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
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16918653C>T	uc009vos.1	-	6	853	c.-35_splice	c.e6+1		NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418													3	33	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974256	16974256	+	RNA	SNP	G	C	C	rs114217985	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974256G>C	uc009vow.2	+	5		c.1066G>C			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GCTCGGGGCCGGACCTATCTC	0.652													7	34	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16975495	16975495	+	RNA	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16975495T>C	uc010och.1	+	9		c.1776T>C			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CTTGCGGAATTGGTGAGGCAC	0.612													7	26	---	---	---	---	PASS
EIF4G3	8672	broad.mit.edu	37	1	21167484	21167484	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21167484C>A	uc001bec.2	-	25	4014	c.3758G>T	c.(3757-3759)GGC>GTC	p.G1253V	EIF4G3_uc010odi.1_Missense_Mutation_p.G857V|EIF4G3_uc010odj.1_Missense_Mutation_p.G1252V|EIF4G3_uc009vpz.2_Missense_Mutation_p.G973V|EIF4G3_uc001bed.2_Missense_Mutation_p.G1253V|EIF4G3_uc001bef.2_Missense_Mutation_p.G1289V|EIF4G3_uc001bee.2_Missense_Mutation_p.G1259V	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	1253	MI.				interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ATGTAGTAGGCCCTGGGCATT	0.473													54	118	---	---	---	---	PASS
ZNF362	149076	broad.mit.edu	37	1	33736126	33736126	+	5'UTR	SNP	T	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33736126T>G	uc001bxc.1	+	2						NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				tggctgggggttcagggaaag	0.065													12	67	---	---	---	---	PASS
RIMS3	9783	broad.mit.edu	37	1	41092246	41092246	+	Silent	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41092246G>T	uc001cfu.1	-	8	1339	c.870C>A	c.(868-870)CTC>CTA	p.L290L	RIMS3_uc001cfv.1_Silent_p.L290L	NM_014747	NP_055562	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	290					neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GGCGCCTGGTGAGGGATCCGA	0.632													20	53	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144815953	144815953	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144815953A>G	uc009wig.1	+	12	1400	c.1324A>G	c.(1324-1326)AAT>GAT	p.N442D	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Missense_Mutation_p.N442D|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Missense_Mutation_p.N171D|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Missense_Mutation_p.N102D	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	442	NBPF 2.					cytoplasm					0						CAACGATGACAATGAAGATGT	0.423													13	150	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828583	144828583	+	Silent	SNP	G	A	A	rs28712116	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828583G>A	uc009wig.1	+	23	2704	c.2628G>A	c.(2626-2628)TTG>TTA	p.L876L	NBPF9_uc010oxn.1_Silent_p.L774L|NBPF9_uc010oxo.1_Silent_p.L801L|NBPF9_uc010oxr.1_Silent_p.L903L|NBPF9_uc010oxt.1_Silent_p.L691L|NBPF9_uc001ekg.1_Silent_p.L203L|NBPF9_uc001ekk.1_Silent_p.L447L|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Silent_p.L203L|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|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|NBPF9_uc001elp.2_Silent_p.L536L|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	876	NBPF 7.					cytoplasm					0						CTGAAGTCTTGCAGGACTCAC	0.468													11	234	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828807	144828807	+	3'UTR	SNP	A	G	G	rs76022554		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828807A>G	uc009wig.1	+	23					NBPF9_uc010oxn.1_3'UTR|NBPF9_uc010oxo.1_3'UTR|NBPF9_uc010oxr.1_3'UTR|NBPF9_uc010oxt.1_3'UTR|NBPF9_uc001ekg.1_3'UTR|NBPF9_uc001ekk.1_3'UTR|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_3'UTR|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|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|NBPF9_uc001elp.2_3'UTR|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						AAGCCGAGAGATGTCATTCCT	0.473													13	131	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145304529	145304529	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145304529T>C	uc001end.3	+	10	1497	c.1462T>C	c.(1462-1464)TCT>CCT	p.S488P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Missense_Mutation_p.S419P|NBPF9_uc010oyg.1_Missense_Mutation_p.S453P|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Missense_Mutation_p.S27P|NBPF10_uc001emq.1_Missense_Mutation_p.S217P	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TAGCCATGGCTCTTATGACTC	0.468													14	597	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891542	148891542	+	RNA	SNP	T	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891542T>G	uc009wkv.1	+	9		c.844T>G								Homo sapiens cDNA, FLJ17483.																		CACCCAAGACTTATACCCAGG	0.368													11	195	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891580	148891580	+	RNA	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891580A>T	uc009wkv.1	+	9		c.882A>T								Homo sapiens cDNA, FLJ17483.																		GAATCAGGGAAGACTCAGTTA	0.358													79	208	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891643	148891643	+	RNA	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891643A>G	uc009wkv.1	+	9		c.945A>G								Homo sapiens cDNA, FLJ17483.																		CCAAAACTGAAATTGAAGATT	0.423													116	243	---	---	---	---	PASS
ADAR	103	broad.mit.edu	37	1	154569310	154569310	+	Silent	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154569310G>A	uc001ffh.2	-	6	2441	c.2241C>T	c.(2239-2241)GTC>GTT	p.V747V	ADAR_uc001ffj.2_Silent_p.V728V|ADAR_uc001ffi.2_Silent_p.V747V|ADAR_uc001ffk.2_Silent_p.V452V	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a	747	DRBM 3.				adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CGGACTGGTCGACCAACTTGA	0.557													11	68	---	---	---	---	PASS
FLAD1	80308	broad.mit.edu	37	1	154956241	154956241	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154956241T>A	uc001fgf.1	+	1	425	c.71T>A	c.(70-72)TTA>TAA	p.L24*	FLAD1_uc001fgc.2_Intron|FLAD1_uc001fgd.1_Nonsense_Mutation_p.L24*|FLAD1_uc001fge.1_Intron|FLAD1_uc001fgg.1_Intron	NM_025207	NP_079483	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase isoform	24					FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)|skin(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AGGATCTGGTTAGAGAAGACT	0.522													9	34	---	---	---	---	PASS
TOMM40L	84134	broad.mit.edu	37	1	161198936	161198936	+	3'UTR	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161198936C>T	uc001fzd.2	+	10					TOMM40L_uc010pkl.1_3'UTR|TOMM40L_uc009wue.2_3'UTR|TOMM40L_uc009wuf.1_RNA|TOMM40L_uc001fze.2_3'UTR	NM_032174	NP_115550	Q969M1	TM40L_HUMAN	translocase of outer mitochondrial membrane 40						protein transport	mitochondrial outer membrane|pore complex	porin activity|voltage-gated anion channel activity			large_intestine(1)	1	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AGTCAGGTGCCCTAGGGCCAA	0.592													18	33	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169510220	169510220	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169510220G>A	uc001ggg.1	-	13	4253	c.4108C>T	c.(4108-4110)CTC>TTC	p.L1370F		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	1370	2-21.|35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	GTCTGGCTGAGGTCTAGAGAA	0.517													5	431	---	---	---	---	PASS
GPR37L1	9283	broad.mit.edu	37	1	202092521	202092521	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202092521G>T	uc001gxj.2	+	1	493	c.430G>T	c.(430-432)GGC>TGC	p.G144C		NM_004767	NP_004758	O60883	ETBR2_HUMAN	G-protein coupled receptor 37 like 1 precursor	144	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2						GTTTGCGGTGGGCATTGTGGG	0.582													24	121	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787831G>T	uc001hfy.2	+	32	5448	c.5308G>T	c.(5308-5310)GAA>TAA	p.E1770*	CR1_uc001hfx.2_Nonsense_Mutation_p.E2220*	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1770	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						TCCAGTGTGTGAACGTGAGTA	0.408													9	408	---	---	---	---	PASS
CEP170	9859	broad.mit.edu	37	1	243333027	243333027	+	Silent	SNP	A	G	G	rs147752333	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243333027A>G	uc001hzs.2	-	12	2154	c.1746T>C	c.(1744-1746)CGT>CGC	p.R582R	CEP170_uc001hzt.2_Silent_p.R484R|CEP170_uc001hzu.2_Silent_p.R484R	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	582						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTGAAACCCAACGTTTGCTTC	0.398													6	245	---	---	---	---	PASS
OR2T12	127064	broad.mit.edu	37	1	248458390	248458390	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248458390A>G	uc010pzj.1	-	1	491	c.491T>C	c.(490-492)TTC>TCC	p.F164S		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	164	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			GCAATATGGGAAGCTCAGGGT	0.587													15	83	---	---	---	---	PASS
LHCGR	3973	broad.mit.edu	37	2	48915918	48915918	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48915918T>C	uc002rwu.3	-	11	1088	c.1018A>G	c.(1018-1020)ACA>GCA	p.T340A	GTF2A1L_uc002rwt.2_Intron	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	340	Extracellular (Potential).				male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	CATCGGGGTGTCTTGGGTAAG	0.428									Familial_Male-Limited_Precocious_Puberty				7	213	---	---	---	---	PASS
TIA1	7072	broad.mit.edu	37	2	70456404	70456404	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70456404T>C	uc002sgj.3	-	4	486	c.269A>G	c.(268-270)GAT>GGT	p.D90G	TIA1_uc002sgk.3_Missense_Mutation_p.D90G|TIA1_uc002sgl.3_RNA|TIA1_uc002sgm.3_Missense_Mutation_p.D90G|TIA1_uc010yqt.1_Missense_Mutation_p.D90G	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding	90					apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0						ACTGCTTGTATCTTTCTTTTG	0.294													7	714	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89100619	89100619	+	RNA	SNP	C	T	T	rs75347118		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89100619C>T	uc010fhg.2	+	13		c.1059C>T			FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_RNA	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TCAACAGCAACTGGATGATGC	0.303													14	107	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97792829	97792829	+	Missense_Mutation	SNP	G	A	A	rs2443919	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97792829G>A	uc010yva.1	+	6	1001	c.757G>A	c.(757-759)GAA>AAA	p.E253K	ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Missense_Mutation_p.E253K|ANKRD36_uc002sxp.3_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	253											0						TTATGAATACGAAAGAAAGAG	0.219													4	173	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97849372	97849372	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97849372T>C	uc010yva.1	+	28	2164	c.1920T>C	c.(1918-1920)GGT>GGC	p.G640G	ANKRD36_uc010fic.2_Silent_p.G359G|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_RNA|ANKRD36_uc002sxq.1_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	640											0						GAATAATGGGTGGTGGGAAAT	0.328													23	248	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608394T>C	uc002thi.2	-	14	1856	c.1609A>G	c.(1609-1611)ACT>GCT	p.T537A		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						GGCTTTGGAGTACTAACGCCA	0.433													9	359	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168103910	168103910	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168103910A>T	uc002udx.2	+	8	6026	c.6008A>T	c.(6007-6009)AAA>ATA	p.K2003I	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.K1828I|XIRP2_uc010fpq.2_Missense_Mutation_p.K1781I|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1828					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						ACTATGGGGAAATCTTGCCAT	0.443													14	48	---	---	---	---	PASS
HOXD3	3232	broad.mit.edu	37	2	177033982	177033982	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177033982A>C	uc002ukt.1	+	2	316	c.140A>C	c.(139-141)CAC>CCC	p.H47P		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	47					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|thyroid gland development		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		AGCACCCCCCACCAGCCCTAC	0.587													8	44	---	---	---	---	PASS
DFNB59	494513	broad.mit.edu	37	2	179318247	179318247	+	Silent	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179318247G>A	uc002umi.3	+	2	467	c.111G>A	c.(109-111)GTG>GTA	p.V37V	PRKRA_uc002umd.2_5'Flank|PRKRA_uc002ume.2_5'Flank|PRKRA_uc002umf.2_5'Flank|PRKRA_uc002umg.2_5'Flank|DFNB59_uc002umj.3_Silent_p.V37V	NM_001042702	NP_001036167	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	37					sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TAAGTCTGGTGGTAAAAAAGA	0.403													7	412	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179665241	179665241	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179665241T>C	uc002und.2	-	4	689	c.464A>G	c.(463-465)GAA>GGA	p.E155G	TTN_uc010zfg.1_Missense_Mutation_p.E155G|TTN_uc010zfh.1_Missense_Mutation_p.E155G|TTN_uc010zfi.1_Missense_Mutation_p.E155G|TTN_uc010zfj.1_Missense_Mutation_p.E155G|TTN_uc002unb.2_Missense_Mutation_p.E155G			Q8WZ42	TITIN_HUMAN	Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.	155							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGGTCGCCTTCTTGTGAAAT	0.488													5	176	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197194348	197194348	+	Silent	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197194348A>T	uc002utm.1	-	5	705	c.522T>A	c.(520-522)GGT>GGA	p.G174G	HECW2_uc002utl.1_5'UTR	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	174	C2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TTCCTGAAGCACCTCCCTCCA	0.413													58	148	---	---	---	---	PASS
PGAP1	80055	broad.mit.edu	37	2	197708784	197708784	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197708784T>C	uc002utw.2	-	25	2467	c.2353A>G	c.(2353-2355)AGA>GGA	p.R785G	PGAP1_uc002utx.2_Missense_Mutation_p.R611G|PGAP1_uc010fsi.2_Missense_Mutation_p.R59G	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase	785	Cytoplasmic (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4						TCACTTCTTCTAGAGTGTTTG	0.323													5	359	---	---	---	---	PASS
ITPR1	3708	broad.mit.edu	37	3	4669521	4669521	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4669521G>A	uc003bqa.2	+	5	586	c.238G>A	c.(238-240)GCC>ACC	p.A80T	ITPR1_uc010hbz.2_Missense_Mutation_p.A80T|ITPR1_uc010hca.1_Missense_Mutation_p.A80T|ITPR1_uc011asu.1_Missense_Mutation_p.A80T|ITPR1_uc010hcb.1_Missense_Mutation_p.A80T	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1	80	Cytoplasmic (Potential).				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		TAAGCCTGGGGCCAACAGCAC	0.522													36	93	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191492	10191492	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191492G>A	uc003bvc.2	+	3	698	c.485G>A	c.(484-486)TGC>TAC	p.C162Y	VHL_uc003bvd.2_Missense_Mutation_p.C121Y	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	162	Interaction with Elongin BC complex.		C -> R (in VHLD; type I).|C -> F (in VHLD; type I; No effect on interaction with HIF1A nor on HIF1A degradation).|C -> Y (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.C162Y(3)|p.C162R(3)|p.C162F(2)|p.C162W(2)|p.C162*(1)|p.C162fs*12(1)|p.C162fs*9(1)|p.L158fs*6(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AAAGAGCGATGCCTCCAGGTT	0.507		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				41	71	---	---	---	---	PASS
MLH1	4292	broad.mit.edu	37	3	37092105	37092105	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37092105T>C	uc003cgl.2	+	19	2292	c.2232T>C	c.(2230-2232)GCT>GCC	p.A744A	MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Silent_p.A503A|MLH1_uc010hge.2_Silent_p.A675A|MLH1_uc003cgn.3_Silent_p.A503A|MLH1_uc011ayc.1_Silent_p.A646A|MLH1_uc011ayd.1_Silent_p.A503A|MLH1_uc003cgo.2_Silent_p.A503A|MLH1_uc010hgk.2_Silent_p.A331A|MLH1_uc010hgn.2_Missense_Mutation_p.L241P|MLH1_uc010hgm.2_RNA|MLH1_uc010hgo.2_3'UTR|MLH1_uc010hgp.2_Silent_p.A127A|MLH1_uc010hgq.2_RNA	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1	744					mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						TGCAGCTTGCTAACCTGCCTG	0.413		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	221	---	---	---	---	PASS
LOC285359	285359	broad.mit.edu	37	3	101431590	101431590	+	RNA	SNP	T	G	G	rs4060654		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101431590T>G	uc003dvj.2	+	1		c.313T>G				NR_002941				Homo sapiens cDNA FLJ12205 fis, clone MAMMA1000931.												0						GAATAAATTTTGAGAAGTTTT	0.413													7	158	---	---	---	---	PASS
CEP70	80321	broad.mit.edu	37	3	138216885	138216885	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138216885G>A	uc003esl.2	-	17	1918	c.1720C>T	c.(1720-1722)CTT>TTT	p.L574F	CEP70_uc011bmk.1_Missense_Mutation_p.L554F|CEP70_uc011bml.1_Missense_Mutation_p.L556F|CEP70_uc011bmm.1_Missense_Mutation_p.L422F	NM_024491	NP_077817	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70 kDa	574					G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			skin(1)	1						AAGATTTCAAGTAGATCATTA	0.343													111	358	---	---	---	---	PASS
XRN1	54464	broad.mit.edu	37	3	142037506	142037506	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142037506A>G	uc003eus.2	-	39	4613	c.4546T>C	c.(4546-4548)TCA>CCA	p.S1516P	XRN1_uc010huu.2_Missense_Mutation_p.S983P|XRN1_uc003eut.2_Missense_Mutation_p.S1516P|XRN1_uc003euu.2_Missense_Mutation_p.S1517P	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a	1516					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						AATACTTGTGAAGGCAAAGGG	0.363													6	360	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506099	195506099	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506099T>C	uc011bto.1	-	3	12428	c.11968A>G	c.(11968-11970)ACT>GCT	p.T3990A	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	886	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCAGAGGAAGTGTCGGTGACA	0.587													5	14	---	---	---	---	PASS
OSTalpha	200931	broad.mit.edu	37	3	195959460	195959460	+	Intron	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195959460G>A	uc003fwd.2	+						OSTalpha_uc010iac.1_3'UTR|OSTalpha_uc003fwe.2_Intron	NM_152672	NP_689885	Q86UW1	OSTA_HUMAN	organic solute transporter alpha							integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)		AGGAAAGAAGGGGCCCCAGAA	0.527													10	56	---	---	---	---	PASS
FAM193A	8603	broad.mit.edu	37	4	2733519	2733519	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2733519C>T	uc010icl.2	+	20	4073	c.3722C>T	c.(3721-3723)GCT>GTT	p.A1241V	FAM193A_uc010ick.2_Missense_Mutation_p.A1400V|FAM193A_uc003gfd.2_Missense_Mutation_p.A1200V|FAM193A_uc011bvm.1_Missense_Mutation_p.A1222V|FAM193A_uc011bvn.1_3'UTR|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	1241										ovary(3)	3						TTGGATTCTGCTAGACAGACC	0.493													33	144	---	---	---	---	PASS
TMEM128	85013	broad.mit.edu	37	4	4239697	4239697	+	Intron	SNP	C	A	A	rs116836858	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4239697C>A	uc003ghr.1	-						TMEM128_uc003ghq.1_Intron|TMEM128_uc003ghs.2_3'UTR|TMEM128_uc011bvv.1_Intron|TMEM128_uc011bvw.1_Intron	NM_032927	NP_116316	Q5BJH2	TM128_HUMAN	transmembrane protein 128							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		TTGACAACTCCAATATGCATC	0.323													11	95	---	---	---	---	PASS
NHEDC1	150159	broad.mit.edu	37	4	103826800	103826800	+	Silent	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826800A>G	uc003hww.2	-	11	1325	c.1203T>C	c.(1201-1203)TCT>TCC	p.S401S	NHEDC1_uc003hwu.2_Silent_p.S401S|NHEDC1_uc010ilm.2_Silent_p.S168S|NHEDC1_uc003hwv.2_RNA|NHEDC1_uc011cev.1_Silent_p.S174S	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	401						integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		GAGTGGCAACAGATATGCCTA	0.303													6	176	---	---	---	---	PASS
TET2	54790	broad.mit.edu	37	4	106162632	106162632	+	Intron	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106162632T>C	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc003hxj.2_Intron|TET2_uc010ilp.1_3'UTR|TET2_uc003hxi.1_3'UTR	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TATCCTTTTGTATATGTCAGA	0.388			Mis N|F		MDS								4	149	---	---	---	---	PASS
C4orf21	55345	broad.mit.edu	37	4	113468532	113468532	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113468532T>A	uc003iau.2	-	24	5718	c.5507A>T	c.(5506-5508)GAT>GTT	p.D1836V	C4orf21_uc003iav.2_RNA|C4orf21_uc003iat.2_Missense_Mutation_p.D294V	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	658						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CTGTTTGGGATCCCCAACAAG	0.358													66	182	---	---	---	---	PASS
CCRN4L	25819	broad.mit.edu	37	4	139966122	139966122	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139966122C>G	uc003ihl.2	+	3	983	c.790C>G	c.(790-792)CAG>GAG	p.Q264E		NM_012118	NP_036250	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like	264					rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)					GAAAACCAACCAGGTGGCCAT	0.498													19	44	---	---	---	---	PASS
SRD5A1	6715	broad.mit.edu	37	5	6663013	6663013	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6663013T>C	uc003jdw.2	+	4	837	c.647T>C	c.(646-648)GTC>GCC	p.V216A	SRD5A1_uc011cml.1_RNA|SRD5A1_uc011cmm.1_Missense_Mutation_p.V169A	NM_001047	NP_001038	P18405	S5A1_HUMAN	steroid-5-alpha-reductase 1	216	Helical; (Potential).				androgen biosynthetic process|cell differentiation|sex determination|sex differentiation	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|electron carrier activity				0					Dutasteride(DB01126)|Finasteride(DB01216)	AGCTGGTCTGTCCAAGGCGCG	0.408													7	576	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54579538	54579538	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54579538T>C	uc003jpx.2	-	11	1578	c.1458A>G	c.(1456-1458)AAA>AAG	p.K486K	DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	486							ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				GATCACGTGGTTTATTGGTTT	0.383													67	577	---	---	---	---	PASS
CRHBP	1393	broad.mit.edu	37	5	76264633	76264633	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76264633T>C	uc003ker.2	+	7	1172	c.892T>C	c.(892-894)TAT>CAT	p.Y298H		NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	298					female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		GACTTTTGAGTATCGTCAGCT	0.448													5	280	---	---	---	---	PASS
BHMT	635	broad.mit.edu	37	5	78423703	78423703	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78423703G>A	uc003kfu.3	+	7	1039	c.934G>A	c.(934-936)GAG>AAG	p.E312K	BHMT_uc011cti.1_Missense_Mutation_p.E159K	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	312	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)	GGCAATTGCAGAGGAGCTGGC	0.537													23	149	---	---	---	---	PASS
C5orf36	285600	broad.mit.edu	37	5	93859664	93859664	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93859664C>T	uc011cuk.1	-	4	528	c.271G>A	c.(271-273)GGA>AGA	p.G91R	C5orf36_uc003kkp.2_Missense_Mutation_p.G91R	NM_001145678	NP_001139150	Q8IV33	K0825_HUMAN	hypothetical protein LOC285600 isoform 1	91											0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)		ATCAAGTCTCCATGAGAAATG	0.328													5	521	---	---	---	---	PASS
FAM193B	54540	broad.mit.edu	37	5	176951610	176951610	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176951610C>T	uc003mhs.3	-	8	3362	c.1773G>A	c.(1771-1773)CTG>CTA	p.L591L	FAM193B_uc003mhr.2_Silent_p.L128L|FAM193B_uc003mht.2_Silent_p.L250L|FAM193B_uc003mhu.2_Silent_p.L303L|FAM193B_uc003mhv.2_Silent_p.L250L|FAM193B_uc003mhw.2_RNA	NM_019057	NP_061930	E9PET5	E9PET5_HUMAN	hypothetical protein LOC54540	624											0						CAGGCTCAGGCAGCTCCTGCT	0.642													7	17	---	---	---	---	PASS
RIOK1	83732	broad.mit.edu	37	6	7395314	7395314	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7395314C>T	uc003mxn.2	+	3	479	c.305C>T	c.(304-306)TCA>TTA	p.S102L	RIOK1_uc003mxm.1_5'UTR	NM_031480	NP_113668	Q9BRS2	RIOK1_HUMAN	RIO kinase 1 isoform 1	102							ATP binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|skin(1)	4	Ovarian(93;0.0418)					GACAGCAGTTCAGCCAAAATG	0.393													28	141	---	---	---	---	PASS
