|muscle cell homeostasis|myeloid cell homeostasis|negative regulation of cholesterol biosynthetic process|negative regulation of neuron apoptosis|neurofilament cytoskeleton organization|ovarian follicle development|peripheral nervous system myelin maintenance|placenta development|platelet activation|platelet degranulation|positive regulation of cytokine production|regulation of blood pressure|regulation of mitochondrial membrane potential|regulation of multicellular organism growth|regulation of organ growth|regulation of T cell differentiation in thymus|relaxation of vascular smooth muscle|removal of superoxide radicals|response to axon injury|response to drug|response to ethanol|response to heat|response to hydrogen peroxide|retina homeostasis|sensory perception of sound|spermatogenesis|thymus development	cytoplasmic vesicle|cytosol|dendrite cytoplasm|extracellular matrix|extracellular space|mitochondrial matrix|neuronal cell body|nucleus|peroxisome|protein complex	chaperone binding|copper ion binding|protein homodimerization activity|protein phosphatase 2B binding|superoxide dismutase activity|zinc ion binding				0						CTGGGGTTTCCGTTGCAGTCC	0.647													12	14	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33076230	33076230	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33076230C>G	uc002ypd.2	-	4	595	c.169G>C	c.(169-171)GAA>CAA	p.E57Q	SFRS15_uc002ype.2_Missense_Mutation_p.E57Q|SFRS15_uc010glu.2_Missense_Mutation_p.E42Q|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Missense_Mutation_p.E57Q	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	57	CID.					nucleus	nucleotide binding|RNA binding				0						ACCTTGTATTCTGGTTTACAC	0.348													44	76	---	---	---	---	PASS
RPL3	6122	broad.mit.edu	37	22	39709724	39709724	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39709724A>T	uc003axi.2	-	8	1030	c.962T>A	c.(961-963)GTC>GAC	p.V321D	RPL3_uc003axh.2_Missense_Mutation_p.V272D|RPL3_uc003axj.2_Missense_Mutation_p.V169D|RPL3_uc010gxx.2_Missense_Mutation_p.V269D|RPL3_uc003axg.2_Missense_Mutation_p.V269D|RPL3_uc003axk.1_Missense_Mutation_p.V169D	NM_000967	NP_000958	P39023	RL3_HUMAN	ribosomal protein L3 isoform a	321					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			breast(1)|kidney(1)	2	Melanoma(58;0.04)					ACCATAGTGGACAAAGCCACC	0.587													3	18	---	---	---	---	PASS
SLC25A6	293	broad.mit.edu	37	X	1505637	1505637	+	Missense_Mutation	SNP	G	A	A	rs143212891		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1505637G>A	uc004cpt.2	-	4	851	c.755C>T	c.(754-756)ACG>ATG	p.T252M	SLC25A6_uc004cpu.2_RNA	NM_001636	NP_001627	P12236	ADT3_HUMAN	adenine nucleotide translocator 3	252	Solcar 3.				active induction of host immune response by virus|apoptosis|energy reserve metabolic process|regulation of insulin secretion|viral infectious cycle	integral to membrane|mitochondrial inner membrane presequence translocase complex	ATP:ADP antiporter activity|protein binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Clodronate(DB00720)	GACGGTGCCCGTGTACATGAT	0.612													44	81	---	---	---	---	PASS
KAZ	23254	broad.mit.edu	37	1	15269725	15269726	+	Intron	DEL	AG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15269725_15269726delAG	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_5'Flank	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						GAGGCCACTCAGAGCAAGAATT	0.510													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35375433	35375433	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35375433delA								DLGAP3 (4449 upstream) : ZMYM6 (73935 downstream)																							GCTTCCTAAGAAAAAAAAACA	0.408													4	2	---	---	---	---	
ZNF684	127396	broad.mit.edu	37	1	41009077	41009077	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41009077delT	uc001cft.1	+							NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			ATTATCCATCTTTTTTTTATT	0.229													4	2	---	---	---	---	
FOXJ3	22887	broad.mit.edu	37	1	42766727	42766729	+	Intron	DEL	ATC	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42766727_42766729delATC	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron|FOXJ3_uc001chh.1_Intron	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ggatgtctaaatctcttcccaga	0.000													4	3	---	---	---	---	
PDZK1IP1	10158	broad.mit.edu	37	1	47654108	47654108	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47654108delG	uc001cqw.2	-							NM_005764	NP_005755	Q13113	PDZ1I_HUMAN	PDZK1 interacting protein 1							integral to membrane					0						TGAGCCTGCAGGAGCTCAGCC	0.577													4	2	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70446814	70446815	+	Intron	DEL	AG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70446814_70446815delAG	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ACACACACCAAGAGAGAGAGAC	0.441													4	2	---	---	---	---	
USP33	23032	broad.mit.edu	37	1	78189345	78189345	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78189345delT	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						ATAtttgttgtttttttttgt	0.109													3	4	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85784769	85784770	+	3'UTR	DEL	TG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85784769_85784770delTG	uc001dlb.2	-	6					DDAH1_uc001dlc.2_3'UTR|uc001dla.1_Intron|DDAH1_uc010osb.1_3'UTR|DDAH1_uc009wco.2_3'UTR	NM_012137	NP_036269	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	GGAAAACTTATGTGATAGTATC	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101117683	101117683	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101117683delA								GPR88 (110101 upstream) : VCAM1 (67614 downstream)																							GAAAAAGGCTAAAACTACAAA	0.423													4	2	---	---	---	---	
COL11A1	1301	broad.mit.edu	37	1	103426301	103426302	+	Intron	INS	-	A	A	rs145064801	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103426301_103426302insA	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGCATGAAGGGAAAAAAAAAGG	0.391													1	6	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145109259	145109260	+	Intron	INS	-	A	A	rs150048477	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109259_145109260insA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						cactccagcccgggggcagagc	0.059													4	3	---	---	---	---	
INTS3	65123	broad.mit.edu	37	1	153721668	153721668	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153721668delA	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_5'Flank|INTS3_uc001fcw.2_5'Flank	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGAGCAGGTAATAGAGATTA	0.527											OREG0013826	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163210220	163210220	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163210220delA								RGS5 (37348 upstream) : NUF2 (81503 downstream)																							catggtggggaaaaaaaaaaa	0.010													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174343665	174343666	+	Intron	INS	-	AT	AT	rs138961682	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174343665_174343666insAT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						CCTAGATATCAATATATAGGTA	0.312													0	6	---	---	---	---	
TPR	7175	broad.mit.edu	37	1	186309101	186309101	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186309101delA	uc001grv.2	-							NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ATACAAGAGGAAAAAAAAATA	0.299			T	NTRK1	papillary thyroid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	192499040	192499040	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192499040delT								RGS21 (162628 upstream) : RGS1 (45817 downstream)																							gagatcacactttttttaatg	0.000													4	2	---	---	---	---	
CFH	3075	broad.mit.edu	37	1	196645303	196645303	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196645303delT	uc001gtj.3	+						CFH_uc001gti.3_Intron|CFH_uc009wyw.2_Intron|CFH_uc009wyx.2_Intron	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						ttatttaatgtttttttttCT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209216996	209216996	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209216996delA								PLXNA2 (799331 upstream) : LOC642587 (385172 downstream)																							TTGGCTATATAATAAAAGGTA	0.303													4	2	---	---	---	---	
INTS7	25896	broad.mit.edu	37	1	212201176	212201176	+	Intron	DEL	T	-	-	rs66579625		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212201176delT	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249	Q9NVH2	INT7_HUMAN	integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		TCGAGATTCCttttttttttc	0.065													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228254474	228254474	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228254474delC								WNT3A (5513 upstream) : ARF1 (15887 downstream)																							ctctctctctctTTTTTTTTT	0.418													5	4	---	---	---	---	
