Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	TranscriptID	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq
ABCD2	225	hgsc.bcm.edu;broad.mit.edu	37	12	40013265	40013266	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ABCD2	NM_005164	exon1	c.153_154insA	p.K51fs	TTTTTTCTTCCCG	.	166.0	10.0	163.0	0.0	.	95
ACACB	32	hgsc.bcm.edu;ucsc.edu	37	12	109617830	109617830	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACACB	NM_001093	exon10	c.C1756T	p.Q586X	CGCTTGCAGGTGG	.	157.0	49.0	152.0	0.0	.	98
ACPT	93650	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	51298214	51298214	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACPT	NM_033068	exon10	c.C1158T	p.I386I	TGCCATCCCCCCA	.	163.0	18.0	178.0	0.0	.	90
ACTN2	88	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	236891012	236891012	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACTN2	NM_001103	exon6	c.C571A	p.H191N	CTCATCCACCGAC	.	163.0	27.0	111.0	0.0	.	95
ADAM15	8751	hgsc.bcm.edu;broad.mit.edu	37	1	155029712	155029713	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADAM15	NM_001261464	exon12	c.1227_1228insA	p.E409fs	CCTGGAGAAAGCC	.	157.0	10.0	76.0	0.0	.	651
ADH1A	124	hgsc.bcm.edu;broad.mit.edu	37	4	100205756	100205757	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADH1A	NM_000667	exon5	c.367_368insG	p.T123fs	GCAGGGTCCCCTG	.	181.0	12.0	210.0	0.0	.	227
ADORA3	140	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	112042806	112042806	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADORA3	NM_000677	exon2	c.G723A	p.L241L	CCATGACAGAGCA	.	212.0	58.0	223.0	0.0	.	156
ADRA1B	147	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	159398905	159398905	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADRA1B	NM_000679	exon2	c.G969A	p.L323L	CACCCTGAAGCCC	.	249.0	131.0	238.0	1.0	.	522
AFAP1L2	84632	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	116060312	116060312	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AFAP1L2	NM_032550	exon14	c.G1680T	p.P560P	CAACGTCGGGGAG	.	88.0	43.0	126.0	0.0	.	136
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu	37	9	88247814	88247815	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AGTPBP1	NM_015239	exon14	c.1658_1659insT	p.C553fs	GTGCAGCAAAGCT	.	163.0	13.0	199.0	0.0	.	158
AGXT2L2	85007	hgsc.bcm.edu;broad.mit.edu	37	5	177642304	177642305	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AGXT2L2	NM_153373	exon9	c.1055_1056insA	p.I352fs	TGTTTGATTTTTT	.	246.0	17.0	215.0	0.0	.	91
AHCYL1	10768	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	110561690	110561690	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AHCYL1	NM_006621	exon14	c.G1335C	p.L445F	CAATTTGAGCTGC	.	154.0	70.0	176.0	0.0	.	91
AK5	26289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	77763544	77763544	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AK5	NM_174858	exon5	c.A611G	p.Q204R	TAAAGCAAAAATT	.	155.0	50.0	156.0	0.0	.	227
ALS2CL	259173	ucsc.edu;bcgsc.ca;mdanderson.org	37	3	46722787	46722787	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ALS2CL	NM_001190707	exon13	c.A1385G	p.H462R	TCCCAGTGGCCCG	.	160.0	27.0	270.0	1.0	.	155
ANKRD12	23253	hgsc.bcm.edu;broad.mit.edu	37	18	9255075	9255076	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD12	NM_015208	exon9	c.1810_1811insA	p.E604fs	CATAAGGAAAAAA	.	198.0	14.0	280.0	0.0	.	92
ANKRD26	22852	hgsc.bcm.edu;broad.mit.edu	37	10	27324037	27324038	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD26	NM_014915	exon24	c.3342_3343insA	p.K1114fs	TTGATACTTTTGT	.	178.0	13.0	159.0	0.0	.	138
ANKRD6	22881	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	90333665	90333665	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD6	NM_001242809	exon12	c.T1107G	p.N369K	TCATAATCACCCT	.	175.0	19.0	226.0	0.0	.	93
ANTXR1	84168	broad.mit.edu;bcgsc.ca	37	2	69472525	69472526	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANTXR1	NM_032208	exon18	c.1603_1604insC	p.S535fs	ATCCCGTCCCCAC	.	87.0	9.0	134.0	0.0	.	94
AP1B1	162	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	22	29736737	29736737	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AP1B1	NM_001127	exon14	c.G1906C	p.D636H	CGAGGTCCAGGTT	.	97.0	11.0	92.0	0.0	.	92
AP3B1	8546	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	77412060	77412060	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AP3B1	NM_003664	exon19	c.1969-2A>G	.	TTTGCCTGTTTAA	.	208.0	22.0	155.0	0.0	.	90
APBB1	322	hgsc.bcm.edu;broad.mit.edu	37	11	6423899	6423900	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APBB1	NM_145689	exon7	c.1161_1162insC	p.P387fs	GCGTCCAGGGGCC	.	185.0	11.0	275.0	0.0	.	136
APEX1	328	hgsc.bcm.edu;broad.mit.edu	37	14	20925388	20925389	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APEX1	NM_080648	exon5	c.678_679insA	p.N226fs	GGGGAACAAAAAG	.	169.0	12.0	206.0	0.0	.	661
AQPEP	0	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	5	115298764	115298764	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_173800	exon1	c.C450G	p.F150L	CCTCTTCCAGGAC	.	71.0	16.0	53.0	0.0	.	.