SCGN	10590	broad.mit.edu	37	6	25670266	25670266	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25670266A>C	uc003nfb.2	+	6	636	c.433A>C	c.(433-435)ATT>CTT	p.I145L	SCGN_uc010jpz.2_Silent_p.P54P	NM_006998	NP_008929	O76038	SEGN_HUMAN	secretagogin precursor	145						extracellular region|transport vesicle membrane	calcium ion binding			ovary(2)|pancreas(1)	3						CAAAAAGGCCATTTCTGAGGC	0.313													28	178	---	---	---	---	PASS
ZNF193	7746	broad.mit.edu	37	6	28195519	28195519	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28195519C>G	uc003nkq.1	+	3	587	c.472C>G	c.(472-474)CTA>GTA	p.L158V	ZNF193_uc003nkr.1_Missense_Mutation_p.L158V|ZNF193_uc010jqz.1_Missense_Mutation_p.L158V	NM_006299	NP_006290	O15535	ZN193_HUMAN	zinc finger protein 193	158					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GATGGTGCCTCTAGCAGAGCA	0.483													6	47	---	---	---	---	PASS
MAS1L	116511	broad.mit.edu	37	6	29454618	29454618	+	Silent	SNP	T	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29454618T>A	uc011dlq.1	-	1	1062	c.1062A>T	c.(1060-1062)CCA>CCT	p.P354P		NM_052967	NP_443199	P35410	MAS1L_HUMAN	MAS1 oncogene-like	354	Cytoplasmic (Potential).					cytoplasm|integral to membrane|nucleus|plasma membrane	G-protein coupled receptor activity			ovary(7)|lung(2)	9						GTTGCTCCATTGGGTCGATGC	0.507													83	183	---	---	---	---	PASS
GLP1R	2740	broad.mit.edu	37	6	39025301	39025301	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39025301C>T	uc003ooj.3	+	3	289	c.229C>T	c.(229-231)CCA>TCA	p.P77S	GLP1R_uc003ooh.2_RNA|GLP1R_uc003ooi.2_RNA	NM_002062	NP_002053	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor precursor	77	Extracellular (Potential).				activation of adenylate cyclase activity|cAMP-mediated signaling|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	glucagon receptor activity|peptide receptor activity, G-protein coupled			lung(3)|breast(1)|pancreas(1)	5					Exenatide(DB01276)|Glucagon recombinant(DB00040)	AGATGGGGAGCCAGGCTCGTT	0.622													8	54	---	---	---	---	PASS
USP49	25862	broad.mit.edu	37	6	41773626	41773626	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41773626G>A	uc003ori.2	-	4	1318	c.1096C>T	c.(1096-1098)CGA>TGA	p.R366*		NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin thioesterase 49	366					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CACATGACTCGGAAGAGGGTG	0.597													4	18	---	---	---	---	PASS
PM20D2	135293	broad.mit.edu	37	6	89868129	89868129	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89868129A>G	uc003pmz.2	+	5	1093	c.998A>G	c.(997-999)AAG>AGG	p.K333R		NM_001010853	NP_001010853	Q8IYS1	P20D2_HUMAN	aminoacylase 1-like 2	333							hydrolase activity				0		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		AATGGAAGAAAGCTAGGAATA	0.333													6	367	---	---	---	---	PASS
FSCN1	6624	broad.mit.edu	37	7	5643128	5643128	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5643128A>T	uc003sou.2	+	3	1105	c.991A>T	c.(991-993)AAT>TAT	p.N331Y	FSCN1_uc003sov.2_Missense_Mutation_p.N53Y|FSCN1_uc003sow.2_Missense_Mutation_p.N53Y	NM_003088	NP_003079	Q16658	FSCN1_HUMAN	fascin 1	331					actin filament bundle assembly|cell migration|cell proliferation	cell junction|cytoplasm|filopodium|invadopodium|stress fiber	actin filament binding|drug binding|protein binding, bridging			ovary(1)	1		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		ATCCCCCAGGAATGCCAGCTG	0.637													5	42	---	---	---	---	PASS
CCDC132	55610	broad.mit.edu	37	7	92982959	92982959	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92982959A>G	uc003umo.2	+	26	2599	c.2471A>G	c.(2470-2472)GAG>GGG	p.E824G	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Missense_Mutation_p.E794G|CCDC132_uc003umr.2_RNA|CCDC132_uc011khz.1_Missense_Mutation_p.E544G	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	824											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TAGGAATTTGAGCAGTTTAAC	0.333													7	511	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94057002	94057002	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94057002G>T	uc003ung.1	+	49	3802	c.3331G>T	c.(3331-3333)GGT>TGT	p.G1111C	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	1111					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTATGACTTTGGTTACGATGG	0.532										HNSCC(75;0.22)			6	108	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100350474	100350474	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100350474T>C	uc003uwj.2	+	14	2911	c.2746T>C	c.(2746-2748)TCC>CCC	p.S916P	ZAN_uc003uwk.2_Missense_Mutation_p.S916P|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	916	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			ACCCACCATCTCCACGGAAAA	0.502													16	693	---	---	---	---	PASS
UPK3BL	100134938	broad.mit.edu	37	7	102279601	102279601	+	Silent	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102279601G>T	uc010lij.1	-	4	581	c.531C>A	c.(529-531)ACC>ACA	p.T177T	UPK3BL_uc003uzy.2_5'Flank|RASA4_uc011klb.1_5'UTR|RASA4_uc011kld.1_Intron|POLR2J2_uc003vai.2_RNA|POLR2J2_uc003vah.2_3'UTR	NM_001114403	NP_001107875	B0FP48	UPK3L_HUMAN	uroplakin-like protein	177	Extracellular (Potential).					integral to membrane					0						TGGACCACTTGGTTTCAGCCA	0.622													5	238	---	---	---	---	PASS
GCC1	79571	broad.mit.edu	37	7	127222158	127222158	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127222158T>C	uc003vma.2	-	2	2656	c.2238A>G	c.(2236-2238)ATA>ATG	p.I746M		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	746	Potential.|GRIP.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2						AGATAGTCAGTATGGCTGTGA	0.527													6	313	---	---	---	---	PASS
JHDM1D	80853	broad.mit.edu	37	7	139813332	139813332	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139813332T>C	uc003vvm.2	-	10	1301	c.1297A>G	c.(1297-1299)AAA>GAA	p.K433E	JHDM1D_uc010lng.2_RNA	NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase	433					midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)					TGCAGTGCTTTCACTCCCTGT	0.353													7	272	---	---	---	---	PASS
LONRF1	91694	broad.mit.edu	37	8	12586770	12586770	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12586770A>C	uc003wwd.1	-	9	1823	c.1760T>G	c.(1759-1761)TTT>TGT	p.F587C	LONRF1_uc011kxv.1_Missense_Mutation_p.F176C|LONRF1_uc010lsp.1_Missense_Mutation_p.F187C	NM_152271	NP_689484	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger	587	Lon.				proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)		TCTTGGCTCAAATACATGGAG	0.388													33	101	---	---	---	---	PASS
CNGB3	54714	broad.mit.edu	37	8	87683231	87683231	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87683231A>G	uc003ydx.2	-	4	480	c.434T>C	c.(433-435)CTC>CCC	p.L145P	CNGB3_uc010maj.2_Missense_Mutation_p.L7P	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	145	Cytoplasmic (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						TTTCTTGTAGAGGGCTGTTCT	0.488													7	391	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110451243	110451243	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110451243G>C	uc003yne.2	+	32	3982	c.3878G>C	c.(3877-3879)AGA>ACA	p.R1293T		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1293	Extracellular (Potential).|IPT/TIG 6.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACAGATATTAGATGCCTTTTG	0.378										HNSCC(38;0.096)			16	285	---	---	---	---	PASS
KIAA0196	9897	broad.mit.edu	37	8	126075885	126075885	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126075885C>T	uc003yrt.2	-	11	1616	c.1287G>A	c.(1285-1287)AAG>AAA	p.K429K	KIAA0196_uc011lir.1_Silent_p.K281K|KIAA0196_uc003yru.1_Silent_p.K3K	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin	429					cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			AAAGCATTTGCTTGAACATCT	0.393													4	222	---	---	---	---	PASS
ABCA1	19	broad.mit.edu	37	9	107546504	107546504	+	3'UTR	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107546504A>G	uc004bcl.2	-	50					NIPSNAP3B_uc004bcj.1_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TCCCACATCAACTTCTGGCTC	0.353													18	94	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135173490	135173490	+	Silent	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135173490G>A	uc004cbk.2	-	13	5941	c.5758C>T	c.(5758-5760)CTG>TTG	p.L1920L	SETX_uc004cbj.2_Silent_p.L1539L|SETX_uc010mzt.2_Silent_p.L1539L	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1920					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GTTGTAGTCAGTAAATCTTTT	0.368													57	127	---	---	---	---	PASS
SLC39A12	221074	broad.mit.edu	37	10	18276482	18276482	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18276482C>A	uc001ipo.2	+	7	1444	c.1171C>A	c.(1171-1173)CAT>AAT	p.H391N	SLC39A12_uc001ipn.2_Missense_Mutation_p.H391N|SLC39A12_uc001ipp.2_Missense_Mutation_p.H391N|SLC39A12_uc010qck.1_Missense_Mutation_p.H257N	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	391	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2						GGTCCTTTTCCATAGCTGTGA	0.547													22	96	---	---	---	---	PASS
FAM21C	253725	broad.mit.edu	37	10	46282020	46282020	+	Intron	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46282020T>C	uc001jcu.2	+						FAM21C_uc001jct.2_Intron|FAM21C_uc010qfi.1_Intron|FAM21C_uc010qfj.1_Intron|FAM21C_uc010qfk.1_Intron|FAM21C_uc001jcw.2_5'UTR	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725											ovary(1)	1						TGTCTTTCTGTTTCCCAAATG	0.398													7	481	---	---	---	---	PASS
GLUD1	2746	broad.mit.edu	37	10	88822546	88822546	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88822546C>T	uc001keh.2	-	6	885	c.788G>A	c.(787-789)GGG>GAG	p.G263E	GLUD1_uc001keg.2_Missense_Mutation_p.G96E|GLUD1_uc010qmp.1_Missense_Mutation_p.G130E	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor	263					glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	ATGGATTCCCCCTTGGCTGAT	0.428													4	192	---	---	---	---	PASS
RBM20	282996	broad.mit.edu	37	10	112572492	112572492	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112572492C>T	uc001kzf.2	+	9	2395	c.2337C>T	c.(2335-2337)CCC>CCT	p.P779P		NM_001134363	NP_001127835	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	779						nucleus	nucleotide binding|RNA binding|zinc ion binding				0						AGGATGCCCCCGGGAGGTCCA	0.592													21	32	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115423676	115423676	+	5'UTR	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115423676A>G	uc001laj.2	-	1					NRAP_uc001lak.2_5'UTR|NRAP_uc001lal.3_5'UTR	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AAGATAGGCAACAGGCAAGAA	0.478													5	151	---	---	---	---	PASS
PDZD8	118987	broad.mit.edu	37	10	119044693	119044693	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119044693T>C	uc001lde.1	-	5	1750	c.1551A>G	c.(1549-1551)TCA>TCG	p.S517S		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	517					intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)		TATGACTTAATGATTGTGCCT	0.398													59	334	---	---	---	---	PASS
FAM45A	404636	broad.mit.edu	37	10	120871395	120871395	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120871395A>C	uc001ldw.2	+	3	331	c.287A>C	c.(286-288)GAT>GCT	p.D96A	FAM45A_uc010qsv.1_Missense_Mutation_p.D88A|FAM45A_uc010qsw.1_5'UTR|FAM45A_uc010qsx.1_RNA|FAM45A_uc010qsy.1_Missense_Mutation_p.D23A|FAM45A_uc010qsz.1_5'UTR|uc001ldx.2_5'Flank	NM_207009	NP_996892	Q8TCE6	FA45A_HUMAN	hypothetical protein LOC404636	96										ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		ACCGCCAAAGATTTTAACCCA	0.299													168	483	---	---	---	---	PASS
OR5D13	390142	broad.mit.edu	37	11	55541194	55541194	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55541194T>C	uc010ril.1	+	1	281	c.281T>C	c.(280-282)ATC>ACC	p.I94T		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	94	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3		all_epithelial(135;0.196)				TACAGAACCATCTCTTTCTCT	0.403													6	352	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944568	55944568	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944568C>T	uc010rjb.1	+	1	475	c.475C>T	c.(475-477)CAC>TAC	p.H159Y		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	159	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					CACATTAATCCACACAATCAG	0.438													4	186	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85406135	85406135	+	3'UTR	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85406135G>A	uc010rth.1	-	18					SYTL2_uc010rtg.1_3'UTR|SYTL2_uc010rti.1_3'UTR|SYTL2_uc010rtj.1_3'UTR|SYTL2_uc001pav.2_3'UTR|SYTL2_uc010rte.1_3'UTR|SYTL2_uc001pax.2_3'UTR|SYTL2_uc001paz.2_3'UTR|SYTL2_uc001pba.2_3'UTR|SYTL2_uc001pay.2_3'UTR|SYTL2_uc001paw.2_3'UTR|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_3'UTR|SYTL2_uc001pbb.2_3'UTR|SYTL2_uc001pbc.2_3'UTR|SYTL2_uc010rtf.1_3'UTR	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTCCTTAGGTGCAATAGATAG	0.378													3	27	---	---	---	---	PASS
PPP2R1B	5519	broad.mit.edu	37	11	111625282	111625282	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111625282T>C	uc001plx.1	-	8	1054	c.970A>G	c.(970-972)AAC>GAC	p.N324D	PPP2R1B_uc001plw.1_Missense_Mutation_p.N324D|PPP2R1B_uc010rwi.1_Missense_Mutation_p.N260D|PPP2R1B_uc010rwj.1_Missense_Mutation_p.N163D|PPP2R1B_uc010rwk.1_Missense_Mutation_p.N324D|PPP2R1B_uc010rwl.1_Missense_Mutation_p.N197D	NM_002716	NP_002707	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein	324	HEAT 8.						protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		ATGGGCAAGTTCTCACCAAGT	0.308													7	453	---	---	---	---	PASS
PRDM10	56980	broad.mit.edu	37	11	129794821	129794821	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129794821A>G	uc001qfm.2	-	13	2078	c.1846T>C	c.(1846-1848)TTC>CTC	p.F616L	PRDM10_uc001qfj.2_Missense_Mutation_p.F530L|PRDM10_uc001qfk.2_Missense_Mutation_p.F526L|PRDM10_uc001qfl.2_Missense_Mutation_p.F530L|PRDM10_uc010sbx.1_Missense_Mutation_p.F526L|PRDM10_uc001qfn.2_Missense_Mutation_p.F612L	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	616	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		GGGCAGGTGAAGTAGCCATCA	0.418													37	78	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2702501	2702501	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2702501T>C	uc009zdu.1	+	19	2966	c.2653T>C	c.(2653-2655)TCT>CCT	p.S885P	CACNA1C_uc009zdv.1_Missense_Mutation_p.S882P|CACNA1C_uc001qkb.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkc.2_Missense_Mutation_p.S885P|CACNA1C_uc001qke.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkf.2_Missense_Mutation_p.S885P|CACNA1C_uc001qjz.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkd.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkg.2_Missense_Mutation_p.S885P|CACNA1C_uc009zdw.1_Missense_Mutation_p.S885P|CACNA1C_uc001qkh.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkl.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkn.2_Missense_Mutation_p.S885P|CACNA1C_uc001qko.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkp.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkr.2_Missense_Mutation_p.S885P|CACNA1C_uc001qku.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkq.2_Missense_Mutation_p.S885P|CACNA1C_uc001qks.2_Missense_Mutation_p.S885P|CACNA1C_uc001qkt.2_Missense_Mutation_p.S885P|CACNA1C_uc001qka.1_Missense_Mutation_p.S420P|CACNA1C_uc001qki.1_Missense_Mutation_p.S621P|CACNA1C_uc001qkj.1_Missense_Mutation_p.S621P|CACNA1C_uc001qkk.1_Missense_Mutation_p.S621P|CACNA1C_uc001qkm.1_Missense_Mutation_p.S621P|CACNA1C_uc001qkw.2_Missense_Mutation_p.S174P	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	885	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CATCTTCAGCTCTAACAACAG	0.552													6	301	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082245	8082245	+	Intron	SNP	T	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082245T>G	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GTGAAATACTTTAAGACACGT	0.254													4	118	---	---	---	---	PASS
CLEC4E	26253	broad.mit.edu	37	12	8693431	8693431	+	5'UTR	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8693431C>T	uc001quo.1	-	1						NM_014358	NP_055173	Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E							integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)					ctctctctctctttttctctc	0.269													5	727	---	---	---	---	PASS
PRH2	5555	broad.mit.edu	37	12	11083284	11083284	+	Missense_Mutation	SNP	A	C	C	rs2923234	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11083284A>C	uc009zhr.2	+	3	162	c.124A>C	c.(124-126)ATA>CTA	p.I42L	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH2_uc001qzh.2_Missense_Mutation_p.I42L|PRH2_uc001qzi.3_Missense_Mutation_p.I42L	NM_001110213	NP_001103683	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 2	42	Inhibits hydroxyapatite formation, binds to hydroxyapatite and calcium.					extracellular space	protein binding				0						TGAGCAGTTCATAGATGAGGA	0.527													5	124	---	---	---	---	PASS
OVCH1	341350	broad.mit.edu	37	12	29629155	29629155	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29629155T>C	uc001rix.1	-	13	1455	c.1455A>G	c.(1453-1455)GAA>GAG	p.E485E		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	485	CUB 2.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TGTGCTTTTCTTCAGAATCAC	0.398													7	414	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29709847	29709847	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29709847G>T	uc001rjb.2	-	10	1769	c.1295C>A	c.(1294-1296)GCT>GAT	p.A432D	TMTC1_uc001riz.2_Missense_Mutation_p.A189D|TMTC1_uc001rja.2_Missense_Mutation_p.A276D|TMTC1_uc001rjc.1_Missense_Mutation_p.A494D	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	540	TPR 2.					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GAGCTGGAGAGCCCTCTGATA	0.498													47	492	---	---	---	---	PASS
C12orf40	283461	broad.mit.edu	37	12	40076779	40076779	+	Silent	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40076779A>T	uc001rmc.2	+	8	1220	c.1053A>T	c.(1051-1053)ACA>ACT	p.T351T	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	351										ovary(6)	6						ACATTTTTACAGTTCCAGAGT	0.323													39	161	---	---	---	---	PASS
LRRK2	120892	broad.mit.edu	37	12	40704394	40704394	+	Silent	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40704394A>G	uc001rmg.3	+	31	4600	c.4479A>G	c.(4477-4479)GAA>GAG	p.E1493E	LRRK2_uc009zjw.2_Silent_p.E331E|LRRK2_uc001rmi.2_Silent_p.E326E	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1493	Roc.				activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CCACCGAGGAATCTGATGCTT	0.428													5	214	---	---	---	---	PASS
FLJ12825	440101	broad.mit.edu	37	12	54515418	54515418	+	RNA	SNP	C	T	T	rs143240436	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54515418C>T	uc001sey.2	+	2		c.3342C>T				NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						tagtggacaacgggcagtctT	0.219													7	77	---	---	---	---	PASS
MYO1A	4640	broad.mit.edu	37	12	57430161	57430161	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57430161C>T	uc001smw.3	-	22	2522	c.2279G>A	c.(2278-2280)CGA>CAA	p.R760Q	MYO1A_uc010sqz.1_Missense_Mutation_p.R598Q|MYO1A_uc009zpd.2_Missense_Mutation_p.R760Q	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	760	IQ 3.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|urinary_tract(1)	7						ATAATTCTTTCGGGCCTGGCA	0.448													5	205	---	---	---	---	PASS
TMTC2	160335	broad.mit.edu	37	12	83290207	83290207	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83290207G>A	uc001szt.2	+	3	1697	c.1265G>A	c.(1264-1266)CGA>CAA	p.R422Q	TMTC2_uc001szr.1_Missense_Mutation_p.R422Q|TMTC2_uc001szs.1_Missense_Mutation_p.R422Q|TMTC2_uc010suk.1_Missense_Mutation_p.R177Q	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat	422						endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						ATTGCAGAGCGAGTATTATAT	0.413													51	537	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	104062492	104062492	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104062492C>A	uc001tjw.2	+	20	2343	c.2157C>A	c.(2155-2157)TGC>TGA	p.C719*		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	719	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						CCCGGTACTGCAATGCCACTG	0.612													10	20	---	---	---	---	PASS
ZMYM2	7750	broad.mit.edu	37	13	20657807	20657807	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20657807A>G	uc001umr.2	+	25	4130	c.3832A>G	c.(3832-3834)ACT>GCT	p.T1278A	ZMYM2_uc001ums.2_Missense_Mutation_p.T1278A|ZMYM2_uc001umt.2_Missense_Mutation_p.T1278A|ZMYM2_uc001umv.2_Missense_Mutation_p.T658A|ZMYM2_uc001umw.2_Missense_Mutation_p.T731A	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	1278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TAAAATTACTACTGGAAAAAG	0.303													76	206	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109535457	109535457	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109535457T>C	uc001vqt.1	+	13	1536	c.1410T>C	c.(1408-1410)CCT>CCC	p.P470P	MYO16_uc010agk.1_Silent_p.P492P|MYO16_uc001vqu.1_Silent_p.P270P	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	470	Myosin head-like 1.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CCTCGCTGCCTCCTCACCTCT	0.562													36	63	---	---	---	---	PASS
OR5AU1	390445	broad.mit.edu	37	14	21624096	21624096	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21624096C>T	uc010tlp.1	-	1	89	c.89G>A	c.(88-90)AGC>AAC	p.S30N		NM_001004731	NP_001004731	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU,	30	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		ACACCTGGGGCTCTGACTGGG	0.478													45	100	---	---	---	---	PASS
C14orf39	317761	broad.mit.edu	37	14	60932762	60932762	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60932762C>T	uc001xez.3	-	11	1017	c.907G>A	c.(907-909)GAA>AAA	p.E303K	C14orf39_uc010apo.2_Missense_Mutation_p.E14K	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	303										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GCAGAACTTTCTTCTTTTATA	0.294													20	151	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68249593	68249593	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68249593A>T	uc001xka.2	-	21	4415	c.4276T>A	c.(4276-4278)TGG>AGG	p.W1426R	ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Missense_Mutation_p.W1426R	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1426					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GCCCGGGACCAATCTCTGGCC	0.542													7	43	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68249594	68249594	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68249594A>T	uc001xka.2	-	21	4414	c.4275T>A	c.(4273-4275)GAT>GAA	p.D1425E	ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Missense_Mutation_p.D1425E	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1425					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CCCGGGACCAATCTCTGGCCA	0.547													7	44	---	---	---	---	PASS
UPF0639	400224	broad.mit.edu	37	14	69967230	69967230	+	Intron	SNP	C	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69967230C>A	uc010ttf.1	+						UPF0639_uc001xli.2_3'UTR	NM_001161498	NP_001154970	B9EJC2	B9EJC2_HUMAN	similar to pleckstrin homology domain protein												0						TCCAGGGGCCCCCAGAACCCC	0.637													3	14	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106110423	106110423	+	RNA	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106110423C>T	uc010tyt.1	-	3641		c.60946G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0						GGTGGGCACTCGACACAACAT	0.612													35	51	---	---	---	---	PASS
TTBK2	146057	broad.mit.edu	37	15	43102877	43102877	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43102877G>A	uc001zqo.2	-	9	1196	c.757C>T	c.(757-759)CCA>TCA	p.P253S	TTBK2_uc010bcy.2_Missense_Mutation_p.P184S|TTBK2_uc001zqp.2_Missense_Mutation_p.P253S|TTBK2_uc010bcz.1_Missense_Mutation_p.P218S	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	253	Protein kinase.				cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CTGAATTCTGGAGGGAGATGT	0.393													50	318	---	---	---	---	PASS
TGM7	116179	broad.mit.edu	37	15	43579799	43579799	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43579799C>T	uc001zrf.1	-	5	632	c.627G>A	c.(625-627)CCG>CCA	p.P209P		NM_052955	NP_443187	Q96PF1	TGM7_HUMAN	transglutaminase 7	209					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)	2		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	AGTCTTTGGCCGGGTTCTTTA	0.488													4	196	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54817772	54817772	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54817772T>C	uc002ack.2	+	23	5483	c.5483T>C	c.(5482-5484)CTA>CCA	p.L1828P		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1828					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AGTACTATTCTAAAAGAACTT	0.393													5	330	---	---	---	---	PASS