RAB4A	5867	broad.mit.edu	37	1	229433514	229433514	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229433514delT	uc001hth.2	+						RAB4A_uc001hti.2_Intron|RAB4A_uc001htj.2_Intron	NM_004578	NP_004569	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family								GDP binding|GTP binding|GTPase activity			ovary(1)	1	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				TTTCCAATTGTTTTTTTCTAT	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23543320	23543321	+	IGR	DEL	CC	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23543320_23543321delCC								None (None upstream) : KLHL29 (212134 downstream)																							CCATCCCCCGCCCCCCCACACA	0.490													4	2	---	---	---	---	
SULT6B1	391365	broad.mit.edu	37	2	37421322	37421322	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37421322delT	uc002rpv.2	-						SULT6B1_uc010fae.1_Intron|SULT6B1_uc010faf.1_Intron|SULT6B1_uc002rpw.2_Intron|SULT6B1_uc010fag.1_Intron|uc002rpx.1_5'Flank			Q6IMI4	ST6B1_HUMAN	Homo sapiens sulfotransferase SULT6B1 (SULT6B1) mRNA, partial 5'UTR; alternate transcript.							cytoplasm	sulfotransferase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(82;0.248)				TGTCTGTAGAttttttttttt	0.149													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46273017	46273018	+	Intron	INS	-	A	A	rs71394869		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46273017_46273018insA	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			ctgtctcaaataaaaaaaaaag	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62788122	62788122	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62788122delT								TMEM17 (25342 upstream) : EHBP1 (112891 downstream)																							TGCTGTACCATTTTCTCTTAC	0.378													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845792	71845793	+	Intron	DEL	GT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845792_71845793delGT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						GGCAGAGGAGgtgtgtgtgtgg	0.183													6	3	---	---	---	---	
POLR1A	25885	broad.mit.edu	37	2	86259773	86259773	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86259773delA	uc002sqs.2	-						POLR1A_uc010ytb.1_Intron	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						CCCAAAAATTAAAAAAAAAAG	0.418													3	3	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87864766	87864766	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87864766delG	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						aagtggcattggaagtgagtg	0.000													4	2	---	---	---	---	
MAP4K4	9448	broad.mit.edu	37	2	102486034	102486035	+	Intron	DEL	TG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102486034_102486035delTG	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_Intron|MAP4K4_uc002tbl.2_Intron	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase						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						CATCTTCTCCTGTCCCTGCTCC	0.450													4	2	---	---	---	---	
IL18R1	8809	broad.mit.edu	37	2	102974342	102974343	+	Intron	DEL	GT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102974342_102974343delGT	uc002tbw.3	+							NM_003855	NP_003846	Q13478	IL18R_HUMAN	interleukin 18 receptor 1 precursor						innate immune response	integral to membrane|plasma membrane	interleukin-1 receptor activity			ovary(2)|pancreas(1)	3						GAGTTTAAGCGTGTGTGTGTGT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118043382	118043382	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118043382delA								None (None upstream) : DDX18 (528873 downstream)																							ataaagacagaaactgaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131138556	131138556	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131138556delA								PTPN18 (5575 upstream) : CFC1B (140280 downstream)																							GCCTTGCTGGAAAAAAAAAGA	0.408													4	2	---	---	---	---	
SLC38A11	151258	broad.mit.edu	37	2	165794366	165794366	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165794366delA	uc002ucv.1	-						SLC38A11_uc002ucu.1_Intron|SLC38A11_uc002ucw.1_Intron	NM_173512	NP_775783	Q08AI6	S38AB_HUMAN	solute carrier family 38, member 11						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1						TCTTCCTTCCAACACCACACA	0.393													4	2	---	---	---	---	
HOXD8	3234	broad.mit.edu	37	2	176995683	176995683	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176995683delT	uc002uko.2	+						uc002ukl.1_5'Flank|uc002ukm.1_5'Flank|HOXD8_uc002ukn.2_Intron|HOXD8_uc002ukp.2_Intron	NM_019558	NP_062458	P13378	HXD8_HUMAN	homeobox D8						anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		TTGGGATGCATTTTTTTTTTA	0.468													2	4	---	---	---	---	
SESTD1	91404	broad.mit.edu	37	2	180119174	180119174	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180119174delA	uc002uni.3	-							NM_178123	NP_835224	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			CTCTCCCTGCAAAACCTAACT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181062821	181062821	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181062821delT								CWC22 (190981 upstream) : UBE2E3 (782291 downstream)																							GCTGGAAACCTTTTTTCATCC	0.323													4	2	---	---	---	---	
SF3B1	23451	broad.mit.edu	37	2	198262521	198262521	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198262521delA	uc002uue.2	-							NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)			actccgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
WNT10A	80326	broad.mit.edu	37	2	219751995	219751996	+	Intron	DEL	GT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219751995_219751996delGT	uc002vjd.1	+							NM_025216	NP_079492	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|female gonad development|hair follicle morphogenesis|odontogenesis|regulation of odontogenesis of dentine-containing tooth|sebaceous gland development|skin development|tongue development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			lung(1)|skin(1)	2		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTGGTGGCAGTGTGTGTGTGT	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73937	73938	+	IGR	INS	-	T	T	rs149000253	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73937_73938insT								None (None upstream) : CHL1 (164712 downstream)																							CAATTTTAAGGTTTTTTTTTTC	0.322													4	2	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16369842	16369842	+	Intron	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16369842delC	uc003cay.2	-						RFTN1_uc010hes.2_Intron|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						GAGTGCTCCACTCAGAAGGTG	0.582													4	2	---	---	---	---	
SMARCC1	6599	broad.mit.edu	37	3	47721723	47721723	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47721723delA	uc003crq.2	-						SMARCC1_uc011bbc.1_Intron|SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		aacaaacaccaaaaaaaaccc	0.139													4	3	---	---	---	---	
GNAI2	2771	broad.mit.edu	37	3	50284737	50284737	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50284737delG	uc003cyq.1	+						GNAI2_uc003cyo.1_Intron|GNAI2_uc003cyp.1_Intron|GNAI2_uc010hlg.1_Intron|GNAI2_uc011bdn.1_Intron	NM_002070	NP_002061	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein),						adenosine receptor signaling pathway|cell cycle|cell division|gamma-aminobutyric acid signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|platelet activation|response to nutrient|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		TCAGGGCTGTGGCAAGTCTGG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	67008091	67008091	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67008091delC								LRIG1 (457246 upstream) : KBTBD8 (40636 downstream)																							tgtctgattacccagCAAAAA	0.080													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115272743	115272743	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115272743delA								ZBTB20 (406616 upstream) : GAP43 (69408 downstream)																							cttgcttgagaaaatgggtgg	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116989464	116989464	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116989464delC								LOC285194 (553579 upstream) : None (None downstream)																							AGCCCCCCAACTATGACCAAA	0.383													4	2	---	---	---	---	
HLTF	6596	broad.mit.edu	37	3	148788845	148788846	+	Intron	DEL	AG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148788845_148788846delAG	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			aaaaaaaaaaagaaaaCTGAGG	0.163													4	3	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155399422	155399422	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155399422delT	uc011bol.1	-							NM_014996	NP_055811	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform b						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GCTTAATTCCTTTTAGGAAAT	0.358													4	2	---	---	---	---	
C3orf55	152078	broad.mit.edu	37	3	157260922	157260922	+	5'Flank	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157260922delA	uc003fbp.3	+						C3orf55_uc011bos.1_5'Flank|C3orf55_uc003fbo.2_5'Flank|C3orf55_uc011bot.1_5'Flank|C3orf55_uc010hvv.2_5'Flank	NM_001130002	NP_001123474	A1A4F0	CC055_HUMAN	hypothetical protein LOC152078 isoform 1												0			Lung(72;0.0215)|LUSC - Lung squamous cell carcinoma(72;0.037)			TCGGCTGGGGAAAAAAACGAG	0.612													3	4	---	---	---	---	