ARHGAP32	9743	hgsc.bcm.edu;broad.mit.edu	37	11	128842442	128842443	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARHGAP32	NM_001142685	exon21	c.3917_3918insC	p.L1306fs	GGGGGAAGGGGAC	.	169.0	11.0	227.0	0.0	.	231
ARHGEF28	64283	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	73153515	73153515	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001080479	exon15	c.C1825A	p.P609T	ATCATACCTGCCA	.	340.0	113.0	300.0	0.0	.	.
ARID2	196528	hgsc.bcm.edu;broad.mit.edu	37	12	46246025	46246026	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARID2	NM_152641	exon15	c.4119_4120insA	p.S1373fs	TTTAAGCAAAAAC	.	198.0	12.0	165.0	0.0	.	100
ARMC9	80210	ucsc.edu;bcgsc.ca;mdanderson.org	37	2	232135735	232135735	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARMC9	NM_025139	exon13	c.T1160G	p.V387G	ACGTGGTGCGGCA	.	290.0	112.0	329.0	2.0	.	91
ATG14	22863	hgsc.bcm.edu;broad.mit.edu	37	14	55844624	55844625	+	Splice_Site	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATG14	NM_014924	exon10	c.1087-2->T	.	ACATGCTAAAAAA	.	197.0	13.0	202.0	0.0	.	90
ATP6V1D	51382	hgsc.bcm.edu;broad.mit.edu	37	14	67819690	67819691	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATP6V1D	NM_015994	exon2	c.109_110insA	p.S37fs	CATCAGATTTTTT	.	184.0	11.0	202.0	0.0	.	659
ATXN3	4287	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	92548653	92548653	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATXN3	NM_004993	exon8	c.A766C	p.S256R	GCATACTTAGCTG	.	149.0	27.0	169.0	0.0	.	522
AUTS2	26053	hgsc.bcm.edu;bcgsc.ca	37	7	70255627	70255627	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AUTS2	NM_015570	exon19	c.3425delA	p.E1142fs	GGCGGGAGCACGA	.	58.0	13.0	66.0	0.0	.	92
AXDND1	126859	hgsc.bcm.edu;broad.mit.edu	37	1	179437688	179437689	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AXDND1	NM_144696	exon17	c.1909_1910insA	p.E637fs	ATAGATGAAAAAA	.	221.0	15.0	149.0	0.0	.	93
B4GALT3	8703	hgsc.bcm.edu;broad.mit.edu	37	1	161143503	161143504	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	B4GALT3	NM_001199873	exon6	c.695_696insC	p.Q232fs	AAGTACTGGGGGT	.	147.0	11.0	130.0	0.0	.	90
BICD1	636	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	32490708	32490708	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BICD1	NM_001714	exon7	c.A2528T	p.Q843L	GCCCACAGACACC	.	105.0	16.0	98.0	0.0	.	153
BRCA1	672	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	41223109	41223109	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BRCA1	NM_007300	exon16	c.G4885A	p.A1629T	ATTCTGCAACTTT	.	262.0	40.0	195.0	0.0	.	3415
BRD2	6046	hgsc.bcm.edu;ucsc.edu	37	6	32948467	32948467	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BRD2	NM_001199455	exon13	c.C2483A	p.S828X	CGTCTTCAGACAC	.	93.0	27.0	136.0	0.0	.	398
BZRAP1	9256	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	56389687	56389687	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BZRAP1	NM_004758	exon17	c.G2495A	p.R832Q	GCCTGTCGCAGCT	.	85.0	15.0	92.0	0.0	.	229
C11orf57	55216	hgsc.bcm.edu;broad.mit.edu	37	11	111953315	111953316	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C11orf57	NM_001082969	exon6	c.501_502insA	p.H167fs	GTCACACAAAAAA	.	242.0	15.0	305.0	0.0	.	155
C11orf86	254439	hgsc.bcm.edu;broad.mit.edu	37	11	66742903	66742904	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C11orf86	NM_001136485	exon1	c.70_71insG	p.W24fs	GAGCCCTGGGGGA	.	178.0	11.0	125.0	0.0	.	68
C2orf42	54980	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	70408519	70408519	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C2orf42	NM_017880	exon3	c.G599A	p.S200N	CCCAAACTGTGCT	.	123.0	19.0	150.0	0.0	.	90
C4BPA	722	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	207318042	207318042	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C4BPA	NM_000715	exon12	c.A1774T	p.T592S	CAATCCACTTTGG	.	150.0	15.0	84.0	0.0	.	154
C6orf141	135398	broad.mit.edu;bcgsc.ca	37	6	49519124	49519125	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145652	exon1	c.619_620insG	p.W207fs	GAACGCTGGGGCC	.	55.0	7.0	78.0	0.0	.	.