ST20	400410	broad.mit.edu	37	15	80191383	80191383	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80191383A>G	uc002bez.3	-	3	810	c.130T>C	c.(130-132)TTC>CTC	p.F44L	ST20_uc002bfa.3_Missense_Mutation_p.F44L|MTHFS_uc002bex.3_5'Flank	NM_001100879	NP_001094349	Q9HBF5	ST20_HUMAN	cervical cancer suppressor-1	44											0						TCAGGACAGAAGAGCATTTCA	0.388													7	529	---	---	---	---	PASS
BLM	641	broad.mit.edu	37	15	91292947	91292947	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91292947C>T	uc002bpr.2	+	3	546	c.449C>T	c.(448-450)ACC>ATC	p.T150I	BLM_uc010uqh.1_Missense_Mutation_p.T150I|BLM_uc010uqi.1_5'UTR|BLM_uc010bnx.2_Missense_Mutation_p.T150I	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	150					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TCTTTAAGTACCATCAATGAT	0.378			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				59	181	---	---	---	---	PASS
RRN3P3	100131998	broad.mit.edu	37	16	22441236	22441236	+	RNA	SNP	G	A	A	rs114681793	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22441236G>A	uc002dkp.2	-	5		c.1170C>T			RRN3P3_uc010vbu.1_RNA	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0						TGTTCCTCTCGATGATGGTGT	0.507													5	136	---	---	---	---	PASS
UBFD1	56061	broad.mit.edu	37	16	23570951	23570951	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23570951A>G	uc002dlv.2	+	3	720	c.518A>G	c.(517-519)GAT>GGT	p.D173G	EARS2_uc002dls.3_5'Flank|EARS2_uc002dlt.3_5'Flank|EARS2_uc002dlu.2_5'Flank	NM_019116	NP_061989	O14562	UBFD1_HUMAN	ubiquitin-binding protein homolog	173											0				GBM - Glioblastoma multiforme(48;0.0331)		GCGCAGCAGGATGCAAAGGCC	0.478													4	80	---	---	---	---	PASS
GAN	8139	broad.mit.edu	37	16	81397479	81397479	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81397479T>C	uc002fgo.2	+	7	1315	c.1167T>C	c.(1165-1167)ATT>ATC	p.I389I		NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin	389	Kelch 3.				cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)				AGGAGCTGATTTCCATGGAGT	0.413													7	588	---	---	---	---	PASS
TRIM16	10626	broad.mit.edu	37	17	15554772	15554772	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15554772A>G	uc002gox.2	-	4	709	c.152T>C	c.(151-153)CTT>CCT	p.L51P	TRIM16_uc002gor.1_Missense_Mutation_p.L51P|TRIM16_uc002goy.2_Intron	NM_006470	NP_006461	O95361	TRI16_HUMAN	tripartite motif-containing 16	51					histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CTCCCTGCCAAGCTTCTCCGA	0.627													5	25	---	---	---	---	PASS
CCDC144A	9720	broad.mit.edu	37	17	16667540	16667540	+	Intron	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16667540A>G	uc002gqk.1	+						CCDC144A_uc002gql.1_Silent_p.V899V|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						GAATTCTTGTATGTTATTTGG	0.328													4	87	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	16723994	16723994	+	RNA	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16723994C>T	uc002gqq.1	-	2		c.673G>A								full-length cDNA clone CS0DI013YN06 of Placenta Cot 25-normalized of Homo sapiens (human).																		AAGTCATCTGCGGCCAGACGG	0.512													9	53	---	---	---	---	PASS
LGALS9C	654346	broad.mit.edu	37	17	18380154	18380154	+	5'UTR	SNP	A	G	G	rs1682220	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18380154A>G	uc002gtw.2	+	1					LGALS9C_uc010vyb.1_5'UTR	NM_001040078	NP_001035167	Q6DKI2	LEG9C_HUMAN	galectin 9 like								sugar binding			ovary(1)	1						TGGTGGCCACAGAGGCGGTGG	0.567													12	42	---	---	---	---	PASS
EFCAB5	374786	broad.mit.edu	37	17	28382907	28382907	+	Silent	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28382907A>G	uc002het.2	+	11	2388	c.2196A>G	c.(2194-2196)GAA>GAG	p.E732E	EFCAB5_uc010wbi.1_Silent_p.E475E|EFCAB5_uc010wbj.1_Silent_p.E676E|EFCAB5_uc010wbk.1_Silent_p.E389E|EFCAB5_uc010csd.2_RNA|EFCAB5_uc010cse.2_Silent_p.E611E|EFCAB5_uc010csf.2_Silent_p.E611E	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	732							calcium ion binding			ovary(1)|skin(1)	2						ACCTTTTAGAAACTACAAAAA	0.333													6	385	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587657	43587657	+	RNA	SNP	C	T	T	rs148404065	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587657C>T	uc002ije.2	-	3		c.1397G>A			uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						GGTGACAACACATCTGTTTTA	0.279													6	266	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630632	44630632	+	3'UTR	SNP	C	T	T	rs142505146	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630632C>T	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						TGTTACACAGCATACAATTCC	0.234													7	93	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630635	44630635	+	3'UTR	SNP	A	G	G	rs150521815	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630635A>G	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						TACACAGCATACAATTCCTGT	0.239													9	99	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45209685	45209685	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45209685G>A	uc002ild.3	-	15	2096	c.1969C>T	c.(1969-1971)CAT>TAT	p.H657Y	CDC27_uc002ile.3_Missense_Mutation_p.H663Y|CDC27_uc002ilf.3_Missense_Mutation_p.H656Y|CDC27_uc010wkp.1_Missense_Mutation_p.H596Y|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	657	TPR 6.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TTTTGGAAATGCATTTCTGCA	0.294													5	378	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234625	45234625	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45234625C>T	uc002ild.3	-	6	728	c.601G>A	c.(601-603)GTT>ATT	p.V201I	CDC27_uc002ile.3_Missense_Mutation_p.V201I|CDC27_uc002ilf.3_Missense_Mutation_p.V201I|CDC27_uc010wkp.1_Missense_Mutation_p.V140I|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	201					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TCCGTAAGAACTGTCTCAGGC	0.338													6	132	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45234626	45234626	+	Silent	SNP	T	G	G	rs76359747		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45234626T>G	uc002ild.3	-	6	727	c.600A>C	c.(598-600)ACA>ACC	p.T200T	CDC27_uc002ile.3_Silent_p.T200T|CDC27_uc002ilf.3_Silent_p.T200T|CDC27_uc010wkp.1_Silent_p.T139T|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	200					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						CCGTAAGAACTGTCTCAGGCT	0.343													6	130	---	---	---	---	PASS
INTS2	57508	broad.mit.edu	37	17	59988926	59988926	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59988926C>T	uc002izn.2	-	7	1009	c.933G>A	c.(931-933)GCG>GCA	p.A311A	INTS2_uc002izm.2_Silent_p.A303A	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	311					snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						TCCGGACTTTCGCATTTGTTC	0.408													4	298	---	---	---	---	PASS
ABCA6	23460	broad.mit.edu	37	17	67110958	67110958	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67110958T>C	uc002jhw.1	-	13	1902	c.1727A>G	c.(1726-1728)AAC>AGC	p.N576S	ABCA6_uc002jhx.1_Missense_Mutation_p.N29S	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	576	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					CAGGCTGAGGTTTTCCTTCAC	0.413													8	316	---	---	---	---	PASS
YES1	7525	broad.mit.edu	37	18	743325	743325	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:743325A>C	uc002kky.2	-	7	1036	c.815T>G	c.(814-816)ATC>AGC	p.I272S	YES1_uc002kkz.2_Missense_Mutation_p.I272S	NM_005433	NP_005424	P07947	YES_HUMAN	viral oncogene yes-1 homolog 1	272					blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)	TTCTCGAGGGATTTCCCAAGC	0.418													42	113	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14542791	14542791	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14542791C>T	uc010dln.2	-	1	809	c.355G>A	c.(355-357)GCT>ACT	p.A119T	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	119										skin(3)	3						TCTCCCCAAGCGCCCACGTTG	0.597													4	52	---	---	---	---	PASS
CTAGE1	64693	broad.mit.edu	37	18	19995469	19995469	+	3'UTR	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19995469C>T	uc002ktv.1	-	1						NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TTCTTGCTGTCGTTCTGGATG	0.423													3	25	---	---	---	---	PASS
CD97	976	broad.mit.edu	37	19	14507236	14507236	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14507236G>C	uc002myl.2	+	5	552	c.429G>C	c.(427-429)CAG>CAC	p.Q143H	CD97_uc002mym.2_Missense_Mutation_p.Q143H|CD97_uc002myn.2_Intron	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor	143	Extracellular (Potential).|EGF-like 3; calcium-binding (Potential).				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)|breast(1)	4						ATACCTGCCAGTGCCTGCCTG	0.582													8	49	---	---	---	---	PASS
MED26	9441	broad.mit.edu	37	19	16687395	16687395	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16687395T>G	uc002nen.1	-	3	1507	c.1246A>C	c.(1246-1248)AAG>CAG	p.K416Q	MED26_uc002nee.2_Intron	NM_004831	NP_004822	O95402	MED26_HUMAN	mediator complex subunit 26	416					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|RNA polymerase II transcription cofactor activity|transcription coactivator activity			ovary(2)	2						CGGACAGGCTTGACGCCCGCC	0.572													4	31	---	---	---	---	PASS
PSG4	5672	broad.mit.edu	37	19	43697425	43697425	+	3'UTR	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43697425C>T	uc002ovy.2	-	6					PSG6_uc010xwk.1_Intron|PSG4_uc002owa.2_RNA|PSG4_uc002owb.2_3'UTR|PSG4_uc002ovz.2_3'UTR	NM_002780	NP_002771	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4 isoform						defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)				aaatttacatcgagttgtcca	0.000													5	111	---	---	---	---	PASS
VSIG10L	147645	broad.mit.edu	37	19	51845047	51845047	+	Silent	SNP	C	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51845047C>G	uc002pwf.2	-	2	255	c.255G>C	c.(253-255)CTG>CTC	p.L85L	VSIG10L_uc002pwd.2_5'Flank	NM_001163922	NP_001157394	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10	85	Extracellular (Potential).|Ser-rich.					integral to membrane					0						TGTTGGAACTCAGGGCCTCAG	0.507													34	114	---	---	---	---	PASS
ZNF665	79788	broad.mit.edu	37	19	53668352	53668352	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53668352C>T	uc010eqm.1	-	4	1491	c.1391G>A	c.(1390-1392)GGT>GAT	p.G464D		NM_024733	NP_079009	Q9H7R5	ZN665_HUMAN	zinc finger protein 665	399	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0196)		GAAGACCTTACCGCAGTCATT	0.433													7	51	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58385546G>T	uc002qqo.2	-	3	1484	c.1212C>A	c.(1210-1212)GAC>GAA	p.D404E	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						AATGTTTTTTGTCAGTGTGAA	0.393													48	338	---	---	---	---	PASS
NOP56	10528	broad.mit.edu	37	20	2637491	2637491	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2637491G>A	uc002wgh.2	+	10	1284	c.1231G>A	c.(1231-1233)GGA>AGA	p.G411R	NOP56_uc010zpy.1_RNA|NOP56_uc002wgi.2_Missense_Mutation_p.G245R|NOP56_uc002wgm.1_Missense_Mutation_p.G158R|SNORD57_uc002wgo.1_5'Flank	NM_006392	NP_006383	O00567	NOP56_HUMAN	nucleolar protein 5A	411	Nop.				rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2						CTATGAGACTGGAGAGATACC	0.512													36	266	---	---	---	---	PASS
ESF1	51575	broad.mit.edu	37	20	13756682	13756682	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13756682T>C	uc002woj.2	-	3	980	c.872A>G	c.(871-873)GAG>GGG	p.E291G	ESF1_uc002wok.1_Missense_Mutation_p.E291G	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	291	Asp-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						atcatcatcctcactatcctc	0.239													9	701	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	21	10862786	10862786	+	IGR	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10862786G>A								None (None upstream) : TPTE (43957 downstream)																							GCAGTCTGGGGCTGAGGTGAA	0.572													9	170	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11020826	11020826	+	RNA	SNP	C	A	A	rs4343554		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11020826C>A	uc002yis.1	-	5		c.1133G>T						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AATACTGACACAGTATGGATG	0.373													5	82	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11020831	11020831	+	RNA	SNP	T	C	C	rs4474962		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11020831T>C	uc002yis.1	-	5		c.1128A>G						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TGACACAGTATGGATGGTAAC	0.378													6	88	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11020869	11020869	+	3'UTR	SNP	G	A	A	rs9981999		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11020869G>A	uc002yit.1	-	10					TPTE_uc002yis.1_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CAGGCAAGTAGTCTTCCTTCT	0.358													7	106	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11049516	11049516	+	3'UTR	SNP	G	A	A	rs468629	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11049516G>A	uc002yit.1	-	4						NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGTAACCGCTGTATCCAGGCA	0.453													159	74	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38119859	38119859	+	Silent	SNP	C	T	T	rs66505048		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38119859C>T	uc003atr.2	+	7	1567	c.1296C>T	c.(1294-1296)TGC>TGT	p.C432C	TRIOBP_uc003atu.2_Silent_p.C260C|TRIOBP_uc003atq.1_Silent_p.C432C|TRIOBP_uc003ats.1_Silent_p.C260C	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	432					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GAACATCCTGCGCCCAGCGGG	0.582													8	355	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38120006	38120006	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38120006T>C	uc003atr.2	+	7	1714	c.1443T>C	c.(1441-1443)TGT>TGC	p.C481C	TRIOBP_uc003atu.2_Silent_p.C309C|TRIOBP_uc003atq.1_Silent_p.C481C|TRIOBP_uc003ats.1_Silent_p.C309C	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	481					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GAACATCCTGTGCCCAGCGGG	0.592													9	191	---	---	---	---	PASS
CSNK1E	1454	broad.mit.edu	37	22	38776379	38776379	+	5'UTR	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38776379T>C	uc003avm.1	-	3					LOC400927_uc010gxm.2_RNA|LOC400927_uc011ans.1_RNA|LOC400927_uc011ant.1_RNA|LOC400927_uc003avr.1_RNA	NM_152221	NP_689407	P49674	KC1E_HUMAN	casein kinase 1 epsilon						DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)					ACTCACCTTTTACTGATAGGT	0.388													12	419	---	---	---	---	PASS
CSNK1E	1454	broad.mit.edu	37	22	38776418	38776418	+	5'UTR	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38776418C>T	uc003avm.1	-	3					LOC400927_uc010gxm.2_RNA|LOC400927_uc011ans.1_RNA|LOC400927_uc011ant.1_RNA|LOC400927_uc003avr.1_RNA	NM_152221	NP_689407	P49674	KC1E_HUMAN	casein kinase 1 epsilon						DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)					TTAAATTCACCTGTGTGTGGG	0.368													11	388	---	---	---	---	PASS
DDX17	10521	broad.mit.edu	37	22	38889717	38889717	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38889717T>C	uc003avy.3	-	10	1488	c.1385A>G	c.(1384-1386)AAT>AGT	p.N462S	DDX17_uc003avx.3_Missense_Mutation_p.N462S|DDX17_uc011anu.1_Missense_Mutation_p.N375S	NM_001098504	NP_001091974	Q92841	DDX17_HUMAN	DEAD box polypeptide 17 isoform 3	383	Helicase C-terminal.				RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)					AAACTTACCATTAAGTACCCA	0.318													56	169	---	---	---	---	PASS
PPARA	5465	broad.mit.edu	37	22	46627961	46627961	+	Silent	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46627961C>T	uc003bgw.1	+	8	1250	c.984C>T	c.(982-984)GAC>GAT	p.D328D	PPARA_uc003bgx.1_Silent_p.D328D|PPARA_uc010hab.1_Silent_p.D328D|PPARA_uc003bhb.1_Silent_p.D328D|PPARA_uc010hac.1_Silent_p.D125D	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,	328	Ligand-binding.|Required for heterodimerization with RXRA.				fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	TGAACAAAGACGGGATGCTGG	0.428													5	201	---	---	---	---	PASS
VCX3A	51481	broad.mit.edu	37	X	6451688	6451688	+	3'UTR	SNP	T	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6451688T>A	uc004crs.2	-	3						NM_016379	NP_057463	Q9NNX9	VCX3_HUMAN	variable charge, X-linked 3A						brain development	nucleolus					0						TTTTATTATCTTCAGAATGGC	0.403													10	102	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													6	136	---	---	---	---	PASS
TCEAL5	340543	broad.mit.edu	37	X	102529084	102529084	+	Silent	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102529084T>C	uc004ejz.1	-	3	703	c.408A>G	c.(406-408)CAA>CAG	p.Q136Q		NM_001012979	NP_001012997	Q5H9L2	TCAL5_HUMAN	transcription elongation factor A (SII)-like 5	136					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(1)|breast(1)	2						GATGCCTTTCTTGTAAGTCCT	0.498													8	446	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130218268	130218268	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130218268C>T	uc004evz.2	+	5	980	c.635C>T	c.(634-636)TCC>TTC	p.S212F	ARHGAP36_uc004ewa.2_Missense_Mutation_p.S200F|ARHGAP36_uc004ewb.2_Missense_Mutation_p.S181F|ARHGAP36_uc004ewc.2_Missense_Mutation_p.S76F	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	212					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						TCAAAAATTTCCTTTCCAATT	0.498													30	52	---	---	---	---	PASS
SPANXE	171489	broad.mit.edu	37	X	140785588	140785588	+	3'UTR	SNP	G	T	T	rs610102	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140785588G>T	uc004fbq.2	-	2						NM_145665	NP_663698	Q8TAD1	SPNXE_HUMAN	SPANX family, member E							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)					AAACTTTATTGTCATTGCCCA	0.458													13	329	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2339	2339	+	5'Flank	SNP	G	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2339G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TCCTCCGCATAAGCCTGCGTC	0.393													27	92	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14469	14469	+	RNA	SNP	A	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14469A>G	uc004cox.3	+	1		c.2133A>G			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CGCTGTAGTATATCCAAAGAC	0.438													21	85	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15840	15840	+	3'UTR	SNP	T	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15840T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		AATCCTAATCCTAATACCAAC	0.403													5	104	---	---	---	---	PASS
HNRNPCL1	343069	broad.mit.edu	37	1	12908384	12908385	+	Intron	INS	-	A	A	rs143606605		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12908384_12908385insA	uc010obf.1	-						LOC649330_uc009vno.2_5'Flank	NM_001013631	NP_001013653	O60812	HNRCL_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleotide binding				0						ATTGCATTTAGAAAAAAAATCA	0.356													6	4	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18631675	18631676	+	Intron	INS	-	GGAT	GGAT	rs150585628	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18631675_18631676insGGAT	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		GATAGGGAAGGggatggatgga	0.243													3	4	---	---	---	---	
C1orf94	84970	broad.mit.edu	37	1	34684572	34684577	+	3'UTR	DEL	ACACAT	-	-	rs3831264	byFrequency	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34684572_34684577delACACAT	uc001bxs.3	+	7					C1orf94_uc001bxt.2_3'UTR	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b								protein binding				0		Myeloproliferative disorder(586;0.0393)				ACACACACACACACATGACCCTCATA	0.374													2	7	---	---	---	---	
HPCAL4	51440	broad.mit.edu	37	1	40154352	40154352	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40154352delC	uc001cdr.2	-						HPCAL4_uc010oix.1_Intron	NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	hippocalcin-like protein 4						central nervous system development	intracellular	calcium ion binding			central_nervous_system(1)	1	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-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;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TCTCAAAGTGCCCACCTATCT	0.512													4	2	---	---	---	---	
PPT1	5538	broad.mit.edu	37	1	40541150	40541150	+	Intron	DEL	T	-	-	rs33944754		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40541150delT	uc001cfb.2	-						PPT1_uc010ojf.1_Intron|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTCTCAAGCCTTTTTTTTTTT	0.423													4	2	---	---	---	---	
ST3GAL3	6487	broad.mit.edu	37	1	44338823	44338823	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44338823delA	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				agactgttgcaaggcagtccg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59096307	59096308	+	IGR	DEL	AC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59096307_59096308delAC								TACSTD2 (53141 upstream) : MYSM1 (29282 downstream)																							tttttCCCTTACACTTTAAAAA	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	85367968	85367968	+	IGR	DEL	A	-	-	rs148433627		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85367968delA								LPAR3 (9072 upstream) : MCOLN2 (23299 downstream)																							attttaaagtaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85981278	85981279	+	Intron	DEL	AC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85981278_85981279delAC	uc001dlc.2	-							NM_001134445	NP_001127917	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)	TATCCAAAGTACCAGTCAAGAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	92022527	92022527	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92022527delG								CDC7 (31207 upstream) : HSP90B3P (78041 downstream)																							ggaaaggctagggtgcataga	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	92082749	92082749	+	IGR	DEL	G	-	-	rs79120152	byFrequency	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92082749delG								CDC7 (91429 upstream) : HSP90B3P (17819 downstream)																							TATCAAAGATGGGGGAAGGAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96088688	96088688	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96088688delT								RWDD3 (375915 upstream) : None (None downstream)																							gataatgccatttccccttct	0.000													4	2	---	---	---	---	
KCNA3	3738	broad.mit.edu	37	1	111218330	111218331	+	5'Flank	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111218330_111218331insT	uc001dzv.1	-							NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(4)|pancreas(1)	5		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAAGTTTCTGATTGGGATTAGC	0.485													4	2	---	---	---	---	
OVGP1	5016	broad.mit.edu	37	1	111970551	111970552	+	5'Flank	INS	-	CC	CC			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111970551_111970552insCC	uc001eba.2	-						OVGP1_uc001eaz.2_5'Flank|OVGP1_uc010owb.1_5'Flank|OVGP1_uc010owc.1_5'Flank	NM_002557	NP_002548	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1 precursor						chitin catabolic process|female pregnancy|single fertilization	transport vesicle	cation binding|chitinase activity			ovary(4)|large_intestine(1)	5		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TCCCTCTCCAACAAAGCAACAG	0.436													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142956513	142956514	+	Intron	DEL	CT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142956513_142956514delCT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		ttagaacttactgtgttccagg	0.089													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144010637	144010637	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144010637delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		ACAGAGCCTCTTTTTTTTCCT	0.448													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145030486	145030486	+	Intron	DEL	T	-	-	rs66508015		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145030486delT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						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)		TGCGTATTTCTTTTTTTTTTC	0.338			T	PDGFRB	MPD								3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145057178	145057179	+	Intron	INS	-	AGA	AGA	rs3978504		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145057178_145057179insAGA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						CACTATTAAGCAGAACACTTTA	0.262													5	3	---	---	---	---	