OSTN	344901	broad.mit.edu	37	3	190953348	190953348	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190953348delG	uc011bsn.1	+							NM_198184	NP_937827	P61366	OSTN_HUMAN	osteocrin precursor						cell differentiation|multicellular organismal development|ossification		hormone activity			pancreas(1)|skin(1)	2	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		gaatgtttctgggggtcacat	0.000													4	2	---	---	---	---	
ATP13A4	84239	broad.mit.edu	37	3	193184990	193184990	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193184990delA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_Intron|ATP13A4_uc003ftf.3_Intron	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		attaaaaATTAAAAAAATATG	0.124													4	2	---	---	---	---	
JAKMIP1	152789	broad.mit.edu	37	4	6170641	6170642	+	Intron	DEL	AA	-	-	rs112687448		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6170641_6170642delAA	uc003giu.3	-						JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_Intron|JAKMIP1_uc003giv.3_Intron|JAKMIP1_uc010ide.2_Intron	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						aaataaaaacaaaaaaaaaaat	0.000													4	2	---	---	---	---	
KIAA0232	9778	broad.mit.edu	37	4	6781551	6781552	+	5'Flank	INS	-	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6781551_6781552insG	uc003gjr.3	+						KIAA0232_uc003gjq.3_5'Flank	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778								ATP binding			ovary(2)	2						TCCAAGTCAGAGGGCACTCAGA	0.510													4	2	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7776866	7776866	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7776866delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron|LOC84740_uc003gkd.3_RNA	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						accccgtgtcaaaaaaaaaTT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19942400	19942400	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19942400delA								None (None upstream) : SLIT2 (312835 downstream)																							ATCAAATGCTAAAATATGTGG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70249492	70249492	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70249492delC								UGT2B28 (88725 upstream) : UGT2B4 (96392 downstream)																							agagtcaccaccagagcacta	0.000													4	2	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86758680	86758680	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86758680delA	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron|ARHGAP24_uc010ikf.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AGAGAAAAACAAAAAAAAACA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117226441	117226441	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117226441delT								MIR1973 (5517 upstream) : TRAM1L1 (778275 downstream)																							ATTTTCCCCCTTTTTCTTGCT	0.328													4	2	---	---	---	---	
LARP1B	55132	broad.mit.edu	37	4	129036098	129036098	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129036098delT	uc003iga.2	+						LARP1B_uc003ifz.1_Intron|LARP1B_uc003igb.1_Intron	NM_018078	NP_060548	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family member 2								RNA binding				0						ATGTTAtttattttttttttt	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190818258	190818260	+	Intron	DEL	ATA	-	-	rs112949874		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190818258_190818260delATA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		gcaggtgcacataatgttttgga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3890748	3890749	+	IGR	INS	-	C	C	rs146161044	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3890748_3890749insC								IRX1 (289232 upstream) : None (None downstream)																							CTCTTGCACTTCAGGGCAAATT	0.564													0	6	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21480147	21480147	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21480147delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						atgtacagacttttttcttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	49414482	49414482	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49414482delA								None (None upstream) : EMB (277551 downstream)																							cagattctacaaaaagagtgt	0.000													6	5	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53448523	53448523	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53448523delA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				TCTGCCTTTTACCTGCATCTC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56300170	56300172	+	IGR	DEL	CCA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56300170_56300172delCCA								MIER3 (32669 upstream) : GPBP1 (169603 downstream)																							GCCATTGCTGCCACCACCACCAC	0.591													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102663639	102663640	+	IGR	DEL	TG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102663639_102663640delTG								C5orf30 (49278 upstream) : NUDT12 (220917 downstream)																							GTGgtgtgtatgtgtgtgtgtg	0.228													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112535724	112535724	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112535724delG	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		gctcctagctggggagaaagg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	153940150	153940150	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153940150delT								HAND1 (82326 upstream) : MIR1303 (125186 downstream)																							ttggtttttgttttttttttt	0.090													4	2	---	---	---	---	
BMP6	654	broad.mit.edu	37	6	7860293	7860293	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7860293delT	uc003mxu.3	+							NM_001718	NP_001709	P22004	BMP6_HUMAN	bone morphogenetic protein 6 preproprotein						BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)					cagtatgttattatggaaagc	0.154													4	2	---	---	---	---	
KLHL32	114792	broad.mit.edu	37	6	97579451	97579451	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97579451delG	uc010kcm.1	+						KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136	Q96NJ5	KLH32_HUMAN	kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GTTTCTTTATGGAGTGAATAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	102784256	102784257	+	IGR	INS	-	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102784256_102784257insT								GRIK2 (266299 upstream) : None (None downstream)																							gaggcctcccgttttttttcgt	0.000													4	2	---	---	---	---	
RTN4IP1	84816	broad.mit.edu	37	6	107035899	107035899	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107035899delG	uc003prj.2	-						RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Intron	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor							mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CTTTGATGGAGATGGAAGGAC	0.403													4	2	---	---	---	---	
RTN4IP1	84816	broad.mit.edu	37	6	107035901	107035901	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107035901delT	uc003prj.2	-						RTN4IP1_uc010kdd.2_Intron|RTN4IP1_uc003prk.2_Intron	NM_032730	NP_116119	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1 precursor							mitochondrion	oxidoreductase activity|zinc ion binding				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TTGATGGAGATGGAAGGACAT	0.403													4	2	---	---	---	---	
ENPP1	5167	broad.mit.edu	37	6	132126429	132126429	+	5'Flank	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132126429delA	uc011ecf.1	+							NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	taaacgtgctacattttgttt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147214239	147214239	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147214239delT	uc003qls.1	-						uc003qlt.1_Intron|uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		CATTTGGAAGTTTTTAACTTA	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170478767	170478768	+	IGR	DEL	AC	-	-	rs113705984		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170478767_170478768delAC								C6orf208 (275798 upstream) : LOC154449 (84654 downstream)																							gtacacacagacacacacacac	0.302													4	2	---	---	---	---	
HEATR2	54919	broad.mit.edu	37	7	782301	782301	+	Intron	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:782301delC	uc010krz.1	+						HEATR2_uc003siz.2_Intron	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2								protein binding			skin(1)	1		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		aaatcacatgcccagctcaaa	0.000													4	2	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11670836	11670836	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11670836delT	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCTTTCATGCTTCAGGTTCTA	0.413										HNSCC(18;0.044)			4	2	---	---	---	---	