USF1	7391	broad.mit.edu	37	1	161011737	161011738	+	Intron	DEL	GA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161011737_161011738delGA	uc001fxi.2	-						F11R_uc010pjw.1_5'Flank|F11R_uc001fxf.3_5'Flank|TSTD1_uc010pjx.1_5'Flank|TSTD1_uc009wtw.2_5'Flank|TSTD1_uc001fxh.3_5'Flank|USF1_uc001fxj.2_Intron	NM_007122	NP_009053	P22415	USF1_HUMAN	upstream stimulatory factor 1 isoform 1						cellular response to insulin stimulus|glucose homeostasis|late viral mRNA transcription|lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter by glucose|response to hypoxia|response to UV	transcription factor complex	bHLH transcription factor binding|histone deacetylase binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			AGGTAGGGTGgagagagagaga	0.446													8	5	---	---	---	---	
C1orf125	126859	broad.mit.edu	37	1	179335930	179335932	+	Intron	DEL	CTC	-	-	rs150638150		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179335930_179335932delCTC	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1												0						TGTTTCACTACTCCATCTAAATA	0.271													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214729774	214729774	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214729774delT								PTPN14 (5132 upstream) : CENPF (46758 downstream)																							TAAATCCTTCTTTTTTCACGT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	224222631	224222632	+	IGR	INS	-	TAAAA	TAAAA	rs112536691		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224222631_224222632insTAAAA								TP53BP2 (188957 upstream) : FBXO28 (79159 downstream)																							TAATCAACAAGTAAAATTAATG	0.287													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230532305	230532306	+	IGR	INS	-	C	C	rs147949837	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230532305_230532306insC								PGBD5 (18938 upstream) : COG2 (245896 downstream)																							ACATTTTGTTGCCCCCCCTCCC	0.520													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232438261	232438261	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232438261delA								DISC1 (261245 upstream) : SIPA1L2 (95453 downstream)																							CAGAAAGCTGAAAAAAACATG	0.473													4	2	---	---	---	---	
LYST	1130	broad.mit.edu	37	1	235891638	235891638	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235891638delA	uc001hxj.2	-						LYST_uc001hxi.2_Intron	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			tttctttattaaaaaaaaagg	0.075									Chediak-Higashi_syndrome				4	2	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241838178	241838179	+	Intron	INS	-	CC	CC			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241838178_241838179insCC	uc001hze.1	+									B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			cctcctttctttctttccttct	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244451558	244451558	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244451558delG								ZNF238 (230782 upstream) : C1orf100 (64379 downstream)																							TCCTTCCTTTGGGGGCCCCCA	0.308													4	2	---	---	---	---	
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198	Q5EBM0	CMPK2_HUMAN	UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					Tacacacacacgcacacacaca	0.198													22	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8167591	8167592	+	Intron	DEL	TC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8167591_8167592delTC	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																		gcactctcattctctctctctc	0.000													6	3	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11340846	11340846	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11340846delA	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		GTTTAAAAAGAAAAAAAAAAA	0.343													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23306094	23306095	+	IGR	DEL	TG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23306094_23306095delTG								None (None upstream) : KLHL29 (449360 downstream)																							ttttgtgtgttgtttgtctttc	0.000													4	2	---	---	---	---	
WDR43	23160	broad.mit.edu	37	2	29165470	29165470	+	Intron	DEL	T	-	-	rs67816126		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29165470delT	uc002rmo.2	+							NM_015131	NP_055946	Q15061	WDR43_HUMAN	WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					TTATGGAAGATtttttttttc	0.169													4	3	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845581	71845582	+	Intron	INS	-	G	G	rs150257500		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845581_71845582insG	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						gtggtagaggtggggttgtgtg	0.000													4	2	---	---	---	---	
TET3	200424	broad.mit.edu	37	2	74273383	74273384	+	5'Flank	INS	-	C	C	rs144991998	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74273383_74273384insC	uc002skb.3	+						TET3_uc010fez.1_5'Flank	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						TTTTCCTTTTTCCCCCTTCTCT	0.485													14	7	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87105478	87105482	+	Intron	DEL	TAATT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87105478_87105482delTAATT	uc002srs.3	+						uc010fgu.1_Intron			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						TTTATTACTCTAATTTATTTTTTCT	0.229													8	5	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87414089	87414090	+	Intron	INS	-	T	T	rs3834719		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87414089_87414090insT	uc002srs.3	+						uc002ssh.2_Intron			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						TTGGGACttaattttttttttt	0.322													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91738347	91738348	+	IGR	INS	-	TCA	TCA			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738347_91738348insTCA								None (None upstream) : LOC654342 (66844 downstream)																							ttcatttcatctcattttatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96610787	96610788	+	5'Flank	INS	-	A	A	rs148448972	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96610787_96610788insA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		actctgtctacaaaaaataaga	0.104													85	84	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97827994	97827995	+	Intron	INS	-	TAA	TAA			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97827994_97827995insTAA	uc010yva.1	+						ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron|ANKRD36_uc002sxq.1_5'Flank	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						TTTCTATGCTTTAATATAATTT	0.178													18	10	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97833083	97833083	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97833083delT	uc010yva.1	+						ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron|ANKRD36_uc002sxq.1_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						TCTTGGGTGATTTTCTTCAGG	0.333													6	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107743686	107743686	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107743686delA								ST6GAL2 (240123 upstream) : LOC729121 (695834 downstream)																							ATACTAGTCTAAAAATGGTTC	0.343													4	2	---	---	---	---	
LOC541471	541471	broad.mit.edu	37	2	112048278	112048278	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112048278delT	uc002the.2	-											Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0						TCTACAGATGTTTTAAAAAAA	0.443													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133711226	133711227	+	Intron	DEL	AG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133711226_133711227delAG	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						acaggcagacagagagagagag	0.198													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151493670	151493670	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151493670delA								RND3 (149490 upstream) : RBM43 (611059 downstream)																							GCATAGGAGGAGGAGAAGGGT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	152050946	152050946	+	IGR	DEL	C	-	-	rs35591602		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152050946delC								RND3 (706766 upstream) : RBM43 (53783 downstream)																							GGATAGGAAACATTTTTAAAT	0.284													4	3	---	---	---	---	
GPD2	2820	broad.mit.edu	37	2	157366209	157366209	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157366209delG	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron|GPD2_uc002tze.1_5'Flank	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						CTCAAGTAAAGGGGGCATGGG	0.373													4	2	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	160084939	160084940	+	Intron	INS	-	T	T	rs148018670	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160084939_160084940insT	uc002uag.2	+						TANC1_uc010zcm.1_Intron|TANC1_uc010fon.2_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						TACTTCCTACCTTTTTTTTAAC	0.495													2	6	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162879588	162879589	+	Intron	INS	-	CC	CC			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162879588_162879589insCC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	cctctgtcccaccagcctgttc	0.094													1	14	---	---	---	---	
GPR155	151556	broad.mit.edu	37	2	175346896	175346896	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175346896delA	uc002uit.2	-						GPR155_uc002uiu.2_Intron|GPR155_uc002uiv.2_Intron|GPR155_uc010fqs.2_Intron	NM_001033045	NP_001028217	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155 isoform 9						intracellular signal transduction|transmembrane transport	integral to membrane				ovary(1)	1						AATACAATGGAAAAAAAAGTG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176789585	176789585	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176789585delA								ATP5G3 (743095 upstream) : KIAA1715 (825 downstream)																							agcaagagagaggaagcaaag	0.000													4	2	---	---	---	---	
ITGA4	3676	broad.mit.edu	37	2	182346182	182346182	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182346182delG	uc002unu.2	+						ITGA4_uc010zfl.1_Intron	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	GACCAATTTTGAGTATCTCTA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	183675073	183675073	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183675073delA								DNAJC10 (31818 upstream) : FRZB (23664 downstream)																							ACAAGGCTCTACTGATTTCTT	0.383													4	2	---	---	---	---	
ITGAV	3685	broad.mit.edu	37	2	187495217	187495218	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187495217_187495218insT	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		gttgggttgtgatataaattat	0.084													5	7	---	---	---	---	
ITGAV	3685	broad.mit.edu	37	2	187495222	187495224	+	Intron	DEL	AAA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187495222_187495224delAAA	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		gttgtgatataaattataatctt	0.089													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187657397	187657397	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187657397delA								FAM171B (26713 upstream) : ZSWIM2 (34810 downstream)																							GCCCCCACTGAAAAAAAAAAA	0.269													2	4	---	---	---	---	
GLS	2744	broad.mit.edu	37	2	191819800	191819800	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191819800delT	uc002usf.2	+						GLS_uc002ush.2_Intron|GLS_uc010zgi.1_Intron|GLS_uc010zgj.1_Intron	NM_014905	NP_055720	O94925	GLSK_HUMAN	glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	AACAAAACAATTTTTTTTTTG	0.229													4	2	---	---	---	---	
STAT4	6775	broad.mit.edu	37	2	192036854	192036854	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192036854delT	uc010zgm.1	-						STAT4_uc010zgn.1_Intron|STAT4_uc010zgo.1_Intron			Q14765	STAT4_HUMAN	Homo sapiens cDNA FLJ60872 complete cds, moderately similar to Signal transducer and activator of transcription 4.						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			CCAAAATGAATTTTTTTTACT	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	196020269	196020269	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196020269delT								None (None upstream) : SLC39A10 (501263 downstream)																							TCTACCTTAATTTTTTTGGCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200383667	200383667	+	IGR	DEL	T	-	-	rs112555132		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200383667delT								FLJ32063 (42009 upstream) : C2orf69 (392312 downstream)																							tgtcctttgattcggtgcttt	0.104													4	2	---	---	---	---	
C2orf60	129450	broad.mit.edu	37	2	200800443	200800450	+	Intron	DEL	ACACACAC	-	-	rs10603476		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200800443_200800450delACACACAC	uc002uvi.3	-						C2orf60_uc002uvj.3_Intron|C2orf60_uc002uvk.3_Intron|C2orf60_uc010fss.2_Intron	NM_001039693	NP_001034782	A2RUC4	TYW5_HUMAN	hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0						CCTGCTTTAAacacacacacacacacac	0.255													5	3	---	---	---	---	
NDUFS1	4719	broad.mit.edu	37	2	207014339	207014340	+	Intron	INS	-	AC	AC	rs141671378	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207014339_207014340insAC	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	ACAATTATATGACATGTGTTTG	0.292													6	6	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223493835	223493836	+	Intron	INS	-	ATG	ATG			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223493835_223493836insATG	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	ACTTGAAAGGTTTATTTTCCAG	0.426													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231691003	231691003	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231691003delT								CAB39 (5214 upstream) : ITM2C (38618 downstream)																							ttccattacgtttttttttTC	0.080													4	2	---	---	---	---	
USP40	55230	broad.mit.edu	37	2	234438438	234438438	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234438438delT	uc010zmr.1	-						USP40_uc010zmt.1_Intron	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GATTTTCAtcttttttttttc	0.114													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239411708	239411708	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239411708delG								ASB1 (50818 upstream) : TWIST2 (344965 downstream)																							aaaaaaaaaagaaTTCAATGT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	625171	625171	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:625171delG	uc003boy.1	+											Homo sapiens cDNA FLJ44328 fis, clone TRACH3002871.																		TGTCTTCTATGGTTACTTGTG	0.338													4	2	---	---	---	---	
CAND2	23066	broad.mit.edu	37	3	12849031	12849032	+	Intron	INS	-	A	A	rs116352565		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12849031_12849032insA	uc003bxk.2	+						CAND2_uc003bxj.2_Intron	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	TBP-interacting protein isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4						AACGAAAAAacaaaaaaaaaac	0.233													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	19066790	19066790	+	IGR	DEL	A	-	-	rs72354182		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19066790delA								SATB1 (586538 upstream) : KCNH8 (123227 downstream)																							caaatagaacaaaaaaaaaat	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	28878190	28878191	+	IGR	DEL	TG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28878190_28878191delTG								ZCWPW2 (311560 upstream) : RBMS3 (444752 downstream)																							GATGAGGAACTGTGTGTGTGTG	0.470													4	2	---	---	---	---	
XYLB	9942	broad.mit.edu	37	3	38404189	38404190	+	Intron	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38404189_38404190insC	uc003cic.2	+						XYLB_uc011ayp.1_Intron|XYLB_uc003cid.1_Intron	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase						D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		TTTGAGGATTGGTGGTTTATGA	0.168													3	4	---	---	---	---	
LIMD1	8994	broad.mit.edu	37	3	45677635	45677636	+	Intron	INS	-	T	T	rs5848761		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45677635_45677636insT	uc003coq.2	+							NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		TTCTCTTGTCCTGCAAGGAGCC	0.520													72	39	---	---	---	---	
LIMD1	8994	broad.mit.edu	37	3	45677639	45677639	+	Intron	DEL	A	-	-	rs5848762		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45677639delA	uc003coq.2	+							NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		CTTGTCCTGCAAGGAGCCTGT	0.517													68	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46695643	46695643	+	IGR	DEL	C	-	-	rs71622505		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46695643delC								TDGF1 (71693 upstream) : ALS2CL (15036 downstream)																							cgtctcaaaacaacaacaaca	0.000													6	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46695645	46695649	+	IGR	DEL	ACAAC	-	-	rs74600368	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46695645_46695649delACAAC								TDGF1 (71695 upstream) : ALS2CL (15030 downstream)																							tctcaaaacaacaacaacaacaaca	0.000													13	6	---	---	---	---	
BAP1	8314	broad.mit.edu	37	3	52440095	52440095	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52440095delC	uc003ddx.2	-						BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1						monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TATTCTCCCTCCCCACTCCAA	0.468			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	61682396	61682396	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61682396delT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		GAGCCCTAGCTTTTTTCAATG	0.458													4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	61728834	61728834	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61728834delT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TATTTTTATCTTTTTTTGCTT	0.488													4	2	---	---	---	---	
PDZRN3	23024	broad.mit.edu	37	3	73657497	73657497	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73657497delA	uc003dpl.1	-							NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		ACCCCCTAACAAAAAAAGAAA	0.423													4	3	---	---	---	---	
CNTN3	5067	broad.mit.edu	37	3	74352195	74352195	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74352195delG	uc003dpm.1	-							NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		GCTTCCTCCTGGGCATTTATG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75995478	75995485	+	IGR	DEL	AGTCAATA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75995478_75995485delAGTCAATA								ZNF717 (160808 upstream) : None (None downstream)																							ATATACATGTAGtcaataagtcaataaa	0.173													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97836266	97836266	+	IGR	DEL	T	-	-	rs63225260		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97836266delT								OR5AC2 (29322 upstream) : OR5H1 (15276 downstream)																							cgctggctccttttttttttt	0.000													5	3	---	---	---	---	
EAF2	55840	broad.mit.edu	37	3	121563040	121563041	+	Intron	INS	-	G	G	rs149030840	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121563040_121563041insG	uc003een.2	+						EAF2_uc003eeo.2_Intron	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)		aggttcatcttgtctaaacagg	0.099													3	5	---	---	---	---	
SEC22A	26984	broad.mit.edu	37	3	122965632	122965633	+	Intron	INS	-	T	T	rs63124060		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122965632_122965633insT	uc003ege.2	+						SEC22A_uc003egf.2_Intron	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)		aatcagtcctctttttttggtc	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	130507855	130507855	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130507855delA								PIK3R4 (42159 upstream) : ATP2C1 (61590 downstream)																							TTGAGGATATAAAACACATTT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150509577	150509577	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150509577delT								SIAH2 (28314 upstream) : CLRN1OS (60694 downstream)																							cacattacactccaggtagcc	0.045													4	2	---	---	---	---	
C3orf55	152078	broad.mit.edu	37	3	157290029	157290029	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157290029delT	uc003fbp.3	+						C3orf55_uc003fbo.2_Intron|C3orf55_uc011bot.1_Intron|C3orf55_uc010hvv.2_Intron	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)			TGTTATTACCTTTTTTTTTAA	0.308													4	5	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171520314	171520314	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171520314delT	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	aatagcatgattaaaaggccc	0.040													3	3	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175345369	175345376	+	Intron	DEL	TGTCTGTA	-	-	rs63431360		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175345369_175345376delTGTCTGTA	uc003fit.2	+						NAALADL2_uc010hwy.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		GACCCATAACTGTCTGTATGATCATTTG	0.173													3	3	---	---	---	---	
ABCC5	10057	broad.mit.edu	37	3	183668075	183668075	+	Intron	DEL	T	-	-	rs4148588		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183668075delT	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GATGCTCTGATTTTTTTTTTT	0.358													4	2	---	---	---	---	
HTR3D	200909	broad.mit.edu	37	3	183756836	183756837	+	3'UTR	INS	-	T	T	rs143758271	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183756836_183756837insT	uc011bqv.1	+	8					HTR3D_uc003fmj.2_3'UTR|HTR3D_uc011bqu.1_3'UTR|HTR3D_uc010hxp.2_3'UTR	NM_001163646	NP_001157118	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine receptor 3 subunit D isoform							integral to membrane|plasma membrane	extracellular ligand-gated ion channel activity|receptor activity				0	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TCAGGCTCTCAGTCAGCCTTGT	0.515													27	15	---	---	---	---	
EHHADH	1962	broad.mit.edu	37	3	184966491	184966492	+	Intron	DEL	AT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184966491_184966492delAT	uc003fpf.2	-						EHHADH_uc011brs.1_Intron	NM_001966	NP_001957	Q08426	ECHP_HUMAN	enoyl-Coenzyme A, hydratase/3-hydroxyacyl							peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)	TCTACAAATAATATATATGCCT	0.272													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187406044	187406044	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187406044delC								SST (17843 upstream) : RTP2 (10003 downstream)																							TGCACCAGGTCCCCACACTCA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	192805184	192805184	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192805184delT								C3orf59 (169234 upstream) : HRASLS (153734 downstream)																							GTTACAGTGATTTTTTTTTTG	0.348													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195518112	195518113	+	In_Frame_Ins	INS	-	GTCTCCTGCGTAACA	GTCTCCTGCGTAACA	rs142781032	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195518112_195518113insGTCTCCTGCGTAACA	uc011bto.1	-	2	798_799	c.338_339insTGTTACGCAGGAGAC	c.(337-339)ACA>ACTGTTACGCAGGAGACA	p.113_113T>TVTQET	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_5'UTR	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	113					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGGAGGAGCTGTCTCCATCAC	0.465													311	137	---	---	---	---	
SH3TC1	54436	broad.mit.edu	37	4	8242814	8242814	+	3'UTR	DEL	T	-	-	rs67520179		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8242814delT	uc003gkv.3	+	18					SH3TC1_uc003gkw.3_3'UTR|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_RNA	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3						ATGGGTTTTGTTTTTTTTTTG	0.552													2	4	---	---	---	---	