FAM188B	84182	broad.mit.edu	37	7	30868499	30868500	+	Intron	DEL	CT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30868499_30868500delCT	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182												0						GAGTAGACTACTCTCTCTCTGA	0.550													4	2	---	---	---	---	
AOAH	313	broad.mit.edu	37	7	36630695	36630696	+	Intron	DEL	AG	-	-	rs145058108		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36630695_36630696delAG	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1						GATTCCAAACAGAGAATTTCCT	0.450													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52222472	52222472	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52222472delG								COBL (837957 upstream) : POM121L12 (880877 downstream)																							ATTTACAAATGGCAGTAAGTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57768423	57768423	+	IGR	DEL	C	-	-	rs113395775		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768423delC								ZNF716 (235158 upstream) : None (None downstream)																							CACTTTGTAACCTGGCAGTCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61834019	61834020	+	IGR	INS	-	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61834019_61834020insA								None (None upstream) : LOC643955 (917652 downstream)																							taaactaaaataagaaagccag	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66847047	66847047	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66847047delA								STAG3L4 (60535 upstream) : None (None downstream)																							AGGGTTGGGGACTGGCAGTCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	74016919	74016919	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74016919delA								GTF2IRD1 (1 upstream) : GTF2I (55111 downstream)																							GTAAAAAAAGAAAAAAAAAAA	0.373													5	4	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76884137	76884137	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76884137delA	uc003uga.2	+							NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TTTTCAGAAGAAAAAAAAGAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84598133	84598134	+	IGR	INS	-	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84598133_84598134insT								SEMA3A (773916 upstream) : SEMA3D (26740 downstream)																							aagcctctgtcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	122849254	122849254	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122849254delA								SLC13A1 (9229 upstream) : IQUB (242984 downstream)																							GACCCTACCCAAAAAAACCAA	0.134													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151944708	151944708	+	Intron	DEL	T	-	-	rs113407913		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151944708delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACTAAAAGAATTTTTAAAGTT	0.264			N		medulloblastoma								4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152100708	152100708	+	Intron	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152100708delC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		tgcactcgtacctttatcaca	0.000			N		medulloblastoma								4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4495167	4495189	+	Intron	DEL	TTTTTTTTTTTTTTTTTTTTTTT	-	-	rs140790537		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4495167_4495189delTTTTTTTTTTTTTTTTTTTTTTT	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTTTAGCCAAttttttttttttttttttttttttttttttttt	0.148													6	3	---	---	---	---	
PSD3	23362	broad.mit.edu	37	8	18431668	18431669	+	Intron	INS	-	A	A	rs7839772	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18431668_18431669insA	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		AAACAAAAAGTAAAAAAAAAGT	0.347													4	2	---	---	---	---	
ASH2L	9070	broad.mit.edu	37	8	37993180	37993180	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37993180delT	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665	Q9UBL3	ASH2L_HUMAN	ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				ATGGTTTTTGTTTCAGATAAT	0.358													86	59	---	---	---	---	
TACC1	6867	broad.mit.edu	37	8	38647239	38647239	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38647239delG	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron	NM_006283	NP_006274	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			aggttcctgaggtgggaaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41950668	41950668	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41950668delT								MYST3 (41163 upstream) : AP3M2 (59796 downstream)																							TGGCCTCAACttttttttgag	0.224													4	2	---	---	---	---	
SGK196	84197	broad.mit.edu	37	8	42971150	42971150	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42971150delT	uc003xpw.2	+							NM_032237	NP_115613	Q9H5K3	SG196_HUMAN	protein kinase-like protein SgK196							integral to membrane	ATP binding|protein kinase activity				0						ccttacctccttcacggtctt	0.000													4	2	---	---	---	---	
PXDNL	137902	broad.mit.edu	37	8	52579237	52579237	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52579237delG	uc003xqu.3	-							NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGAGTCCTAGGAGCCACCCA	0.463													4	2	---	---	---	---	
ADHFE1	137872	broad.mit.edu	37	8	67349608	67349608	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67349608delG	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			gtggctaagaggtaatcagtg	0.095													4	2	---	---	---	---	
LY96	23643	broad.mit.edu	37	8	74926044	74926044	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74926044delT	uc003yad.2	+							NM_015364	NP_056179	Q9Y6Y9	LY96_HUMAN	MD-2 protein precursor						cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)			cagaatgtgcttgtggggaat	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16153798	16153798	+	IGR	DEL	G	-	-	rs143780644	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16153798delG								C9orf93 (181903 upstream) : BNC2 (255704 downstream)																							CCCTAGGTCTGGGTAGGTGGT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	27732646	27732646	+	IGR	DEL	A	-	-	rs140453581		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27732646delA								C9orf72 (158804 upstream) : LINGO2 (215882 downstream)																							GAtgccattgaaaaaaaaatt	0.124													4	2	---	---	---	---	
DDX58	23586	broad.mit.edu	37	9	32457558	32457558	+	Intron	DEL	A	-	-	rs7865082	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32457558delA	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CAATTGGAGGAAAAAAAAAAA	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32857760	32857760	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32857760delG								TMEM215 (68563 upstream) : APTX (114849 downstream)																							CACTGGATGTGGCGATCTCCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67912130	67912130	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67912130delA								FAM27B (117941 upstream) : None (None downstream)																							AAACTTTACCAAAAAGTACCA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68427396	68427396	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68427396delC								FAM27B (633207 upstream) : MIR1299 (574843 downstream)																							CTCTGCCCAGCCCCCTAGTTC	0.438													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68494353	68494353	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68494353delA								FAM27B (700164 upstream) : MIR1299 (507886 downstream)																							ATTTGAGAGGAAAGCTGGTGC	0.383													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73304438	73304438	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73304438delA	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						aaattactttaaaaaaaaaac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	94246887	94246887	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94246887delG								NFIL3 (60743 upstream) : ROR2 (78486 downstream)																							GAGGGTGTATGGGCATCCTGG	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102109085	102109085	+	IGR	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102109085delC								SEC61B (116185 upstream) : NR4A3 (475052 downstream)																							ATGAACTAGACCAACAAAGTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	17502679	17502680	+	IGR	INS	-	AA	AA			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17502679_17502680insAA								ST8SIA6 (6425 upstream) : PTPLA (129280 downstream)																							acagtaaactgaaaaaaaaatc	0.000													4	2	---	---	---	---	
CCNY	219771	broad.mit.edu	37	10	35725597	35725597	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35725597delT	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0						ATACGTTACCTTTTTAGAACT	0.403													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47058600	47058601	+	Intron	DEL	CA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47058600_47058601delCA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						aaacacacatcacacacacaac	0.203													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47090757	47090758	+	Intron	DEL	AG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47090757_47090758delAG	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						gtagatattcagagtccttgtt	0.153													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65732710	65732710	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65732710delG								REEP3 (350739 upstream) : ANXA2P3 (852575 downstream)																							TTTGCAGGGTGGCCAAGAGAA	0.438													4	2	---	---	---	---	