CPZ	8532	broad.mit.edu	37	4	8614091	8614093	+	Intron	DEL	GGA	-	-	rs33936982		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8614091_8614093delGGA	uc003glm.2	+						CPZ_uc003gll.2_Intron|CPZ_uc003gln.2_Intron|CPZ_uc003glo.2_Intron|CPZ_uc003glp.2_Intron	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1						proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						TGACTGTTGTGGAGGACCCAGGC	0.498													4	2	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	15987514	15987515	+	Intron	INS	-	GT	GT	rs55689632		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15987514_15987515insGT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						AAACATTATAAATATTTAATCT	0.312													111	62	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	15987515	15987516	+	Intron	INS	-	TGCT	TGCT	rs55689632		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15987515_15987516insTGCT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						AACATTATAAATATTTAATCTG	0.317													110	63	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18087507	18087507	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18087507delA								LCORL (64122 upstream) : None (None downstream)																							ACGGTAAAGGAAAAAAAAAAG	0.194													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	20660998	20660998	+	IGR	DEL	A	-	-	rs67653056		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20660998delA								SLIT2 (40210 upstream) : PACRGL (36907 downstream)																							taataataataaaaaaaaaaa	0.214													3	3	---	---	---	---	
ARAP2	116984	broad.mit.edu	37	4	36120323	36120323	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36120323delA	uc003gsq.1	-							NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						CCCCGCTCCCAAAAAAAGTGA	0.348													4	2	---	---	---	---	
APBB2	323	broad.mit.edu	37	4	40895623	40895623	+	Intron	DEL	A	-	-	rs10714456		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40895623delA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc011byt.1_Intron	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						tttgctatttaaaaaaatgta	0.060													2	4	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47288610	47288610	+	Intron	DEL	A	-	-	rs35730377		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47288610delA	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	AAAAGACAAGAAAAAAATAAA	0.348													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49107744	49107744	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49107744delC								CWH43 (43651 upstream) : None (None downstream)																							ttccattccacccggattgat	0.000													5	3	---	---	---	---	
TMEM165	55858	broad.mit.edu	37	4	56290930	56290940	+	Intron	DEL	CCATCTCTTAT	-	-	rs138731419	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56290930_56290940delCCATCTCTTAT	uc003hax.2	+						TMEM165_uc011bzy.1_Intron	NM_018475	NP_060945	Q9HC07	TM165_HUMAN	transmembrane protein 165							integral to membrane					0	Lung NSC(11;0.00545)|Glioma(25;0.08)|all_neural(26;0.101)|all_epithelial(27;0.135)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0103)			TAATTACCTACCATCTCTTATAGAGGTATTA	0.251													20	12	---	---	---	---	
RUFY3	22902	broad.mit.edu	37	4	71656817	71656825	+	Intron	DEL	AGAAAGAGA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71656817_71656825delAGAAAGAGA	uc003hfq.2	+						RUFY3_uc011cax.1_Intron|RUFY3_uc003hfr.2_Intron|RUFY3_uc011cay.1_Intron	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			TAAAGCAAACAGAAAGAGAATAATGACTT	0.278													13	6	---	---	---	---	
DCK	1633	broad.mit.edu	37	4	71895356	71895357	+	3'UTR	INS	-	CT	CT			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71895356_71895357insCT	uc003hfx.2	+	7					DCK_uc011cbb.1_3'UTR	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	tggttccagtatcagcatagtg	0.109													3	3	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77459417	77459417	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77459417delA	uc011cbx.1	+							NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			aagctgttggaaaaAaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90259809	90259809	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90259809delT								GPRIN3 (30648 upstream) : SNCA (385442 downstream)																							CCACAGTAGCTTTTTTTGTGT	0.408													4	2	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	93566819	93566819	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93566819delC	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	ctgctcactacccccatgagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117893016	117893017	+	IGR	DEL	AC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117893016_117893017delAC								MIR1973 (672092 upstream) : TRAM1L1 (111699 downstream)																							CTTCATGcatacacacacacac	0.312													4	2	---	---	---	---	
SLC7A11	23657	broad.mit.edu	37	4	139140176	139140176	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139140176delT	uc011chb.1	-							NM_014331	NP_055146	Q9UPY5	XCT_HUMAN	solute carrier family 7, (cationic amino acid						blood coagulation|cellular nitrogen compound metabolic process|leukocyte migration|response to toxin	integral to membrane|plasma membrane	cystine:glutamate antiporter activity|protein binding			skin(1)	1	all_hematologic(180;0.166)				L-Cystine(DB00138)|L-Glutamic Acid(DB00142)|Sulfasalazine(DB00795)	CATTTGTTTGTTTTTTATGAC	0.363													3	4	---	---	---	---	
TTC29	83894	broad.mit.edu	37	4	147691583	147691584	+	Intron	INS	-	T	T	rs5862769		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147691583_147691584insT	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)					AACGTTTTCACTTTTTTTTTTT	0.257													3	5	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148668318	148668318	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148668318delC	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTTTTTTTTTCCCCCAAAGTA	0.423													4	2	---	---	---	---	
FNIP2	57600	broad.mit.edu	37	4	159814631	159814636	+	Intron	DEL	CAATAA	-	-	rs77228157	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159814631_159814636delCAATAA	uc003iqe.3	+							NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		GTATGATAGTCAATAACAATTAGTTT	0.189													20	9	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183565284	183565284	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183565284delG	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		CTGGGTGCTCGGGTCTGTGTT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185422998	185423000	+	IGR	DEL	TTC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185422998_185423000delTTC								IRF2 (27272 upstream) : CASP3 (125852 downstream)																							cccaagacaattcttcttcttcc	0.138													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190553492	190553492	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190553492delT								None (None upstream) : FRG1 (308482 downstream)																							TCTCCCTACATTTTTTAATAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5703662	5703662	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5703662delT								KIAA0947 (213325 upstream) : FLJ33360 (606892 downstream)																							CTTAGTTGTATCCAGTTGGAA	0.368													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10397692	10397692	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10397692delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CATTTCTGGGTTTTTTTTTTG	0.418													5	3	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16818442	16818443	+	Intron	DEL	TC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16818442_16818443delTC	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ATGTCACCTATCTCTCTCTCTC	0.193													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32574069	32574069	+	IGR	DEL	A	-	-	rs78357220		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32574069delA								ZFR (129225 upstream) : SUB1 (11536 downstream)																							GCAAAACattaaaaaaaaatt	0.189													4	2	---	---	---	---	
PRLR	5618	broad.mit.edu	37	5	35195102	35195102	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35195102delA	uc003jjm.2	-							NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	tctgtgggggaaaacgggtat	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	38648760	38648760	+	Intron	DEL	A	-	-	rs67604856		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38648760delA	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																		gtctcaaaagaaaaaaaaaag	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56817843	56817843	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56817843delG								ACTBL2 (39207 upstream) : PLK2 (931969 downstream)																							tgataagggagggccatgggg	0.000													4	2	---	---	---	---	
RAB3C	115827	broad.mit.edu	37	5	58008952	58008952	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58008952delT	uc003jrp.2	+							NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		ACATAGACTGTTTTTGAACAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	64397106	64397107	+	IGR	INS	-	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64397106_64397107insG								CWC27 (82516 upstream) : ADAMTS6 (47457 downstream)																							GACTTGCACCAGGGGGCAGAGT	0.559											OREG0016633	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	5	70623216	70623216	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70623216delC								NAIP (215353 upstream) : PMCHL2 (48396 downstream)																							GGTTTGGCTTCCCCCCCAAAA	0.259													6	3	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80742368	80742369	+	Intron	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80742368_80742369insC	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTTATTCAGAAATTTTCTAAAT	0.277													3	3	---	---	---	---	
POLR3G	10622	broad.mit.edu	37	5	89797503	89797503	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89797503delA	uc003kjq.2	+						POLR3G_uc011cuc.1_Intron	NM_006467	NP_006458	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)		CTTCAGTCTTAAAAAAAAAAA	0.289													3	5	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102285571	102285571	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102285571delT	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	TAATACCTTATTATATTAAAT	0.323													53	56	---	---	---	---	
PDE6A	5145	broad.mit.edu	37	5	149310918	149310918	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149310918delT	uc003lrg.3	-							NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A						cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			aagtttttaattttttttttt	0.249													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166982514	166982514	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166982514delT	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		ACTGTACGGCTTTTTGTACAA	0.398													4	2	---	---	---	---	
GNB2L1	10399	broad.mit.edu	37	5	180665900	180665900	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180665900delT	uc003mni.1	-						GNB2L1_uc003mnh.1_Intron|GNB2L1_uc003mnk.1_Intron|GNB2L1_uc003mnj.1_Intron|GNB2L1_uc003mnl.1_Intron|GNB2L1_uc011dhk.1_3'UTR	NM_006098	NP_006089	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein),						apoptosis|cell cycle|gastrulation|interspecies interaction between organisms|negative regulation of cell growth|negative regulation of phagocytosis|negative regulation of translation|negative regulation of Wnt receptor signaling pathway|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of gastrulation|positive regulation of GTPase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein homooligomerization|positive regulation of protein phosphorylation|regulation of cell cycle|regulation of cell division|regulation of establishment of cell polarity|regulation of protein localization|rhythmic process	cytoskeleton|dendrite|midbody|nucleus|perikaryon|perinuclear region of cytoplasm|phagocytic cup|small ribosomal subunit	ion channel inhibitor activity|protein kinase C binding|protein phosphatase binding|protein tyrosine kinase inhibitor activity|receptor tyrosine kinase binding|SH2 domain binding				0	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		TTAACTGTCATTTGCTGAAAG	0.274													14	9	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3380193	3380194	+	Intron	DEL	GT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3380193_3380194delGT	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc010jno.2_Intron	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				gtgtggatgcgtgtgtgtgtgt	0.327													5	3	---	---	---	---	
FAM8A1	51439	broad.mit.edu	37	6	17602638	17602638	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17602638delG	uc003ncc.2	+							NM_016255	NP_057339	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1							integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			TGGATTCTCTGTTACTCTATT	0.254													9	8	---	---	---	---	
ZSCAN16	80345	broad.mit.edu	37	6	28096341	28096341	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28096341delT	uc003nkm.2	+						uc010jqw.1_Intron|uc003nkk.1_Intron|uc003nkl.1_Intron	NM_025231	NP_079507	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)	1						GGGGGTGACATTTTAGGCAAA	0.428													4	2	---	---	---	---	
CSNK2B	1460	broad.mit.edu	37	6	31635959	31635961	+	Intron	DEL	TAT	-	-	rs146750326	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31635959_31635961delTAT	uc003nvr.1	+						BAT4_uc003nvn.2_5'Flank|BAT4_uc003nvo.3_5'Flank|BAT4_uc003nvp.3_5'Flank|BAT4_uc003nvq.2_5'Flank|CSNK2B_uc010jta.1_3'UTR|CSNK2B_uc003nvs.1_Intron|LY6G5B_uc003nvt.1_5'Flank	NM_001320	NP_001311	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide						adiponectin-mediated signaling pathway|axon guidance|cellular protein complex assembly|negative regulation of cell proliferation|regulation of DNA binding|Wnt receptor signaling pathway	cytosol|nucleus|protein kinase CK2 complex	identical protein binding|protein domain specific binding|protein kinase regulator activity|receptor binding|transcription factor binding				0						AATTCAGACCTATTCCAAAATGC	0.404													11	6	---	---	---	---	
MAPK14	1432	broad.mit.edu	37	6	36034813	36034814	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36034813_36034814insT	uc003olp.2	+						MAPK14_uc011dth.1_Intron|MAPK14_uc003olo.2_Intron|MAPK14_uc003olq.2_Intron|MAPK14_uc003olr.2_Intron|MAPK14_uc011dti.1_Intron	NM_001315	NP_001306	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14 isoform 1						activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|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 activity|MAP kinase kinase activity|protein binding			ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	6						TATGTTTACAATTTTTTTTTTA	0.342													4	4	---	---	---	---	
HMGCLL1	54511	broad.mit.edu	37	6	55442034	55442042	+	Intron	DEL	ATAGAAAAA	-	-	rs59821254		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55442034_55442042delATAGAAAAA	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron|HMGCLL1_uc003pcp.2_Intron	NM_019036	NP_061909	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			ttacgataagATAGAAAAAATCACAATTC	0.177													27	20	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57386124	57386124	+	Intron	DEL	A	-	-	rs11347363		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57386124delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTAGCTGGAGAAAAAAAACCC	0.363													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57512788	57512789	+	Splice_Site	INS	-	TA	TA	rs79832250		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57512788_57512789insTA	uc003pdx.2	+	15	1702	c.1615_splice	c.e15+1			NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tgcactctgttgtgtaattgtg	0.129													15	13	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57512794	57512796	+	Splice_Site	DEL	ATT	-	-	rs78697028		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57512794_57512796delATT	uc003pdx.2	+	16	1720	c.1633_splice	c.e16-1			NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ctgttgtgtaattgtgacacaat	0.118													12	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57542931	57542931	+	IGR	DEL	G	-	-	rs112793267		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57542931delG								PRIM2 (29556 upstream) : GUSBL2 (703228 downstream)																							agacctgtaagataataaatg	0.040													7	5	---	---	---	---	
DDX43	55510	broad.mit.edu	37	6	74115935	74115936	+	Intron	INS	-	GG	GG	rs143908408	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74115935_74115936insGG	uc003pgw.2	+						DDX43_uc011dyn.1_Intron	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43							intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						ttagtagagacggtttctctat	0.000													9	11	---	---	---	---	
DSE	29940	broad.mit.edu	37	6	116579587	116579588	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116579587_116579588insT	uc011ebf.1	+									Q9UL01	DSE_HUMAN	Homo sapiens squamous cell carcinoma antigen recognized by T cell (SART-2) mRNA, complete cds.						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		CTTAGTTGTAATTTTTTTGCTT	0.366													5	3	---	---	---	---	
ENPP3	5169	broad.mit.edu	37	6	132066293	132066293	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132066293delA	uc003qcu.3	+						ENPP3_uc010kfq.2_Intron|ENPP3_uc003qcv.2_Intron	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		aatgttatggaaaaaaaagtg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134121377	134121378	+	Intron	INS	-	CAGGAT	CAGGAT	rs141963897	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134121377_134121378insCAGGAT	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																		gtgaagagaaactaggaccccc	0.000													6	7	---	---	---	---	
MAS1	4142	broad.mit.edu	37	6	160327841	160327841	+	5'Flank	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160327841delT	uc003qsz.2	+							NM_002377	NP_002368	P04201	MAS_HUMAN	MAS1 oncogene						anatomical structure morphogenesis|cell proliferation|protein kinase C signaling cascade	integral to plasma membrane	angiotensin type II receptor activity			ovary(2)|lung(2)	4		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		TCTGTTAAACTTTTTTTTAAT	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165322087	165322088	+	IGR	INS	-	G	G	rs146567609	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165322087_165322088insG								None (None upstream) : C6orf118 (371067 downstream)																							gtaaaagctttggggggaccaa	0.000													4	2	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	167184290	167184290	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167184290delA	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|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|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		TGTTTAACTTAAAAAAAAAAT	0.433													3	5	---	---	---	---	
TCP10	6953	broad.mit.edu	37	6	167789428	167789431	+	Intron	DEL	AGTT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167789428_167789431delAGTT	uc003qvv.1	-						TCP10_uc003qvu.2_Intron|TCP10_uc003qvw.2_3'UTR	NM_004610	NP_004601	Q12799	TCP10_HUMAN	t-complex 10							cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		GCATGGAAACAGTTAGGAGCCCTC	0.569													16	13	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21714476	21714476	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21714476delA	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						ccaactgcagaaaaaaaaaag	0.000									Kartagener_syndrome				4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	32463330	32463333	+	IGR	DEL	AACC	-	-	rs5883353		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32463330_32463333delAACC								PDE1C (124389 upstream) : LSM5 (61612 downstream)																							CGTAGATGGAAACCAAGAAGCAAT	0.348													3	6	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32623219	32623219	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32623219delA	uc003tcv.1	+						AVL9_uc011kai.1_Intron|uc003tcw.2_Intron|AVL9_uc010kwj.1_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						tgagcctaggatgtcaaggct	0.005													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34118338	34118338	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34118338delT	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						AAACGACCACTTTTTTTTTTA	0.383													6	3	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48278659	48278659	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48278659delT	uc003toq.2	+						ABCA13_uc010kyr.2_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						AAAATATAACTTTTTTTTTTT	0.343													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	50219487	50219487	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50219487delG								C7orf72 (20129 upstream) : IKZF1 (124891 downstream)																							AGACCCCAAAGGCAAAGAAAA	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57696574	57696579	+	5'Flank	DEL	GGGGGT	-	-	rs150717737	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57696574_57696579delGGGGGT	uc003tso.1	+											Homo sapiens macronuclear mRNA.																		tgagaatggcgggggtgagaatggcg	0.029													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61804274	61804274	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61804274delC								None (None upstream) : LOC643955 (947398 downstream)																							TAAATACTATCATTTTTCACT	0.284													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65976420	65976420	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65976420delA								NCRNA00174 (111025 upstream) : LOC493754 (17026 downstream)																							catctcgaacaaaaaaaaaaa	0.244													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66874270	66874270	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66874270delT								STAG3L4 (87758 upstream) : None (None downstream)																							AAACCTTACCTTTTTTTTTTC	0.423													3	6	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69483196	69483196	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69483196delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TGTAGGACTCTTTTTTTTTTA	0.303													4	2	---	---	---	---	
STYXL1	51657	broad.mit.edu	37	7	75650263	75650264	+	Intron	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75650263_75650264insA	uc003uej.3	-						STYXL1_uc011kgf.1_Intron|STYXL1_uc011kgg.1_Intron|STYXL1_uc003ueh.2_Intron|STYXL1_uc003uek.3_Intron|STYXL1_uc003uel.2_Intron|STYXL1_uc003uem.2_Intron|STYXL1_uc010ldg.1_Intron|STYXL1_uc010ldh.1_Intron|STYXL1_uc003uen.1_Intron	NM_016086	NP_057170	Q9Y6J8	STYL1_HUMAN	map kinase phosphatase-like protein MK-STYX						intracellular signal transduction|protein dephosphorylation	intracellular	protein binding|protein tyrosine/serine/threonine phosphatase activity				0						gaagggaggggaacaaatgaaa	0.134													4	2	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	91937252	91937253	+	Intron	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91937252_91937253insA	uc003ulw.2	+							NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ctcagcctccccagtagctggg	0.000													4	5	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	91937257	91937257	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91937257delA	uc003ulw.2	+							NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			cctccccagtagctgggacta	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100930709	100930709	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100930709delG								FIS1 (35116 upstream) : RABL5 (25940 downstream)																							ACTCACACTTGGGGGGCTGCC	0.537													4	2	---	---	---	---	