GOT1	2805	broad.mit.edu	37	10	101162638	101162639	+	Intron	DEL	AG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101162638_101162639delAG	uc001kpr.2	-						GOT1_uc009xwh.2_Intron|GOT1_uc001kpq.1_Intron	NM_002079	NP_002070	P17174	AATC_HUMAN	aspartate aminotransferase 1						aspartate catabolic process|cellular response to insulin stimulus|gluconeogenesis|response to glucocorticoid stimulus	cytosol	L-aspartate:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding				0		Ovarian(717;0.028)|Colorectal(252;0.234)		Epithelial(162;4.76e-10)|all cancers(201;3.84e-08)	L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	TTAACATACCAGAGAGAGAGAC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120429869	120429869	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120429869delA								PRLHR (74709 upstream) : C10orf46 (3765 downstream)																							TGGCATGGAGAATGGAGGGAG	0.478													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583153	127583154	+	Intron	DEL	AA	-	-	rs66768561		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583153_127583154delAA	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ATATGATTACAAAGTGTTTCAC	0.312													4	3	---	---	---	---	
KNDC1	85442	broad.mit.edu	37	10	135022930	135022931	+	Intron	DEL	GT	-	-	rs142395560		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135022930_135022931delGT	uc001llz.1	+							NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		ggcgggtatagtgtgtgtgtgc	0.104													5	4	---	---	---	---	
DCHS1	8642	broad.mit.edu	37	11	6667909	6667909	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6667909delT	uc001mem.1	-							NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGTCCCCGGTCCTGCTACTT	0.572													4	2	---	---	---	---	
C11orf85	283129	broad.mit.edu	37	11	64729920	64729924	+	5'Flank	DEL	GTAAC	-	-	rs2307666		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64729920_64729924delGTAAC	uc001ocb.1	-						C11orf85_uc001occ.1_Intron|C11orf85_uc001ocd.1_Intron	NM_001037225	NP_001032302	Q3KP22	CK085_HUMAN	hypothetical protein LOC283129												0						TTACGTCCCAGTAACTATTATTAAG	0.376													4	2	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76867524	76867524	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76867524delA	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						TATCTGAACGAAGGTGAAGGA	0.512													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99193149	99193151	+	Intron	DEL	TTT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99193149_99193151delTTT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TCAggaaaacttttttaaaaatc	0.123													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107365636	107365640	+	IGR	DEL	GCCTC	-	-	rs67219576	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107365636_107365640delGCCTC								CWF19L2 (37064 upstream) : ALKBH8 (7814 downstream)																							agccacactggcctcctgcggttct	0.000													4	2	---	---	---	---	
POU2AF1	5450	broad.mit.edu	37	11	111225390	111225390	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111225390delT	uc001plg.3	-							NM_006235	NP_006226	Q16633	OBF1_HUMAN	POU class 2 associating factor 1						humoral immune response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			kidney(1)	1		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		CATCTCCCCCTTCAATTCTGC	0.483			T	BCL6	NHL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115767566	115767566	+	IGR	DEL	A	-	-	rs35465239		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115767566delA								CADM1 (392325 upstream) : BUD13 (851322 downstream)																							GGTGTTAAGGAAAACAACATT	0.507													4	2	---	---	---	---	
TMPRSS4	56649	broad.mit.edu	37	11	117946644	117946645	+	5'Flank	INS	-	G	G	rs150381383	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117946644_117946645insG	uc010rxo.1	+						TMPRSS4_uc010rxp.1_5'Flank|TMPRSS4_uc010rxq.1_5'Flank|TMPRSS4_uc010rxr.1_5'Flank|TMPRSS4_uc010rxs.1_5'Flank|TMPRSS4_uc009yzu.2_5'Flank|uc001prx.1_Intron|uc001pry.1_Intron|uc001prz.1_Intron|uc009yzs.1_Intron|uc001psa.1_Intron	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1						proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TCCCCTGGCCAGGGGGCAGCTC	0.262													3	4	---	---	---	---	
PATE2	399967	broad.mit.edu	37	11	125648107	125648108	+	Intron	INS	-	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125648107_125648108insA	uc001qcu.2	-						PATE2_uc010sbj.1_Intron	NM_212555	NP_997720	Q6UY27	PATE2_HUMAN	prostate and testis expressed 2 precursor							extracellular space					0						tttctccaattaaAAAAATCTT	0.134													4	2	---	---	---	---	
ST14	6768	broad.mit.edu	37	11	130042018	130042018	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130042018delT	uc001qfw.2	+							NM_021978	NP_068813	Q9Y5Y6	ST14_HUMAN	matriptase						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|skin(2)|central_nervous_system(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	ttttggttgcttttttttttg	0.000													3	4	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132946603	132946604	+	Intron	INS	-	TCA	TCA	rs140457401	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132946603_132946604insTCA	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		cctcatcattgtcatcatcatc	0.416													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134650197	134650198	+	IGR	INS	-	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134650197_134650198insT								B3GAT1 (368385 upstream) : None (None downstream)																							TTTAAATAGCATTTTTTTTTCC	0.327													4	2	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3307516	3307517	+	Intron	DEL	GT	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3307516_3307517delGT	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			acagctcaccgtaccagcacag	0.000													3	4	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	6032163	6032164	+	Intron	INS	-	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6032163_6032164insC	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						AGGAAGTGCGGCCCCCCGACTG	0.302													3	3	---	---	---	---	
CASC1	55259	broad.mit.edu	37	12	25313731	25313731	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25313731delT	uc001rgl.2	-						CASC1_uc001rgk.2_Intron|CASC1_uc001rgm.3_Intron|CASC1_uc001rgj.2_Intron|CASC1_uc010sje.1_Intron|CASC1_uc010sjf.1_Intron|CASC1_uc010sjg.1_Intron|CASC1_uc010sjh.1_Intron	NM_001082973	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1 isoform b											ovary(2)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			tttaaaacaatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	33741772	33741772	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33741772delA								SYT10 (149018 upstream) : ALG10 (433444 downstream)																							aagtagggtgaaaggaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	49265327	49265328	+	IGR	DEL	AA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49265327_49265328delAA								RND1 (5674 upstream) : CCDC65 (32565 downstream)																							CCTCAGTCCTAAGCAATAACTT	0.540													4	2	---	---	---	---	
KRT85	3891	broad.mit.edu	37	12	52756440	52756440	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52756440delG	uc001sag.2	-							NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85						epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTCCTTGATGGCGGTCACAG	0.547													4	2	---	---	---	---	
SPRYD3	84926	broad.mit.edu	37	12	53470733	53470733	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53470733delA	uc001sbt.1	-						SPRYD3_uc010snw.1_Intron	NM_032840	NP_116229	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3											central_nervous_system(1)	1						actctgtcttaaaaaaaaaaa	0.179													5	3	---	---	---	---	
MON2	23041	broad.mit.edu	37	12	62978891	62978893	+	Intron	DEL	AAA	-	-	rs72114101		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62978891_62978893delAAA	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron|MON2_uc001srg.2_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		acacacacacaaaacaaaaaaaa	0.000													3	3	---	---	---	---	
LGR5	8549	broad.mit.edu	37	12	71946539	71946540	+	Intron	DEL	AA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71946539_71946540delAA	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9						GAAAGAAACTAAAAGATCATCA	0.421													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	86640612	86640612	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86640612delA	uc001tai.3	-						MGAT4C_uc001tal.3_Intron|MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron|MGAT4C_uc010sum.1_Intron|MGAT4C_uc001tah.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						CTTGCTATCTAATATCTCaaa	0.264													4	2	---	---	---	---	
HSP90B1	7184	broad.mit.edu	37	12	104325828	104325828	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104325828delT	uc001tkb.1	+						HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Intron|LOC253724_uc010swf.1_5'Flank|LOC253724_uc009zuh.2_5'Flank	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1						actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	AAAGTTGGGATTTTTTTTTTT	0.348													4	2	---	---	---	---	
RBM19	9904	broad.mit.edu	37	12	114355936	114355936	+	Intron	DEL	A	-	-	rs77946057		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114355936delA	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TTTTCTTATTAAAAAAAAAAA	0.398													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	122057899	122057899	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122057899delG								KDM2B (38979 upstream) : ORAI1 (6556 downstream)																							GCTGGCACCagggctggctgg	0.244													4	2	---	---	---	---	
GALNT9	50614	broad.mit.edu	37	12	132685940	132685941	+	Intron	INS	-	GGCCCCATCC	GGCCCCATCC	rs141720371	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132685940_132685941insGGCCCCATCC	uc001ukc.3	-						GALNT9_uc009zyr.2_Intron|GALNT9_uc001ukb.2_Intron|GALNT9_uc001uka.2_Intron	NM_001122636	NP_001116108	Q9HCQ5	GALT9_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TCAGATGCTGAGGCCCCATCCA	0.629													4	2	---	---	---	---	
CDK8	1024	broad.mit.edu	37	13	26840746	26840746	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26840746delG	uc001uqr.1	+						CDK8_uc001uqs.1_Intron|CDK8_uc001uqt.1_Intron	NM_001260	NP_001251	P49336	CDK8_HUMAN	cyclin-dependent kinase 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		AGAAGTGTCTGGGTTAAATAA	0.378													4	2	---	---	---	---	
SLC46A3	283537	broad.mit.edu	37	13	29274923	29274924	+	3'UTR	INS	-	TT	TT			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29274923_29274924insTT	uc001usi.2	-	5					SLC46A3_uc001usg.2_3'UTR|SLC46A3_uc001usj.2_3'UTR|SLC46A3_uc001ush.2_3'UTR	NM_181785	NP_861450	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3 isoform a						transmembrane transport	integral to membrane				central_nervous_system(1)|skin(1)	2		Lung SC(185;0.0367)		all cancers(112;0.159)		TAGAAATATTATCATGCCTGTC	0.282													8	5	---	---	---	---	
MYCBP2	23077	broad.mit.edu	37	13	77739179	77739179	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77739179delT	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTTCtttttattttttttgta	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78241975	78241975	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78241975delG								SCEL (22579 upstream) : SLAIN1 (30495 downstream)																							GCACACATCAGCACATCAAAG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81229630	81229630	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81229630delG								SPRY2 (314544 upstream) : None (None downstream)																							AAGAAGGGACGGAAGTCAAGT	0.483													4	2	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95672857	95672857	+	3'UTR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95672857delT	uc001vmd.3	-	31					ABCC4_uc010afj.2_3'UTR|ABCC4_uc010afk.2_3'UTR	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	TAGTCAATGCTTGCAATAATT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106375342	106375342	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106375342delT	uc001vqf.1	+											Homo sapiens cDNA FLJ25324 fis, clone TST00330.																		tttgtacttgtttttttccct	0.000													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110863718	110863718	+	Intron	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110863718delC	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CCATCTGCCTCCCCAGTTTGG	0.587													4	2	---	---	---	---	
MCF2L	23263	broad.mit.edu	37	13	113691013	113691014	+	Intron	INS	-	TTC	TTC	rs150383781	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113691013_113691014insTTC	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron	NM_001112732	NP_001106203	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				AGCTCGCGCctttcttcaggtg	0.347													2	4	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	72483490	72483490	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72483490delT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		ttttttggaattttttttggc	0.000													4	2	---	---	---	---	
C14orf142	84520	broad.mit.edu	37	14	93670353	93670353	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93670353delT	uc001ybl.1	-							NM_032490	NP_115879	Q9BXV9	CN142_HUMAN	hypothetical protein LOC84520												0		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.177)|all cancers(159;0.198)|COAD - Colon adenocarcinoma(157;0.203)		TCtttttttctttttttttga	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20114037	20114037	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20114037delG								None (None upstream) : GOLGA6L6 (623057 downstream)																							gtggcgttttgttttttgtct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20398991	20398991	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20398991delA								None (None upstream) : GOLGA6L6 (338103 downstream)																							TTCTGGGTGTAGGGGATGTTT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20849218	20849218	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20849218delT								GOLGA8C (68192 upstream) : BCL8 (20838 downstream)																							TTCATTTTAGTTTTTTTTCAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20867625	20867628	+	IGR	DEL	GAGT	-	-	rs61049442		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20867625_20867628delGAGT								GOLGA8C (86599 upstream) : BCL8 (2428 downstream)																							AAGAAAATAAGAGTAAGTTTAATG	0.157													4	2	---	---	---	---	
LTK	4058	broad.mit.edu	37	15	41803050	41803050	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41803050delT	uc001zoa.3	-						LTK_uc001zob.3_Intron|LTK_uc010ucx.1_Intron|LTK_uc010bcg.2_Intron	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1						apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CAATCCTGCCTTTCTGCCCCT	0.313										TSP Lung(18;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	51161356	51161356	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51161356delT								SPPL2A (103446 upstream) : AP4E1 (39590 downstream)																							TTGATAGGGATTTTTTTTTCT	0.428													4	2	---	---	---	---	
CGNL1	84952	broad.mit.edu	37	15	57767850	57767852	+	Intron	DEL	TCT	-	-	rs79013528		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57767850_57767852delTCT	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TCCCAAAGAATCTTCTTCTTGCA	0.453													4	2	---	---	---	---	
IGDCC3	9543	broad.mit.edu	37	15	65622307	65622307	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65622307delG	uc002aos.2	-						IGDCC3_uc002aor.1_5'Flank	NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule											ovary(3)	3						CCACTCCCAAGTGGGAGTGGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70082522	70082524	+	IGR	DEL	CAC	-	-	rs35874419		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70082522_70082524delCAC								LOC145837 (218743 upstream) : C15orf50 (45049 downstream)																							TCAGAGCTCTCACCACCACCACC	0.527													2	5	---	---	---	---	
PARP6	56965	broad.mit.edu	37	15	72553349	72553349	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72553349delA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599	Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0						TGAGAGAGAGAAAAAAAAATA	0.423													4	2	---	---	---	---	
CD276	80381	broad.mit.edu	37	15	73988042	73988042	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73988042delA	uc002avv.1	+						CD276_uc010bjd.1_Intron|CD276_uc002avu.1_Intron|CD276_uc002avw.1_Intron|CD276_uc010ulb.1_Intron	NM_001024736	NP_001019907	Q5ZPR3	CD276_HUMAN	CD276 antigen isoform a						cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding			skin(1)	1						ggtttaagggaaaaaaaatga	0.050													4	2	---	---	---	---	
CCDC33	80125	broad.mit.edu	37	15	74551885	74551885	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74551885delT	uc002axo.2	+							NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5						GGCCTCCCCCTCCCACCCAGT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77851288	77851288	+	IGR	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77851288delG								HMG20A (73345 upstream) : LINGO1 (54081 downstream)																							catatgaagtggcggtttatg	0.080													4	2	---	---	---	---	
KIAA1024	23251	broad.mit.edu	37	15	79731826	79731827	+	Intron	INS	-	G	G			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79731826_79731827insG	uc002bew.1	+							NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251							integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4						ATGTGGGATATGGTGGCAGTCA	0.322													4	2	---	---	---	---	