LAMB4	22798	broad.mit.edu	37	7	107749452	107749452	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107749452delT	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8						TTAAAAAGTGTTTTTTTTTTC	0.338													8	4	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116860028	116860028	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116860028delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7_uc011knn.1_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TTAGGATATATTTTTCTCCCT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117655098	117655099	+	IGR	INS	-	TCTGGAGCAC	TCTGGAGCAC	rs140493172		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117655098_117655099insTCTGGAGCAC								CTTNBP2 (141537 upstream) : NAA38 (168987 downstream)																							CCTGGCCAGGGACTCACCCACC	0.480													41	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131644384	131644387	+	IGR	DEL	AAGG	-	-	rs72124207		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131644384_131644387delAAGG								PODXL (403008 upstream) : PLXNA4 (163705 downstream)																							GTCAGGAAACAAGGAGGGAGGAGC	0.544													4	2	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138356664	138356665	+	Intron	INS	-	A	A	rs77651439		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138356664_138356665insA	uc011kqh.1	-							NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						CCAACAGTGGCAGTGGTGAGAC	0.515													23	16	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138356730	138356731	+	Intron	INS	-	G	G	rs5887895		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138356730_138356731insG	uc011kqh.1	-							NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						CGCCCTCAGTTGCTGTGTTCAC	0.550													71	51	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141563611	141563612	+	IGR	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141563611_141563612insA								PRSS37 (22326 upstream) : OR9A4 (55064 downstream)																							CTCTGTCCTGGGGACAATCCTT	0.366													3	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151953413	151953413	+	Intron	DEL	A	-	-	rs111762726		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151953413delA	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)		tttgcatggcaaaaaaaaaat	0.005			N		medulloblastoma								4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151971449	151971450	+	Intron	INS	-	C	C	rs79820593		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151971449_151971450insC	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)		AGACTCACAGAAAAAAACACAA	0.287			N		medulloblastoma								7	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152110157	152110157	+	Intron	DEL	A	-	-	rs11335639		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152110157delA	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)		CACTTCTGAGAAAAAAAACAA	0.254			N		medulloblastoma								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	7778919	7778919	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7778919delT								DEFB4A (24683 upstream) : FAM66E (33616 downstream)																							TGCTTCTGGGttttttttctt	0.333													4	2	---	---	---	---	
RBPMS	11030	broad.mit.edu	37	8	30264872	30264872	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30264872delG	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858	Q93062	RBPMS_HUMAN	RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)		ttttttGGGTGGGGGGGTGCT	0.318													5	4	---	---	---	---	
EFCAB1	79645	broad.mit.edu	37	8	49642082	49642082	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49642082delA	uc003xqo.2	-						EFCAB1_uc003xqn.3_Intron|EFCAB1_uc011ldj.1_Intron|EFCAB1_uc010lxx.2_Intron|EFCAB1_uc011ldk.1_Intron	NM_024593	NP_078869	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1 isoform a								calcium ion binding				0		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)				accctgtctcaaaaaaaaaaa	0.129													6	5	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51286554	51286555	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51286554_51286555insT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				AGCCTACACAATTTTTTTTTAT	0.371													4	2	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69699988	69699989	+	Intron	INS	-	A	A	rs146026747	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69699988_69699989insA	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TAACTTTCTAGAAAAAAAAAGC	0.312													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70236669	70236669	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70236669delT								C8orf34 (505413 upstream) : SULF1 (142190 downstream)																							ATCCAGGGAGTTTTTTTAGTT	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92891717	92891717	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92891717delT								SLC26A7 (481337 upstream) : RUNX1T1 (79435 downstream)																							AAAAAAAAAATTTTTTGACTT	0.333													4	2	---	---	---	---	
CCNE2	9134	broad.mit.edu	37	8	95892737	95892737	+	3'UTR	DEL	T	-	-	rs144325537		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95892737delT	uc003yhc.2	-	12						NM_057749	NP_477097	O96020	CCNE2_HUMAN	cyclin E2						cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	cytosol|nucleoplasm	protein kinase binding				0	Breast(36;8.75e-07)					TGAGGCTGGATTTTTTTTTTA	0.269													4	2	---	---	---	---	
EBAG9	9166	broad.mit.edu	37	8	110573290	110573290	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110573290delT	uc003ynf.2	+						EBAG9_uc003yng.2_Intron	NM_198120	NP_936056	O00559	RCAS1_HUMAN	estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)			TAATAAGGACTTTTTTTTTTG	0.289													13	7	---	---	---	---	
COLEC10	10584	broad.mit.edu	37	8	120114450	120114457	+	Intron	DEL	CCTCCCTC	-	-	rs111495463		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120114450_120114457delCCTCCCTC	uc003yoo.2	+							NM_006438	NP_006429	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 precursor							collagen|cytoplasm	mannose binding			ovary(2)|skin(1)	3	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			TTCACtccttcctccctccctccctccc	0.125													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	121892820	121892820	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121892820delT								SNTB1 (68511 upstream) : HAS2 (732451 downstream)																							ccccatcaggttttttatgca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122397343	122397343	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122397343delT								SNTB1 (573034 upstream) : HAS2 (227928 downstream)																							AACCAAGGTCTTTTTTTTTCT	0.448													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136063342	136063343	+	IGR	DEL	TG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136063342_136063343delTG								MIR30D (246154 upstream) : LOC286094 (183031 downstream)																							TATGTGTGTATGTGTGTGTGTG	0.391													4	2	---	---	---	---	
C9orf46	55848	broad.mit.edu	37	9	5622137	5622137	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5622137delA	uc003zjd.2	-							NM_018465	NP_060935	Q9HBL7	CI046_HUMAN	hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)		ccaacccaataaagtgaatat	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33617692	33617703	+	5'Flank	DEL	GGATGTAACACG	-	-	rs113178723		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33617692_33617703delGGATGTAACACG	uc003ztf.1	+											Homo sapiens patient CS-1 clone 1 T cell receptor beta chain CDR3 (TCRB) mRNA, partial cds.																		GCAGAGAGATGGATGTAACACGGGTCATGAGC	0.349											OREG0019139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	10	---	---	---	---	
DNAI1	27019	broad.mit.edu	37	9	34489849	34489849	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34489849delA	uc003zum.2	+							NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1						cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		actctgtctcaaaaaaaaaaG	0.244									Kartagener_syndrome				5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44097478	44097479	+	IGR	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44097478_44097479insC								FAM75A6 (466748 upstream) : FAM27C (892757 downstream)																							ATATCCAGCTTCCCCTCAAAAA	0.312													25	71	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68430746	68430746	+	IGR	DEL	T	-	-	rs113456947		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430746delT								FAM27B (636557 upstream) : MIR1299 (571493 downstream)																							TTTTACTAGCTTCTTATATCC	0.313													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	77842967	77842968	+	IGR	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77842967_77842968insT								OSTF1 (80854 upstream) : PCSK5 (662592 downstream)																							aataatttctcttttttttcta	0.025													4	2	---	---	---	---	
AGTPBP1	23287	broad.mit.edu	37	9	88284712	88284712	+	Intron	DEL	A	-	-	rs35265103		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88284712delA	uc011ltd.1	-						AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Intron|AGTPBP1_uc011lte.1_Intron	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1						C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						AGTTATATGCAAAAAAAAAAA	0.214													5	3	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113243811	113243817	+	Intron	DEL	CTGTCTA	-	-	rs3841727		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113243811_113243817delCTGTCTA	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						AGGACTCCTCCTGTCTATCGCTATTTC	0.348													5	6	---	---	---	---	
ROD1	9991	broad.mit.edu	37	9	114994286	114994286	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114994286delG	uc004bfw.2	-						ROD1_uc004bfv.2_Intron|ROD1_uc004bfx.2_Intron|ROD1_uc011lwu.1_Intron|ROD1_uc004bfy.2_Intron|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1						gaagagaagagaagagaagag	0.100													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118778493	118778494	+	IGR	INS	-	TC	TC			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118778493_118778494insTC								C9orf27 (91116 upstream) : PAPPA (137577 downstream)																							atttttgccaacatttgctatt	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118778496	118778497	+	IGR	INS	-	AGG	AGG			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118778496_118778497insAGG								C9orf27 (91119 upstream) : PAPPA (137574 downstream)																							tttgccaacatttgctatttct	0.000													13	6	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123888360	123888360	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123888360delT	uc004bkx.1	+						CEP110_uc004bky.1_Intron|CEP110_uc004bkz.1_Intron|CEP110_uc004bla.1_Intron	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						ACAGTTGGGCTTTTTTTTTTC	0.303													5	3	---	---	---	---	
MED27	9442	broad.mit.edu	37	9	134941272	134941272	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134941272delT	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		TCTGCTGACATTCCCTTTTAT	0.507													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1599331	1599331	+	Intron	DEL	C	-	-	rs10706282		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1599331delC	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		gtccatggcgccccccgtctt	0.000													3	3	---	---	---	---	
PITRM1	10531	broad.mit.edu	37	10	3194619	3194619	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3194619delT	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|PITRM1_uc001igw.1_Intron			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						CCATGTTCCATTTCCACCTTC	0.617													4	2	---	---	---	---	
AKR1CL1	340811	broad.mit.edu	37	10	5202343	5202344	+	Intron	INS	-	A	A	rs138192813	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5202343_5202344insA	uc009xhz.2	-							NR_027916				Homo sapiens cDNA FLJ16347 fis, clone TESTI2036288, moderately similar to PROSTAGLANDIN-F SYNTHASE 1 (EC 1.1.1.188).												0						TCTAGAATGGGAAAAAAAAATG	0.426													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8795674	8795674	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8795674delT								GATA3 (678512 upstream) : None (None downstream)																							GAAAACTGCCTTTTTTTCTCC	0.413													4	2	---	---	---	---	
UPF2	26019	broad.mit.edu	37	10	12076804	12076805	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12076804_12076805insT	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)				attccgtctcaaaataaataaa	0.134													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	15780109	15780109	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15780109delA								ITGA8 (18339 upstream) : FAM188A (40066 downstream)																							AAGAAACTTTAAAAAATCTAA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	28939527	28939527	+	IGR	DEL	A	-	-	rs148885642		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28939527delA								WAC (29606 upstream) : BAMBI (26897 downstream)																							ctttcgggggaaaaaaaaaaa	0.025													12	8	---	---	---	---	
CCNY	219771	broad.mit.edu	37	10	35728462	35728462	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35728462delC	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						ctctctctctctttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37008431	37008431	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37008431delA								None (None upstream) : ANKRD30A (406354 downstream)																							tggcaaaaggaaaaaaaacag	0.010													4	2	---	---	---	---	
LOC100129055	100129055	broad.mit.edu	37	10	38465355	38465355	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38465355delT	uc001izn.2	+							NR_024524				Homo sapiens cDNA clone IMAGE:4825074.												0						TGGCTCCCCCTTTGTCCTTAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42392387	42392387	+	IGR	DEL	A	-	-	rs66654883		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42392387delA								None (None upstream) : LOC441666 (434928 downstream)																							aatggattcgaaatgtaatca	0.000													11	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42641630	42641630	+	IGR	DEL	T	-	-	rs77529483		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42641630delT								None (None upstream) : LOC441666 (185685 downstream)																							tttcacttcatttcatcattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42653182	42653182	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42653182delT								None (None upstream) : LOC441666 (174133 downstream)																							AAAAGAGAAATTCTTTCATTG	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45736261	45736261	+	IGR	DEL	A	-	-	rs35312527		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45736261delA								LOC100133308 (86217 upstream) : OR13A1 (61841 downstream)																							AGGCAGTGAGAAAAAAAAATA	0.373													3	4	---	---	---	---	
C10orf128	170371	broad.mit.edu	37	10	50379919	50379920	+	Intron	INS	-	C	C	rs150277741		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50379919_50379920insC	uc001jhn.3	-						C10orf128_uc001jhl.3_Intron|C10orf128_uc001jhm.3_Intron|C10orf128_uc010qgo.1_Intron|C10orf128_uc001jho.3_Intron	NM_001010863	NP_001010863	Q5T292	CJ128_HUMAN	hypothetical protein LOC170371 precursor							integral to membrane				lung(1)	1						CATCCAGGCCTCTTTGAGCTGT	0.559													4	2	---	---	---	---	
FAM13C	220965	broad.mit.edu	37	10	61029485	61029486	+	Intron	INS	-	CAATGGCAT	CAATGGCAT	rs146306829	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61029485_61029486insCAATGGCAT	uc001jkn.2	-						FAM13C_uc001jko.2_Intron|FAM13C_uc010qid.1_Intron|FAM13C_uc010qie.1_Intron|FAM13C_uc010qif.1_Intron|FAM13C_uc001jkp.2_Intron	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1											ovary(2)	2						ATCAAGGCCTGCAATGGCATCC	0.436													6	5	---	---	---	---	
WAPAL	23063	broad.mit.edu	37	10	88227434	88227434	+	Intron	DEL	T	-	-	rs7914748		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88227434delT	uc001kdo.2	-						WAPAL_uc009xsv.2_Intron|WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_Intron	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog						cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1						CTCTAAAAAAttttttttttt	0.139													4	2	---	---	---	---	
AGAP11	119385	broad.mit.edu	37	10	88753100	88753100	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88753100delT	uc001kee.2	+						AGAP11_uc001kef.2_5'Flank	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						ATGAGTTTACTTTTTTTTTTA	0.303													4	3	---	---	---	---	
TNKS2	80351	broad.mit.edu	37	10	93622951	93622959	+	3'UTR	DEL	GTTTTTTCA	-	-	rs74594203		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93622951_93622959delGTTTTTTCA	uc001khp.2	+	27						NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related						positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				AATATTTCCTGTTTTTTCAGCACTTTAAC	0.330													5	3	---	---	---	---	
IDE	3416	broad.mit.edu	37	10	94275019	94275019	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94275019delT	uc001kia.2	-							NM_004969	NP_004960	P14735	IDE_HUMAN	insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TAAAAGTGTCttttttttttt	0.144													4	2	---	---	---	---	
ABCC2	1244	broad.mit.edu	37	10	101567651	101567652	+	Intron	DEL	TT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101567651_101567652delTT	uc001kqf.2	+							NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),							apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	tagtaatccattaattgacttt	0.054													15	12	---	---	---	---	
ABCC2	1244	broad.mit.edu	37	10	101567654	101567657	+	Intron	DEL	ATTG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101567654_101567657delATTG	uc001kqf.2	+							NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),							apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	taatccattaattgactttgtgac	0.044													16	12	---	---	---	---	
CCDC147	159686	broad.mit.edu	37	10	106152248	106152248	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106152248delA	uc001kyh.2	+							NM_001008723	NP_001008723	Q5T655	CC147_HUMAN	coiled-coil domain containing 147											ovary(2)|central_nervous_system(2)|skin(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AGAATAGATTAAAAAAAAAAC	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111740793	111740793	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111740793delG	uc001kyr.1	-											Homo sapiens mRNA; cDNA DKFZp686J1229 (from clone DKFZp686J1229).																		TTTGAATAATGGGGGAGAGGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112180077	112180077	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112180077delT								SMNDC1 (115370 upstream) : DUSP5 (77548 downstream)																							gccaacagcctggaatggcac	0.159													4	2	---	---	---	---	
C10orf46	143384	broad.mit.edu	37	10	120500993	120500996	+	Intron	DEL	CACC	-	-	rs12778436	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120500993_120500996delCACC	uc001lds.1	-						C10orf46_uc010qst.1_Intron	NM_153810	NP_722517	Q86Y37	CJ046_HUMAN	chromosome 10 open reading frame 46						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)		CACACACACACACCCCCTCACTTC	0.456													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583238	127583239	+	Intron	INS	-	T	T	rs142355498		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583238_127583239insT	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)				GACCTGCACTGTTGTTTCTTCT	0.302													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134760038	134760044	+	IGR	DEL	CAGCACC	-	-	rs75239062		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134760038_134760044delCAGCACC								C10orf93 (3974 upstream) : GPR123 (124389 downstream)																							Gcccagcactcagcacccagcacccag	0.271													4	3	---	---	---	---	
KCNQ1	3784	broad.mit.edu	37	11	2482706	2482707	+	Intron	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2482706_2482707insC	uc001lwn.2	+						KCNQ1_uc009ydo.1_Intron|KCNQ1_uc009ydp.1_5'UTR|KCNQ1_uc001lwo.2_5'UTR	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	GCCTGGGGCTGTGAGAGGCCCG	0.639													13	6	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7468231	7468231	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7468231delT	uc001mfe.2	+						SYT9_uc009yfi.2_Intron|uc001mff.1_Intron|uc001mfg.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		CCTGGTGCCCTTTTGCTTCAC	0.542													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	33005748	33005748	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33005748delC	uc001mtz.1	+	15	4870	c.4514delC	c.(4513-4515)ACCfs	p.T1505fs		NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	Error:Variant_position_missing_in_Q2KHR3_after_alignment										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					GTTAGCAGCACCAGAAGATCA	0.279													4	2	---	---	---	---	
PDHX	8050	broad.mit.edu	37	11	34968884	34968885	+	Intron	DEL	AC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34968884_34968885delAC	uc001mvt.2	+						PDHX_uc010rep.1_Intron|PDHX_uc010req.1_Intron	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			gcatacacatacacacacacac	0.074													4	2	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46567012	46567012	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46567012delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		accctgtctcaaaaaaaaaaT	0.219													3	3	---	---	---	---	
KIAA0652	9776	broad.mit.edu	37	11	46666126	46666126	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666126delA	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)		CTACTTGTTCaaaaaaaaaat	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	49327167	49327167	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49327167delA								FOLH1 (96945 upstream) : LOC440040 (252913 downstream)																							TAAAGTTAGcaaaaaaaaaaa	0.204													4	3	---	---	---	---	
PITPNM1	9600	broad.mit.edu	37	11	67262282	67262283	+	Intron	INS	-	GA	GA	rs67466581		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67262282_67262283insGA	uc001olx.2	-						PITPNM1_uc001olw.2_Intron|PITPNM1_uc001oly.2_Intron|PITPNM1_uc001olz.2_Intron	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,						brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3						CGAGAGTGGGCGAGTGGGCGAG	0.703													4	2	---	---	---	---	
IL18BP	10068	broad.mit.edu	37	11	71710837	71710837	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71710837delC	uc001ore.1	+						IL18BP_uc001orf.1_Intron|IL18BP_uc009ysu.1_Intron|IL18BP_uc001org.1_5'UTR|IL18BP_uc001orh.1_5'UTR|IL18BP_uc001ori.2_Intron|IL18BP_uc009ysv.1_5'Flank	NM_001039659	NP_001034748	O95998	I18BP_HUMAN	interleukin 18 binding protein isoform a						T-helper 1 type immune response	extracellular region	interleukin-18 binding|receptor antagonist activity				0						TGTCACTTGACCCCCCCAGCT	0.413													4	2	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72549650	72549650	+	3'UTR	DEL	A	-	-	rs113447165		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72549650delA	uc009ytl.2	-	20					FCHSD2_uc010rrg.1_3'UTR|FCHSD2_uc001oth.3_3'UTR|ATG16L2_uc009ytj.1_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			AAATGACAACAAAAAAAAAAG	0.453													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82332144	82332144	+	IGR	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82332144delG								None (None upstream) : FAM181B (110909 downstream)																							atgtgatttagggagggggct	0.000													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84163156	84163156	+	Intron	DEL	A	-	-	rs5793122		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84163156delA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				AAAGGTTAACAAAAAAAAAAA	0.204													2	4	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107673652	107673652	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107673652delA	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		TTTTTGATCTAGAGTCTTGAA	0.363													72	31	---	---	---	---	
ZW10	9183	broad.mit.edu	37	11	113629070	113629070	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113629070delA	uc001poe.2	-						ZW10_uc009yyv.2_Intron	NM_004724	NP_004715	O43264	ZW10_HUMAN	centromere/kinetochore protein zw10						cell division|ER to Golgi vesicle-mediated transport|establishment of mitotic spindle orientation|meiosis|mitotic cell cycle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|protein complex assembly|protein localization to kinetochore|protein transport|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|endoplasmic reticulum membrane|kinetochore microtubule|nucleus|spindle pole	centromeric DNA binding|protein binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		TTCAAAAACCAAAAAAAAAAA	0.323													9	4	---	---	---	---	
FAM118B	79607	broad.mit.edu	37	11	126131050	126131051	+	Intron	INS	-	AAATGTA	AAATGTA	rs78366918		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126131050_126131051insAAATGTA	uc001qdf.2	+						FAM118B_uc009zca.2_Intron|FAM118B_uc001qdg.2_Intron	NM_024556	NP_078832	Q9BPY3	F118B_HUMAN	hypothetical protein LOC79607												0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		GCCTGTatgtgaaatgtaaaat	0.381													5	5	---	---	---	---	