BTBD1	53339	broad.mit.edu	37	15	83713601	83713601	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83713601delT	uc002bjn.2	-						BTBD1_uc002bjo.2_Intron	NM_025238	NP_079514	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1 isoform 1							cytoplasmic mRNA processing body|protein complex	protein binding			ovary(1)|central_nervous_system(1)	2				all cancers(203;0.000186)		CTCCATAGTGTTTTTTTTCAT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95074912	95074913	+	IGR	INS	-	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95074912_95074913insC								MCTP2 (47732 upstream) : LOC145820 (901409 downstream)																							GTCCTTGCTTTCCCCATCATTT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102094891	102094891	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102094891delA								PCSK6 (64704 upstream) : TM2D3 (78289 downstream)																							CCGCCCCGGGAAGGGACTGCT	0.597													4	2	---	---	---	---	
PALB2	79728	broad.mit.edu	37	16	23619548	23619548	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23619548delT	uc002dlx.1	-							NM_024675	NP_078951	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2						double-strand break repair via homologous recombination	nucleoplasm	DNA binding|protein binding			lung(3)|breast(3)|ovary(2)|skin(1)|kidney(1)|pancreas(1)	11				GBM - Glioblastoma multiforme(48;0.0167)		GTTCTtcttcttttttttttt	0.199			F|N|Mis			Wilms tumor|medulloblastoma|AML ,breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia_type_N|Fanconi_Anemia|PALB2-associated_Familial_Breast_and_Pancreatic_Cancer|Pancreatic_Cancer_Familial_Clustering_of				4	2	---	---	---	---	
MVP	9961	broad.mit.edu	37	16	29841797	29841798	+	Intron	INS	-	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29841797_29841798insC	uc002dui.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc010bzh.1_RNA|MVP_uc010vdz.1_Intron|MVP_uc002duj.2_5'UTR|MVP_uc010vea.1_5'Flank	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein						mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						CACCCCAGGCTCCCCAGGTTCA	0.599													37	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31112383	31112384	+	IGR	DEL	TG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31112383_31112384delTG								PRSS53 (6107 upstream) : BCKDK (7278 downstream)																							gccacacagctgtgtgtgtgtg	0.000													4	2	---	---	---	---	
ITGAM	3684	broad.mit.edu	37	16	31342788	31342789	+	Intron	INS	-	TTG	TTG	rs144797541	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31342788_31342789insTTG	uc002ebq.2	+						ITGAM_uc002ebr.2_Intron|ITGAM_uc010can.2_Intron	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						AGTCGCCCTCCTTGTAGTTTCT	0.530													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32094264	32094264	+	IGR	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32094264delT								ZNF267 (165638 upstream) : HERC2P4 (68346 downstream)																							gtgggtatcatgaaaattatg	0.095													3	3	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55845122	55845122	+	Intron	DEL	C	-	-	rs147594975		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55845122delC	uc002eim.2	-						CES1_uc010ccf.2_Intron|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	GCAAAGTTTACAAAAAAAAAA	0.284													4	2	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55845123	55845123	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55845123delA	uc002eim.2	-						CES1_uc010ccf.2_Intron|CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	CAAAGTTTACAAAAAAAAAAA	0.289													4	3	---	---	---	---	
NLRC5	84166	broad.mit.edu	37	16	57111993	57111994	+	Intron	INS	-	G	G	rs142860883	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57111993_57111994insG	uc002ekk.1	+						NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_Intron|NLRC5_uc002eko.1_Intron|NLRC5_uc002ekq.1_Intron|NLRC5_uc002ekr.1_Intron	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)				TCGGGAGCAGTGGGGGGGTCCA	0.649													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64401495	64401495	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64401495delA								None (None upstream) : CDH11 (579190 downstream)																							GATTCTCAGTAAAAAAGCTAA	0.403													4	2	---	---	---	---	
VAC14	55697	broad.mit.edu	37	16	70814574	70814574	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70814574delG	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				ctacaattgtgtgagtgacat	0.239													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78477777	78477777	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78477777delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TTTCCAGTGATTTTTGGCTGC	0.388													4	2	---	---	---	---	
CRK	1398	broad.mit.edu	37	17	1326699	1326700	+	3'UTR	INS	-	A	A			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1326699_1326700insA	uc002fsl.2	-	3					CRK_uc002fsm.2_3'UTR	NM_016823	NP_058431	P46108	CRK_HUMAN	v-crk sarcoma virus CT10 oncogene homolog						actin cytoskeleton organization|activation of MAPKK activity|blood coagulation|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of transcription from RNA polymerase II promoter	cytosol|endosome|nucleus|plasma membrane	protein binding|SH2 domain binding			lung(2)|central_nervous_system(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.083)		ACAGAATGCTTATATAAACTAG	0.351													13	8	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2921210	2921211	+	Intron	INS	-	GT	GT	rs142119866	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2921210_2921211insGT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						CCTCTGTGACCgtgtgtgtgtg	0.475													4	2	---	---	---	---	
ASGR1	432	broad.mit.edu	37	17	7079869	7079870	+	Intron	DEL	CA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7079869_7079870delCA	uc002ges.3	-						ASGR1_uc010clx.1_Intron	NM_001671	NP_001662	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1						receptor-mediated endocytosis	integral to plasma membrane	asialoglycoprotein receptor activity|metal ion binding|sugar binding			breast(1)|central_nervous_system(1)	2						atctcattctcacacacacaca	0.000													4	2	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	19985132	19985133	+	Intron	DEL	AC	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19985132_19985133delAC	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						CCACATTACAACACACACACAA	0.559													4	2	---	---	---	---	
TMEM11	8834	broad.mit.edu	37	17	21102179	21102180	+	Intron	DEL	GA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21102179_21102180delGA	uc002gyp.2	-						TMEM11_uc002gyq.2_Intron	NM_003876	NP_003867	P17152	TMM11_HUMAN	transmembrane protein 11						mitochondrion organization	integral to mitochondrial inner membrane|integral to plasma membrane	protein binding				0						GCAGGAAAGGGAGAGAGAGAGA	0.535													8	4	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21197000	21197014	+	Intron	DEL	AGGGCAGGGCTGTGG	-	-	rs36014964		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21197000_21197014delAGGGCAGGGCTGTGG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GGGCAGAGGCAGGGCAGGGCTGTGGAGGGCAGAGC	0.651													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	38515902	38515902	+	5'Flank	DEL	G	-	-	rs113614211		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38515902delG	uc010cxa.1	+											Homo sapiens cDNA FLJ40933 fis, clone UTERU2007081.																		tcagctacttggggggggggc	0.000													3	3	---	---	---	---	
DBF4B	80174	broad.mit.edu	37	17	42819161	42819162	+	Intron	INS	-	C	C	rs146660683	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42819161_42819162insC	uc002ihf.2	+						DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)				CTGCACTGTTTCCCCCAGAGCA	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46103486	46103487	+	IGR	DEL	AC	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46103486_46103487delAC								CDK5RAP3 (44340 upstream) : COPZ2 (48 downstream)																							CCTTATATGAacacacacacac	0.490											OREG0024510	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SGCA	6442	broad.mit.edu	37	17	48242564	48242564	+	5'Flank	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48242564delC	uc002iqi.2	+						SGCA_uc010wmh.1_5'Flank|SGCA_uc002iqj.2_5'Flank|SGCA_uc010wmi.1_5'Flank	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor						muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2						GGTGCCTCCTCCGCTCACCTG	0.418													4	2	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60142663	60142663	+	5'Flank	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60142663delG	uc002izo.2	-							NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						GGGGAGGGCCGGGGGGGGGGT	0.478													3	3	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65521779	65521779	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65521779delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			TCATTTATCCTTCAGGTGCTC	0.483													4	2	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	71025726	71025726	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71025726delT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						CCACTCAATCttttttttttt	0.303													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77183580	77183580	+	Intron	DEL	C	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77183580delC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			GACCTTCCTGCCCCAGCCCTG	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10030695	10030695	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10030695delA								VAPA (70678 upstream) : APCDD1 (423930 downstream)																							TGTTCACATCAAAAAAATGGA	0.139													4	2	---	---	---	---	