DDX12	440081	broad.mit.edu	37	12	9573309	9573310	+	Intron	INS	-	CCC	CCC	rs66804813		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9573309_9573310insCCC	uc010sgs.1	-						DDX12_uc001qvx.3_5'Flank|DDX12_uc001qvy.1_5'Flank	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						gagggagggagCCCCCATGGAG	0.446													58	30	---	---	---	---	
STRAP	11171	broad.mit.edu	37	12	16033969	16033969	+	5'Flank	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16033969delA	uc001rdc.3	+						STRAP_uc010shw.1_5'Flank|STRAP_uc001rdd.3_5'Flank	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated						mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				TGTGTGAGACAAAAGGGAGAG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16342393	16342396	+	IGR	DEL	ATTA	-	-	rs66881403		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16342393_16342396delATTA								DERA (152079 upstream) : MGST1 (157680 downstream)																							AAATTATTTTATTAATTCTAATGC	0.260													3	4	---	---	---	---	
ANO6	196527	broad.mit.edu	37	12	45792990	45792991	+	Intron	INS	-	T	T	rs147009974	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45792990_45792991insT	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						tttgttttttgtttttttgaga	0.183													4	2	---	---	---	---	
CELA1	1990	broad.mit.edu	37	12	51740388	51740391	+	Intron	DEL	CTGG	-	-	rs57614420		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51740388_51740391delCTGG	uc001ryi.1	-							NM_001971	NP_001962	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			breast(1)	1						AGGGTTGCGACTGGACCATATCCA	0.510													8	32	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54202969	54202969	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54202969delT								CALCOCO1 (81662 upstream) : HOXC13 (129607 downstream)																							ACCCTTTGAATTTTACCACAT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55215260	55215262	+	IGR	DEL	GGT	-	-	rs76239927		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55215260_55215262delGGT								DCD (173111 upstream) : MUCL1 (33037 downstream)																							CTCTGGCCCAGGTGGTGGTGGTG	0.532													4	2	---	---	---	---	
RBMS2	5939	broad.mit.edu	37	12	56980357	56980359	+	Intron	DEL	TAA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56980357_56980359delTAA	uc001sln.2	+						RBMS2_uc010sqp.1_Intron|RBMS2_uc010sqq.1_Intron|RBMS2_uc009zou.2_Intron	NM_002898	NP_002889	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting						RNA processing	nucleus	nucleotide binding|RNA binding				0						ttttttttactaatttttttagt	0.025													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77779101	77779102	+	IGR	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77779101_77779102insA								E2F7 (319741 upstream) : NAV3 (445967 downstream)																							TAAGTTCCTTTAAAAAAAAGAA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	85866124	85866124	+	IGR	DEL	A	-	-	rs116046023	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85866124delA								ALX1 (170565 upstream) : RASSF9 (332207 downstream)																							ggaggcttttagaggactctt	0.000													4	2	---	---	---	---	
ATP2B1	490	broad.mit.edu	37	12	90015716	90015716	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90015716delT	uc001tbh.2	-						ATP2B1_uc001tbg.2_Intron|ATP2B1_uc001tbf.2_Intron	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						AATACTGAAATTTTTTTTTTT	0.264													6	3	---	---	---	---	
PLEKHG7	440107	broad.mit.edu	37	12	93155399	93155399	+	Intron	DEL	G	-	-	rs11283164		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93155399delG	uc001tcj.2	+							NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						aagaaagaaagaagaaagaaa	0.070													64	30	---	---	---	---	
LTA4H	4048	broad.mit.edu	37	12	96434042	96434042	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96434042delG	uc010suy.1	-						LTA4H_uc010suz.1_Intron	NM_000895	NP_000886	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1						AGTTAATGCAGTGCCCTCACA	0.368													4	2	---	---	---	---	
LTA4H	4048	broad.mit.edu	37	12	96438461	96438461	+	5'Flank	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96438461delA	uc010suy.1	-						LTA4H_uc010suz.1_5'Flank	NM_000895	NP_000886	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1						TATTGATATGAAAAAAAATAA	0.378													4	3	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109877328	109877339	+	5'Flank	DEL	CCACAGCCTCTA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109877328_109877339delCCACAGCCTCTA	uc010sxo.1	+						MYO1H_uc010sxn.1_Intron			Q8N1T3	MYO1H_HUMAN	SubName: Full=cDNA FLJ54829, moderately similar to Myosin Ic; SubName: Full=Myosin IH, isoform CRA_a;							myosin complex	motor activity				0						GTGGTCATCTCCACAGCCTCTACCACTTTGGC	0.311													18	9	---	---	---	---	
OAS3	4940	broad.mit.edu	37	12	113385942	113385945	+	Intron	DEL	TTTG	-	-	rs45548934		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113385942_113385945delTTTG	uc001tug.2	+							NM_006187	NP_006178	Q9Y6K5	OAS3_HUMAN	2'-5'oligoadenylate synthetase 3						interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	microsome	ATP binding|nucleotidyltransferase activity|RNA binding			central_nervous_system(1)	1						GGTTTTGCACTTTGTTTATGTGTC	0.466													8	11	---	---	---	---	
RNF10	9921	broad.mit.edu	37	12	120990203	120990203	+	Intron	DEL	A	-	-	rs112757664		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120990203delA	uc001typ.3	+						RNF10_uc010szk.1_Intron|RNF10_uc001tyq.3_Intron	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10						negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					actccgtctcaaaaaaaaaaG	0.164													8	5	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	125022151	125022151	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125022151delA	uc001ugj.1	-						NCOR2_uc010tay.1_5'Flank|NCOR2_uc010taz.1_5'Flank|NCOR2_uc010tbc.1_5'Flank	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		ttgtgagtgtaaagtgCCCTC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130819237	130819237	+	IGR	DEL	C	-	-	rs67320079		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130819237delC								FZD10 (168953 upstream) : PIWIL1 (3377 downstream)																							attaaaaaaaCAACAACAACA	0.259													4	2	---	---	---	---	
ZMYM2	7750	broad.mit.edu	37	13	20633359	20633359	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20633359delA	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		TTTCTTTCTTAAAAAAAAAAA	0.299													4	2	---	---	---	---	
ATP5EP2	432369	broad.mit.edu	37	13	28519646	28519646	+	RNA	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28519646delA	uc001uru.2	+	1		c.304delA				NR_002162				Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2 (ATP5EP2), transcript variant 6, non-coding RNA.											ovary(1)	1						ATTTCATGGGAAAAAAAAATC	0.284													6	4	---	---	---	---	
SUGT1L1	283507	broad.mit.edu	37	13	41398933	41398933	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41398933delA	uc001uxp.1	-							NR_003365				Homo sapiens cDNA FLJ35913 fis, clone TESTI2010239.												0						TCCTAAAAAGAAAAAAAAAAT	0.224													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51739680	51739689	+	IGR	DEL	CAAGAGGAAG	-	-	rs145186525		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51739680_51739689delCAAGAGGAAG								GUCY1B2 (84682 upstream) : FAM124A (56818 downstream)																							taaaggagaacaagaggaagcaaccaagga	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59783742	59783743	+	IGR	INS	-	GG	GG	rs144037370	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59783742_59783743insGG								None (None upstream) : DIAPH3 (455982 downstream)																							ATATACTGGGCGGGGGGGAAAA	0.351													5	3	---	---	---	---	
PIBF1	10464	broad.mit.edu	37	13	73539212	73539212	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73539212delA	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		aaaagaaaacaaaaaaaaTTA	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83104420	83104421	+	IGR	DEL	TG	-	-	rs72217036		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83104420_83104421delTG								None (None upstream) : None (None downstream)																							tgtttgtgtatgtgtgtgtgtg	0.282													5	3	---	---	---	---	
DCT	1638	broad.mit.edu	37	13	95117701	95117702	+	Intron	INS	-	A	A	rs146133280	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95117701_95117702insA	uc001vlv.3	-						DCT_uc010afh.2_Intron	NM_001922	NP_001913	P40126	TYRP2_HUMAN	dopachrome tautomerase isoform 1						epidermis development|melanin biosynthetic process from tyrosine	cytosol|integral to membrane|melanosome membrane|microsome	copper ion binding|dopachrome isomerase activity|oxidoreductase activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		GATTTTGATATTTTTTTTTTAA	0.252													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22111983	22111983	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22111983delT								OR10G2 (8985 upstream) : OR4E2 (21314 downstream)																							tcagtcactatttttttttct	0.070													4	2	---	---	---	---	
SRP54	6729	broad.mit.edu	37	14	35492300	35492300	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35492300delG	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127	P61011	SRP54_HUMAN	signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		AGAAAAATAAGCTTGTTATTA	0.333													30	20	---	---	---	---	
SRP54	6729	broad.mit.edu	37	14	35492302	35492318	+	Intron	DEL	TTGTTATTAGTTAACAG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35492302_35492318delTTGTTATTAGTTAACAG	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127	P61011	SRP54_HUMAN	signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		AAAAATAAGCTTGTTATTAGTTAACAGACGGAAAAGA	0.336													26	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38355303	38355303	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38355303delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		ttattttttctttttttgaca	0.000													4	2	---	---	---	---	
PRPF39	55015	broad.mit.edu	37	14	45554177	45554177	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45554177delT	uc001wvz.3	+						uc001wvx.1_5'Flank|PRPF39_uc001wvy.3_Intron|PRPF39_uc010and.2_Intron	NM_017922	NP_060392	Q86UA1	PRP39_HUMAN	PRP39 pre-mRNA processing factor 39 homolog						mRNA processing|RNA splicing	nucleus	binding			ovary(1)|breast(1)	2						TCAAATGTTGTTTTTTTCGTT	0.294													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50196448	50196449	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50196448_50196449insT	uc010anj.1	-						KLHDC1_uc001www.2_Intron|KLHDC1_uc010tqg.1_Intron|KLHDC1_uc010tqh.1_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		GATAAAACATGAAAATACTAAC	0.292													6	3	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79115799	79115799	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79115799delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TCTTTTTCTTAAAAAAAAAAT	0.358													5	3	---	---	---	---	
MARK3	4140	broad.mit.edu	37	14	103915226	103915226	+	Intron	DEL	A	-	-	rs80102122		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103915226delA	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			TGTTGGGGGGATTATGTGTTT	0.249													56	37	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106349516	106349516	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106349516delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ACTCCATGGCTCTGTGGTGCT	0.657													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106821595	106821596	+	Intron	DEL	TT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106821595_106821596delTT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TCACTGTTTCTTTTTTTTTTTC	0.109													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106919168	106919168	+	RNA	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106919168delC	uc010tyt.1	-	245		c.10611delG			uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						ACGTTAACCTCCCCCTCACTG	0.557													9	6	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106919176	106919177	+	RNA	INS	-	TG	TG	rs145658629	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106919176_106919177insTG	uc010tyt.1	-	244		c.10603_10604insCA			uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						CTCCCCCTCACTGTCTCTAGTA	0.545													13	6	---	---	---	---	
SNRPN	6638	broad.mit.edu	37	15	25206097	25206097	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25206097delT	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNURF_uc001ywu.2_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718	P63162	RSMN_HUMAN	small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)		ccctaccttcttttttttcat	0.005									Prader-Willi_syndrome				4	2	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31841875	31841875	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31841875delA	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GGTAGAATATAAAGGGAATAC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38027990	38027990	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38027990delC								MEIS2 (634490 upstream) : TMCO5A (198837 downstream)																							TCATTCAGTTCCAGTTTCATT	0.423													4	2	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38641774	38641775	+	Intron	INS	-	AAT	AAT	rs34352434		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641774_38641775insAAT	uc001zka.3	+							NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TAATTAATAGATAGGTAAAGTT	0.317									Legius_syndrome				50	44	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38641777	38641778	+	Intron	INS	-	TA	TA	rs114258866	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641777_38641778insTA	uc001zka.3	+							NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TTAATAGATAGGTAAAGTTTTC	0.317									Legius_syndrome				16	44	---	---	---	---	
TRPM7	54822	broad.mit.edu	37	15	50882045	50882046	+	Intron	INS	-	TTTTTTG	TTTTTTG	rs148695282	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50882045_50882046insTTTTTTG	uc001zyt.3	-						TRPM7_uc010bew.1_Intron	NM_017672	NP_060142	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AGGTTACAGttttttttgtttt	0.178													22	11	---	---	---	---	
HERC1	8925	broad.mit.edu	37	15	63952920	63952920	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63952920delA	uc002amp.2	-							NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						ccctactttgaaaaaaaaata	0.129													4	2	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	67872870	67872875	+	Intron	DEL	TTACTC	-	-	rs66514950		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67872870_67872875delTTACTC	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc010ujw.1_Intron	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						ATCAACACTTTTACTCTTAAAGATAA	0.306													9	6	---	---	---	---	
ITGA11	22801	broad.mit.edu	37	15	68596330	68596331	+	Intron	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68596330_68596331insC	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	TGGGGGAGCTGCATCCTCTTCC	0.668													4	2	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	68933189	68933191	+	Intron	DEL	GAG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68933189_68933191delGAG	uc002arj.3	+						CORO2B_uc010bic.2_Intron	NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						GGCTGGGGTAGAGgaggaggagc	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70771292	70771293	+	IGR	DEL	AC	-	-	rs114323145	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70771292_70771293delAC								TLE3 (381036 upstream) : UACA (175602 downstream)																							aaaaacagagacacacacacac	0.267													4	2	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	77154590	77154600	+	Intron	DEL	CTTTTATAAAA	-	-	rs144502115		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77154590_77154600delCTTTTATAAAA	uc002bby.2	-						SCAPER_uc002bbx.2_5'Flank|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						AACAATAAGGCTTTTATAAAACCATGTGTGT	0.294													20	15	---	---	---	---	
C15orf26	161502	broad.mit.edu	37	15	81409885	81409885	+	Intron	DEL	T	-	-	rs143700340		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81409885delT	uc010blp.1	+							NM_173528	NP_775799	Q6P656	CO026_HUMAN	hypothetical protein LOC161502												0						TCACAGCTACttttttttttt	0.408													16	13	---	---	---	---	
TMC3	342125	broad.mit.edu	37	15	81660812	81660813	+	Intron	INS	-	T	T	rs55873314		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81660812_81660813insT	uc002bgo.1	-						TMC3_uc010blr.1_Intron|TMC3_uc002bgp.2_Intron	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3							integral to membrane				ovary(1)|liver(1)	2						AATGGAGTTACACAAATACTTC	0.282													10	9	---	---	---	---	
TMC3	342125	broad.mit.edu	37	15	81660814	81660815	+	Intron	INS	-	TACTCTACT	TACTCTACT	rs56061003		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81660814_81660815insTACTCTACT	uc002bgo.1	-						TMC3_uc010blr.1_Intron|TMC3_uc002bgp.2_Intron	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3							integral to membrane				ovary(1)|liver(1)	2						TGGAGTTACACAAATACTTCAT	0.282													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96533704	96533704	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96533704delA								LOC145820 (482630 upstream) : NR2F2 (335453 downstream)																							AAAGTGAGAGAAAAAGGGAAG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102284543	102284543	+	5'Flank	DEL	G	-	-	rs112440991		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102284543delG	uc010usj.1	+											RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		AAATTGGGTAGGGTGAAGGGG	0.502													13	7	---	---	---	---	
SRL	6345	broad.mit.edu	37	16	4247598	4247598	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4247598delT	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284	Q86TD4	SRCA_HUMAN	sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5						aatttttgtatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5836446	5836447	+	IGR	DEL	AG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5836446_5836447delAG								FAM86A (688657 upstream) : A2BP1 (232685 downstream)																							GTGTTTATGCAGAGTTGAAATA	0.312													8	4	---	---	---	---	
RRN3	54700	broad.mit.edu	37	16	15179184	15179184	+	Intron	DEL	T	-	-	rs71743255		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15179184delT	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Intron	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						TGTGCTTTACTTTTTTTTTTA	0.244													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27178480	27178480	+	IGR	DEL	A	-	-	rs11367962		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27178480delA								C16orf82 (97994 upstream) : JMJD5 (36327 downstream)																							CAGAATCGCCACCCAGACCCA	0.542													6	3	---	---	---	---	
CCL17	6361	broad.mit.edu	37	16	57444578	57444578	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57444578delC	uc002elj.1	+						CCL17_uc010ccz.1_Intron	NM_002987	NP_002978	Q92583	CCL17_HUMAN	small inducible cytokine A17 precursor						cell-cell signaling|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|inflammatory response|multicellular organismal development	extracellular space	chemokine activity			ovary(1)	1						TCTGGAAGTTCCCTTGGCATC	0.517													3	3	---	---	---	---	
MLKL	197259	broad.mit.edu	37	16	74724952	74724953	+	Intron	DEL	TT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74724952_74724953delTT	uc002fdb.2	-						MLKL_uc002fdc.2_Intron	NM_152649	NP_689862	Q8NB16	MLKL_HUMAN	mixed lineage kinase domain-like isoform 1								ATP binding|protein binding|protein kinase activity			stomach(2)	2						gggaaAGTTGtttttttttttt	0.010													4	2	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77870204	77870204	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77870204delC	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						CCACCGTGAGCCCCAGGATAA	0.507													4	2	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83984579	83984580	+	Intron	DEL	CA	-	-	rs71392792		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83984579_83984580delCA	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_5'Flank	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						tacatactggcacacacgtaca	0.000													4	3	---	---	---	---	
CTU2	348180	broad.mit.edu	37	16	88780681	88780690	+	Intron	DEL	TGTGCGCGGG	-	-	rs7191439	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88780681_88780690delTGTGCGCGGG	uc002flm.2	+						CTU2_uc002fln.2_Intron|CTU2_uc010chz.2_Intron|CTU2_uc010cia.2_Intron	NM_001012759	NP_001012777	Q2VPK5	CTU2_HUMAN	cytoplasmic tRNA 2-thiolation protein 2 isoform						tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding			skin(1)	1						gggtgtgtgctgtgcgcgggtgtgtgcggg	0.405													15	7	---	---	---	---	
ZNF276	92822	broad.mit.edu	37	16	89801921	89801921	+	Intron	DEL	G	-	-	rs146246550		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89801921delG	uc002fos.3	+						ZNF276_uc010ciq.2_Intron|ZNF276_uc002fop.2_Intron|ZNF276_uc002foq.3_Intron|ZNF276_uc010cir.2_Intron|ZNF276_uc002for.3_Intron|ZNF276_uc010cis.2_Intron|ZNF276_uc002fot.3_Intron|ZNF276_uc010vpm.1_Intron|ZNF276_uc010cit.1_Intron	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GCACTTCCTTGGGTTTGGTCC	0.413													3	3	---	---	---	---	
DNAH2	146754	broad.mit.edu	37	17	7646597	7646597	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7646597delT	uc002giu.1	+						DNAH2_uc002git.2_Frame_Shift_Del_p.F763fs|DNAH2_uc010vuk.1_Frame_Shift_Del_p.F681fs	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GTCATTTTACTTTTTTTTTTC	0.338													7	6	---	---	---	---	
TBC1D28	254272	broad.mit.edu	37	17	18541853	18541854	+	Intron	DEL	CC	-	-	rs72222771		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18541853_18541854delCC	uc002gud.2	-							NM_001039397	NP_001034486	Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28							intracellular	Rab GTPase activator activity			ovary(1)	1						CTGAGAGGCACCCACCCAGGCC	0.604													40	24	---	---	---	---	
TBC1D28	254272	broad.mit.edu	37	17	18541856	18541857	+	Intron	INS	-	TGGT	TGGT			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18541856_18541857insTGGT	uc002gud.2	-							NM_001039397	NP_001034486	Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28							intracellular	Rab GTPase activator activity			ovary(1)	1						AGAGGCACCCACCCAGGCCAAA	0.599													49	22	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21518846	21518847	+	IGR	DEL	TT	-	-	rs74411889		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518846_21518847delTT								C17orf51 (41115 upstream) : FAM27L (306523 downstream)																							ATTCCCTTCATTTTTTTTTTCT	0.371													21	11	---	---	---	---	
C17orf75	64149	broad.mit.edu	37	17	30658580	30658580	+	3'UTR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30658580delC	uc002hhg.2	-	10						NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TTTCACAACTCTCACATACAT	0.323													4	2	---	---	---	---	
C17orf75	64149	broad.mit.edu	37	17	30658583	30658584	+	3'UTR	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30658583_30658584insT	uc002hhg.2	-	10						NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			CACAACTCTCACATACATTATC	0.317													4	2	---	---	---	---	
ARHGAP23	57636	broad.mit.edu	37	17	36638146	36638147	+	Intron	INS	-	AGAT	AGAT			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36638146_36638147insAGAT	uc010wdp.1	+						ARHGAP23_uc002hqc.2_Intron	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23						signal transduction	intracellular	GTPase activator activity			lung(1)	1						CAGCCCTGGGCATCTGGTTTCT	0.515													18	9	---	---	---	---	