GNAL	2774	broad.mit.edu	37	18	11868300	11868300	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11868300delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_Intron	NM_001142339	NP_001135811	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						actccatctcaaaaaaaaaaa	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62346197	62346198	+	IGR	INS	-	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62346197_62346198insT								C18orf20 (529937 upstream) : None (None downstream)																							TTATGCTTTTATTTTTTTTCAT	0.267													4	2	---	---	---	---	
ZFR2	23217	broad.mit.edu	37	19	3871980	3871980	+	5'Flank	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3871980delA	uc002lyw.2	-						ZFR2_uc010xhx.1_5'Flank|ZFR2_uc002lyx.3_5'Flank|ZFR2_uc010xhy.1_5'Flank	NM_015174	NP_055989	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2 isoform 1							intracellular	nucleic acid binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		gaggctctccaaaaaaaaaag	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5815164	5815165	+	IGR	DEL	TG	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5815164_5815165delTG								DUS3L (23915 upstream) : NRTN (8653 downstream)																							TGTGCACCCCTGTGTGTGTGTG	0.589													4	3	---	---	---	---	
VAV1	7409	broad.mit.edu	37	19	6792383	6792383	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6792383delA	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron|VAV1_uc002mfv.1_Intron	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						GGCAAGAATTAAAAAAAAAAA	0.254													3	4	---	---	---	---	
ZNF788	388507	broad.mit.edu	37	19	12223137	12223137	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12223137delA	uc002mtd.2	+	3	1412	c.775delA	c.(775-777)AAAfs	p.K259fs		NR_027049				RecName: Full=Zinc finger protein 788;												0						GGAATGTGGGAAATCATACTA	0.383													4	2	---	---	---	---	
LGI4	163175	broad.mit.edu	37	19	35623554	35623555	+	Intron	INS	-	C	C			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35623554_35623555insC	uc002nxx.2	-						LGI4_uc002nxy.1_Intron|LGI4_uc002nxz.1_Intron|LGI4_uc002nya.2_Intron	NM_139284	NP_644813	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4							extracellular region				pancreas(1)	1	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			caccacccactcccatcaacac	0.035													4	2	---	---	---	---	
FCGBP	8857	broad.mit.edu	37	19	40384321	40384324	+	Intron	DEL	AGAA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40384321_40384324delAGAA	uc002omp.3	-							NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			gaggacacagagaaagaaatggga	0.088													6	3	---	---	---	---	
IL4I1	259307	broad.mit.edu	37	19	50398581	50398582	+	Intron	INS	-	G	G	rs150991128	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50398581_50398582insG	uc002pqt.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 1 precursor							lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)		CCCTTCTGTATGGAGGTGGGGG	0.614													5	5	---	---	---	---	
NLRP2	55655	broad.mit.edu	37	19	55505987	55505987	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55505987delT	uc002qij.2	+						NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2						apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TAAGtttttgttttttttttt	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1488839	1488840	+	IGR	INS	-	T	T			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1488839_1488840insT								SIRPB2 (16606 upstream) : SIRPD (26059 downstream)																							taatgttaagatttttttttct	0.000													4	2	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20563452	20563452	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20563452delT	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						TGACTTATCCTGGATTTATAA	0.224													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29645743	29645743	+	Intron	DEL	G	-	-	rs146031080	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29645743delG	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						actggataaagaaaatgtggt	0.000													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41179092	41179092	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41179092delT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGGATTAGGGTTTTTTTTTAG	0.378													4	2	---	---	---	---	
SDC4	6385	broad.mit.edu	37	20	43959228	43959228	+	Intron	DEL	G	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43959228delG	uc002xnu.2	-						SDC4_uc010zws.1_Intron	NM_002999	NP_002990	P31431	SDC4_HUMAN	syndecan 4 precursor							extracellular region|integral to plasma membrane	cytoskeletal protein binding|thrombospondin receptor activity				0		Myeloproliferative disorder(115;0.0122)				AAGGAGAAGAGACACTCAGCG	0.537													31	17	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45648115	45648115	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45648115delT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				TCCTATTAACTTTTTTTTTTT	0.393													4	2	---	---	---	---	
ATP9A	10079	broad.mit.edu	37	20	50385906	50385907	+	5'Flank	DEL	CA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50385906_50385907delCA	uc002xwg.1	-						ATP9A_uc010gih.1_5'Flank	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4						TTCACGGTCTCACACACACACC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54182316	54182316	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54182316delA								DOK5 (914607 upstream) : CBLN4 (390181 downstream)																							TGGAGAGGGGAAAAAATCTGG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	21798492	21798493	+	IGR	DEL	GA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21798492_21798493delGA								None (None upstream) : C21orf131 (316421 downstream)																							TGTCTGGGAGGAGAGAGAGAGG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44359382	44359385	+	IGR	DEL	TTTT	-	-	rs35669654		TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44359382_44359385delTTTT								NDUFV3 (29610 upstream) : PKNOX1 (35258 downstream)																							ttgtttcttgtttttttttttttt	0.216													4	2	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18501961	18501961	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18501961delA	uc002zng.3	-						MICAL3_uc002znh.2_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		accctgtctcaaaaaaaaaaG	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20745000	20745001	+	IGR	DEL	CA	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20745000_20745001delCA								RIMBP3 (283214 upstream) : ZNF74 (3478 downstream)																							TTGAGAGAACCACACACACACA	0.490													3	4	---	---	---	---	
RAB36	9609	broad.mit.edu	37	22	23488568	23488568	+	Intron	DEL	G	-	-	rs147076751	by1000genomes	TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23488568delG	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	NM_004914	NP_004905	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		taatttttttggttttttttt	0.000													4	3	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33916416	33916416	+	Intron	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33916416delA	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				GCTGTTCTCCAAATCCCACAA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	43890280	43890280	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43890280delA								NDP (57359 upstream) : EFHC2 (116849 downstream)																							TCATTTGTATACAATTCCCGT	0.318													2	16	---	---	---	---	
GNL3L	54552	broad.mit.edu	37	X	54570904	54570904	+	Intron	DEL	T	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54570904delT	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1						ACCGAGTGACttttttttttt	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28815410	28815410	+	IGR	DEL	A	-	-			TCGA-B0-5699-01A-11D-1534-10	TCGA-B0-5699-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28815410delA								None (None upstream) : None (None downstream)																							aattgaatggaaaaaatggaa	0.000													4	3	---	---	---	---	