GRB7	2886	broad.mit.edu	37	17	37902900	37902901	+	Intron	INS	-	AAG	AAG			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37902900_37902901insAAG	uc002hsr.2	+						GRB7_uc002hss.2_Intron|GRB7_uc010cwc.2_Intron|GRB7_uc002hst.2_Intron	NM_005310	NP_005301	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7						blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly	cytosol|focal adhesion|stress granule	phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			aaagaaaaagaaaaaagaaaag	0.272													5	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43893770	43893770	+	Intron	DEL	C	-	-	rs68004164		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43893770delC	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron|CRHR1_uc010das.1_Intron|CRHR1_uc002ijo.1_Intron	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		ATGTCCTCTGCCTGCCTGGGG	0.587													10	10	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43893773	43893777	+	Intron	DEL	GCCTG	-	-	rs66475418		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43893773_43893777delGCCTG	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron|CRHR1_uc010das.1_Intron|CRHR1_uc002ijo.1_Intron	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		TCCTCTGCCTGCCTGGGGCCTTGGC	0.605													7	10	---	---	---	---	
SAMD14	201191	broad.mit.edu	37	17	48202122	48202125	+	Intron	DEL	TGCA	-	-	rs149885965	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48202122_48202125delTGCA	uc002iqg.2	-						SAMD14_uc002iqe.2_5'Flank|SAMD14_uc002iqf.2_Intron	NM_174920	NP_777580	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14												0						CCTGCACGCGTGcacgcgcgcgcg	0.309													9	4	---	---	---	---	
SKA2	348235	broad.mit.edu	37	17	57228357	57228357	+	Intron	DEL	T	-	-	rs111657703	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57228357delT	uc002ixd.2	-						SKA2_uc010dde.1_Intron|SKA2_uc002ixe.2_Intron	NM_182620	NP_872426	Q8WVK7	SKA2_HUMAN	spindle and KT associated 2 isoform 1						cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						AGTTAAAAGGTTTTTTTTTTT	0.249													17	8	---	---	---	---	
YPEL2	388403	broad.mit.edu	37	17	57474735	57474736	+	3'UTR	DEL	TT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57474735_57474736delTT	uc002ixm.1	+	5						NM_001005404	NP_001005404	Q96QA6	YPEL2_HUMAN	yippee-like 2							nucleolus					0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)					TCTCTGTCTCTTTGCTTTGTAT	0.500													4	2	---	---	---	---	
HELZ	9931	broad.mit.edu	37	17	65119433	65119433	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65119433delA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					AGCATATTACaaaaaaaaaaa	0.239													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71857666	71857666	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71857666delT								C17orf54 (32990 upstream) : RPL38 (342129 downstream)																							CCTATGAGCATTTTCCACTCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75844200	75844200	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75844200delC								SEPT9 (347524 upstream) : FLJ45079 (30909 downstream)																							GGAGTAAGCGCCCCCAACTGG	0.428													4	2	---	---	---	---	
CYTH1	9267	broad.mit.edu	37	17	76696603	76696603	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76696603delT	uc002jvw.2	-						CYTH1_uc010wtw.1_Intron|CYTH1_uc010wtx.1_Intron	NM_017456	NP_059430	Q15438	CYH1_HUMAN	cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						CTGCCAATGAttttttttttc	0.229													8	4	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34092653	34092653	+	Intron	DEL	C	-	-	rs34586462		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34092653delC	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AAAACATCTGCCATAGGTAAA	0.373													4	3	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34092657	34092664	+	Intron	DEL	AGGTAAAA	-	-	rs34982026		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34092657_34092664delAGGTAAAA	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CATCTGCCATAGGTAAAACAGGTTTTAC	0.385													3	3	---	---	---	---	
PIK3C3	5289	broad.mit.edu	37	18	39573568	39573568	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39573568delT	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						CAGTATACTCTTTTTTTTTTT	0.204										TSP Lung(28;0.18)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39774007	39774007	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39774007delC	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																		TTCCTTCTGGCCTATAGACCT	0.353													4	2	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42620288	42620289	+	Intron	INS	-	TAG	TAG	rs150044374	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42620288_42620289insTAG	uc010dni.2	+							NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		acttgatggattagtagcacct	0.163									Schinzel-Giedion_syndrome				3	3	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46217838	46217839	+	Intron	INS	-	C	C			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46217838_46217839insC	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						ATTCTAGATTTCCCTCCAGTCA	0.446													4	2	---	---	---	---	
ZNF626	199777	broad.mit.edu	37	19	20806648	20806649	+	3'UTR	DEL	CA	-	-	rs71893877		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20806648_20806649delCA	uc002npb.1	-	4					ZNF626_uc002npc.1_3'UTR	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						TATGCTTTGCCACATTCTTCAC	0.203													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	22500220	22500220	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22500220delT								ZNF676 (120467 upstream) : ZNF98 (73679 downstream)																							GTGGCAAAACttttttttttt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31400212	31400213	+	IGR	DEL	GA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31400212_31400213delGA								ZNF536 (351247 upstream) : DKFZp566F0947 (240570 downstream)																							GGATgatggggagagagaggca	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33023521	33023530	+	IGR	DEL	TGTCTCTCTG	-	-	rs71922504		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33023521_33023530delTGTCTCTCTG								DPY19L3 (48285 upstream) : PDCD5 (48574 downstream)																							tctctctgtatgtctctctgtgtctctctg	0.181													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	37492219	37492223	+	IGR	DEL	TTTTT	-	-	rs56159108		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37492219_37492223delTTTTT								ZNF568 (3385 upstream) : ZNF420 (77159 downstream)																							ttttgttttgtttttgtttttcaga	0.161													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39727753	39727754	+	IGR	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39727753_39727754insA								SYCN (32847 upstream) : IL28B (6519 downstream)																							caggtgtggggagaggagagag	0.228													4	2	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41055990	41055990	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41055990delA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc010egy.1_Intron|SPTBN4_uc002ooa.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			catctcaaagaaaaaaaaaaa	0.239													6	6	---	---	---	---	
LYPD5	284348	broad.mit.edu	37	19	44306390	44306395	+	Intron	DEL	CCCCCA	-	-	rs72214885		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44306390_44306395delCCCCCA	uc002oxm.3	-						LYPD5_uc002oxn.3_Intron	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A							anchored to membrane|plasma membrane					0		Prostate(69;0.0352)				ggagtccaggcccccagtctctcctc	0.102													16	8	---	---	---	---	
STRN4	29888	broad.mit.edu	37	19	47234392	47234392	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47234392delC	uc002pfl.2	-						STRN4_uc002pfm.2_Intron|STRN4_uc010xyf.1_Intron|STRN4_uc010xyg.1_Intron	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1							cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		AGAGGGCCAGCCCCCAACCCT	0.572													4	2	---	---	---	---	
BBC3	27113	broad.mit.edu	37	19	47733077	47733078	+	Intron	DEL	AC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47733077_47733078delAC	uc002pgf.3	-						BBC3_uc010xyl.1_Intron|BBC3_uc010eky.2_Intron|BBC3_uc010ekz.2_Intron|hsa-mir-3191|MI0014236_5'Flank	NM_014417	NP_055232	Q9BXH1	BBC3_HUMAN	BCL2 binding component 3 isoform 4						activation of caspase activity|activation of pro-apoptotic gene products|cellular response to hypoxia|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of growth|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|positive regulation of thymocyte apoptosis|protein insertion into mitochondrial membrane involved in induction of apoptosis|reduction of endoplasmic reticulum calcium ion concentration|release of cytochrome c from mitochondria|release of sequestered calcium ion into cytosol	cytosol|mitochondrial outer membrane	protein binding|protein binding				0		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.000179)|OV - Ovarian serous cystadenocarcinoma(262;0.00029)|Epithelial(262;0.0103)|GBM - Glioblastoma multiforme(486;0.0234)		acacatacatacacacacacac	0.446													4	2	---	---	---	---	
PPP2R1A	5518	broad.mit.edu	37	19	52724951	52724954	+	Intron	DEL	CTTT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52724951_52724954delCTTT	uc002pyp.2	+						PPP2R1A_uc010ydk.1_Intron|PPP2R1A_uc002pyq.2_Intron	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		TGTCTATTTGCTTTTCCTACGAtt	0.044			Mis		clear cell ovarian carcinoma								11	5	---	---	---	---	
PPP2R1A	5518	broad.mit.edu	37	19	52724960	52724961	+	Intron	DEL	CG	-	-	rs112592853	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52724960_52724961delCG	uc002pyp.2	+						PPP2R1A_uc010ydk.1_Intron|PPP2R1A_uc002pyq.2_Intron	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GCTTTTCCTACGAttataatta	0.045			Mis		clear cell ovarian carcinoma								6	5	---	---	---	---	
SSC5D	284297	broad.mit.edu	37	19	56001420	56001420	+	Intron	DEL	G	-	-	rs10716127		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56001420delG	uc002qlg.3	+							NM_001144950	NP_001138422	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine-rich glycoprotein							extracellular region|membrane	scavenger receptor activity				0						TGCCCCCCCCGAGGGGAGAGG	0.706													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7513020	7513020	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7513020delC								BMP2 (752110 upstream) : HAO1 (350611 downstream)																							TGCAAAAGGACCCCCACTCTA	0.338													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15804885	15804886	+	Intron	DEL	TC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15804885_15804886delTC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ATCTTAAGTGTCTCTCTCTCTC	0.277													4	2	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25436620	25436620	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25436620delT	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc002wuw.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						taatcccagctacttgggagg	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25899953	25899953	+	IGR	DEL	A	-	-	rs140359127		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25899953delA								FAM182B (51167 upstream) : LOC100134868 (90482 downstream)																							ATGAGGAAATAAAAAAACTAG	0.214													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25907772	25907773	+	IGR	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25907772_25907773insT								FAM182B (58986 upstream) : LOC100134868 (82662 downstream)																							AAAAATTCATCTTTTTTTAAac	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26142426	26142427	+	IGR	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26142426_26142427insA								C20orf191 (47749 upstream) : MIR663 (46395 downstream)																							ATCTTTTAGATATTCAGAGGTT	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26147215	26147215	+	IGR	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26147215delT								C20orf191 (52538 upstream) : MIR663 (41607 downstream)																							AATTTTAATCTGTTTAGATTT	0.318													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29646794	29646796	+	Intron	DEL	AAA	-	-	rs112811287		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29646794_29646796delAAA	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						aaaatgagacaaaaattgtctgt	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34664142	34664142	+	IGR	DEL	T	-	-	rs113482157		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34664142delT								LOC647979 (25260 upstream) : EPB41L1 (15284 downstream)																							TTCACCCAACTTTTTTTTTTC	0.418													5	6	---	---	---	---	
CTSZ	1522	broad.mit.edu	37	20	57580018	57580018	+	Intron	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57580018delC	uc002yai.2	-						CTSZ_uc002yaj.3_Intron	NM_001336	NP_001327	Q9UBR2	CATZ_HUMAN	cathepsin Z preproprotein						proteolysis	endoplasmic reticulum|extracellular space|lysosome	cysteine-type endopeptidase activity			kidney(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)			TCACCTGACTCCCTCTCAAAG	0.567													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10909809	10909810	+	Intron	INS	-	TT	TT			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10909809_10909810insTT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaacctaactctctttccagtc	0.000													11	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11068910	11068911	+	Intron	DEL	AT	-	-	rs147061174		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11068910_11068911delAT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ttctcttatcatatgtgtaatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11186277	11186277	+	IGR	DEL	A	-	-	rs112747514		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11186277delA								BAGE (87340 upstream) : None (None downstream)																							atgggattagaaatctcctgc	0.000													3	3	---	---	---	---	
C21orf131	387486	broad.mit.edu	37	21	22142476	22142476	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22142476delT	uc002ykz.3	-						C21orf131_uc002yky.3_Intron|C21orf131_uc002yla.3_Intron|C21orf131_uc002ylb.3_Intron|C21orf131_uc002ylc.3_Intron	NR_024090				Homo sapiens cDNA FLJ37207 fis, clone BRALZ2007576.												0						TATCTCTGGGTTTACTTCTCT	0.413													4	2	---	---	---	---	
GABPA	2551	broad.mit.edu	37	21	27121587	27121588	+	Intron	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27121587_27121588insA	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2						TATTTGACAGGGTgaaacagat	0.149													5	3	---	---	---	---	
SON	6651	broad.mit.edu	37	21	34948508	34948509	+	Intron	INS	-	T	T	rs111372529		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34948508_34948509insT	uc002yse.1	+						SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysh.2_Intron|DONSON_uc002ysi.1_Intron	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F						anti-apoptosis|cytokinesis|mRNA processing|regulation of cell cycle|regulation of RNA splicing|RNA splicing|spindle pole body separation	nuclear speck	DNA binding|double-stranded RNA binding			ovary(4)|skin(2)	6						TTTGCAGTCCCTTTCCCAAATG	0.287													4	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	37981280	37981280	+	IGR	DEL	C	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37981280delC								CLDN14 (32413 upstream) : SIM2 (90711 downstream)																							agaacatcttccccagaaatt	0.000													4	2	---	---	---	---	
DSCR6	53820	broad.mit.edu	37	21	38380677	38380686	+	Intron	DEL	TGAGTAAGGT	-	-	rs72350961		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38380677_38380686delTGAGTAAGGT	uc002yvv.2	+						DSCR6_uc011aec.1_Intron|DSCR6_uc010gnd.2_Intron	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6							nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)				GGAACCTGAATGAGTAAGGTGTTAATCAGA	0.476													4	4	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	39906277	39906290	+	Intron	DEL	CAAATGAACACCTG	-	-	rs111755368		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39906277_39906290delCAAATGAACACCTG	uc010gnw.2	-						ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				TTTCTATTGCCAAATGAACACCTGTTTCAGAGTC	0.308													9	5	---	---	---	---	
COL18A1	80781	broad.mit.edu	37	21	46930960	46930960	+	Intron	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46930960delA	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron|SLC19A1_uc010gpy.1_Intron|COL18A1_uc002zhj.2_Intron|COL18A1_uc002zhk.2_Intron	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		acacccccccacaaacaccca	0.144													16	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	18843723	18843724	+	Intron	INS	-	A	A			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18843723_18843724insA	uc002zoe.2	+											Homo sapiens cDNA FLJ76361 complete cds.																		AGGGGCACCCCACGGCCTGGAG	0.619													9	8	---	---	---	---	
CLTCL1	8218	broad.mit.edu	37	22	19214071	19214072	+	Intron	INS	-	G	G	rs150400931	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19214071_19214072insG	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)					GTGGGTCCCAAATCCCTGGCTG	0.569			T	?	ALCL								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20206898	20206899	+	IGR	INS	-	G	G			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20206898_20206899insG								LOC150197 (10838 upstream) : RTN4R (22041 downstream)																							cttttaattctgagggctcgct	0.040													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22905655	22905656	+	Intron	INS	-	T	T	rs73879649	by1000genomes	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22905655_22905656insT	uc011aim.1	+						LOC648691_uc011ais.1_Intron					Parts of antibodies, mostly variable regions.												0						taaACATATGATTTTTTTTTCC	0.183													2	4	---	---	---	---	
RAB36	9609	broad.mit.edu	37	22	23498332	23498333	+	Intron	INS	-	AA	AA	rs56254210		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23498332_23498333insAA	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)		TGTCCTCCAAGACCCACTGAGA	0.594													4	3	---	---	---	---	
SMTN	6525	broad.mit.edu	37	22	31485629	31485629	+	Intron	DEL	G	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31485629delG	uc003ajl.1	+						SMTN_uc003ajk.1_Intron|SMTN_uc003ajm.1_Intron|SMTN_uc011ale.1_Intron|SMTN_uc011alf.1_Intron|SMTN_uc003ajn.1_Intron|SMTN_uc011alg.1_5'Flank	NM_006932	NP_008863	P53814	SMTN_HUMAN	smoothelin isoform c						muscle organ development|smooth muscle contraction	actin cytoskeleton|cytoplasm	actin binding|structural constituent of muscle			large_intestine(2)|pancreas(1)	3						CCTCAGTGGTGGGGGTGGCGT	0.612													4	2	---	---	---	---	
JOSD1	9929	broad.mit.edu	37	22	39087685	39087685	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39087685delT	uc003awf.2	-							NM_014876	NP_055691	Q15040	JOS1_HUMAN	Josephin domain containing 1								peptidase activity				0	Melanoma(58;0.04)					tttctttttctttttttgaga	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45258902	45258903	+	IGR	DEL	CT	-	-	rs10597263		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45258902_45258903delCT								PRR5-ARHGAP8 (240 upstream) : PHF21B (18142 downstream)																							gctggggtgactctgttctccc	0.000													3	6	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50564212	50564212	+	Intron	DEL	G	-	-	rs138241	byFrequency	TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50564212delG	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron|MOV10L1_uc011arq.1_Intron|MOV10L1_uc010hao.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TAATGTTtttgtttgtttgtt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6587828	6587829	+	IGR	INS	-	GGAT	GGAT	rs111533413		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6587828_6587829insGGAT								VCX3A (134669 upstream) : HDHD1A (379132 downstream)																							gaaggatagaaggatggatgga	0.000													4	2	---	---	---	---	
SCML2	10389	broad.mit.edu	37	X	18276526	18276527	+	Intron	INS	-	GTAG	GTAG	rs68080340		TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18276526_18276527insGTAG	uc004cyl.2	-						SCML2_uc004cyk.3_Intron|SCML2_uc010nfd.1_Intron|SCML2_uc011miz.1_Intron|SCML2_uc010nfc.2_Intron	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2						anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)					CCTAAAAATATGTAAATATATT	0.267													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	26274621	26274621	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26274621delA								MAGEB6 (60859 upstream) : VENTXP1 (301833 downstream)																							TTCTCTGGGGAAAAAAAAATA	0.323													3	3	---	---	---	---	
SLC9A7	84679	broad.mit.edu	37	X	46529366	46529367	+	Intron	DEL	TT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46529366_46529367delTT	uc004dgu.1	-						SLC9A7_uc004dgv.1_Intron	NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7						regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2						TATCTGAACATTTCATTTTTAA	0.391													4	2	---	---	---	---	
SLC9A7	84679	broad.mit.edu	37	X	46529371	46529373	+	Intron	DEL	TTT	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46529371_46529373delTTT	uc004dgu.1	-						SLC9A7_uc004dgv.1_Intron	NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7						regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2						GAACATTTCATTTTTAAAAGTTG	0.389													4	2	---	---	---	---	
MAGED1	9500	broad.mit.edu	37	X	51644532	51644533	+	Intron	DEL	TG	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51644532_51644533delTG	uc004dpm.2	+						MAGED1_uc004dpn.2_Intron|MAGED1_uc004dpo.2_Intron	NM_001005332	NP_001005332	Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1 isoform b						apoptosis|induction of apoptosis by extracellular signals|negative regulation of epithelial cell proliferation|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|plasma membrane|protein complex	protein binding			ovary(3)	3	Ovarian(276;0.236)					agtattccattgtgtgtgtgtg	0.015										Multiple Myeloma(10;0.10)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	65181420	65181420	+	IGR	DEL	A	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65181420delA								MSN (219628 upstream) : MIR223 (57292 downstream)																							AAAACAACATAAAAAACAAGG	0.398													4	2	---	---	---	---	
DIAPH2	1730	broad.mit.edu	37	X	95953488	95953488	+	Intron	DEL	T	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:95953488delT	uc004efu.3	+						DIAPH2_uc004eft.3_Intron|DIAPH2_uc004efs.2_Intron	NM_006729	NP_006720	O60879	DIAP2_HUMAN	diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4						TGACAAACTATTTTTGTGTTG	0.393													4	2	---	---	---	---	
SYTL4	94121	broad.mit.edu	37	X	99934109	99934110	+	Intron	INS	-	T	T			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99934109_99934110insT	uc004egd.3	-						SYTL4_uc004egc.2_5'Flank|SYTL4_uc010nnb.2_Intron|SYTL4_uc010nnc.2_Intron|SYTL4_uc004ege.3_Intron|SYTL4_uc004egf.3_Intron	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4						exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCTGTCTGCAGCCCTCCTCTTT	0.436													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139115413	139115414	+	IGR	INS	-	ATC	ATC			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139115413_139115414insATC								CXorf66 (67736 upstream) : SOX3 (469738 downstream)																							ggtgggtatggtggaggtggtg	0.163													5	3	---	---	---	---	
MAMLD1	10046	broad.mit.edu	37	X	149583705	149583706	+	Intron	DEL	CA	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149583705_149583706delCA	uc011mxu.1	+						MAMLD1_uc011mxt.1_Intron			Q13495	MAMD1_HUMAN	RecName: Full=Mastermind-like domain-containing protein 1;          Short=Protein CG1; AltName: Full=F18;						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					tacaaagggccacaaggaaact	0.000													4	2	---	---	---	---	
FLNA	2316	broad.mit.edu	37	X	153587539	153587547	+	Intron	DEL	AGGGATGGC	-	-			TCGA-CW-5588-01A-01D-1534-10	TCGA-CW-5588-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153587539_153587547delAGGGATGGC	uc004fkk.2	-						FLNA_uc011mzn.1_5'Flank|FLNA_uc010nuu.1_Intron	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2						actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GTTGGGGCAAAGGGATGGCGGCTGTATGA	0.627													9	10	---	---	---	---	