CAND2	23066	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	12854821	12854821	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CAND2	NM_001162499	exon7	c.T940G	p.Y314D	CCCAACTACAACT	.	171.0	62.0	250.0	0.0	.	72
CAPN3	825	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	15	42703132	42703132	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CAPN3	NM_000070	exon22	c.G2314A	p.D772N	TACGCAGACAAAC	.	204.0	51.0	240.0	0.0	.	514
CASP8AP2	9994	hgsc.bcm.edu;broad.mit.edu	37	6	90577003	90577004	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CASP8AP2	NM_012115	exon8	c.3994_3995insA	p.E1332fs	TGTACTGAAAAAA	.	168.0	10.0	145.0	0.0	.	24
CBX4	8535	hgsc.bcm.edu;broad.mit.edu	37	17	77808830	77808831	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CBX4	NM_003655	exon5	c.611_612insG	p.A204fs	CCTTTGGCCCCCG	.	206.0	12.0	78.0	0.0	.	228
CCDC141	285025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	179702272	179702272	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCDC141	NM_173648	exon23	c.C3674T	p.S1225F	AGAGGGGACTCAG	.	103.0	14.0	111.0	0.0	.	78
CCDC146	57639	broad.mit.edu;bcgsc.ca	37	7	76889333	76889334	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCDC146	NM_020879	exon8	c.766_767insA	p.E256fs	GAAATGGAAAAGA	.	91.0	9.0	123.0	0.0	.	70
CCDC168	643677	hgsc.bcm.edu;broad.mit.edu	37	13	103396690	103396691	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001146197	exon4	c.6357_6358insA	p.N2119fs	TTGTAAGTTTTTT	.	155.0	10.0	177.0	0.0	.	.
CCDC168	643677	hgsc.bcm.edu;broad.mit.edu	37	13	103397069	103397070	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001146197	exon4	c.5978_5979insA	p.M1993fs	GTTAACATTTTTT	.	188.0	15.0	220.0	0.0	.	.
CCR2	729230	ucsc.edu;bcgsc.ca	37	3	46399449	46399449	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCR2	NM_001123041	exon2	c.A431G	p.H144R	TTGTCCATGCTGT	.	387.0	75.0	501.0	1.0	.	568
CDC37L1	55664	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	4706065	4706065	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDC37L1	NM_017913	exon7	c.G967A	p.V323M	AACTCGGTGGTAC	.	269.0	58.0	291.0	0.0	.	90
CDK12	51755	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	37627327	37627327	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDK12	NM_016507	exon2	c.G1242C	p.K414N	AGCAAAGATGGAT	.	174.0	26.0	119.0	0.0	.	1055
CDK12	51755	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	37687306	37687306	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDK12	NM_016507	exon14	c.C4210T	p.R1404C	GACCTCCGTTTTG	.	112.0	13.0	138.0	0.0	.	1055
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu	37	22	46930690	46930691	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CELSR1	NM_014246	exon1	c.2378_2379insC	p.H793fs	GTGTAATGGGAGC	.	167.0	10.0	139.0	0.0	.	525
CEP85L	387119	hgsc.bcm.edu;broad.mit.edu	37	6	118886846	118886847	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001178035	exon4	c.875_876insT	p.P292fs	TGAATGGGAACTC	.	300.0	27.0	287.0	0.0	.	.
CFTR	1080	broad.mit.edu;bcgsc.ca	37	7	117232304	117232305	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CFTR	NM_000492	exon14	c.2083_2084insA	p.E695fs	TTTGGGGAAAAAA	.	79.0	9.0	67.0	0.0	.	518
CLASP2	23122	ucsc.edu;bcgsc.ca	37	3	33626378	33626378	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CLASP2	NM_015097	exon22	c.G2106C	p.L702L	TGTGGTCAGAACT	.	194.0	47.0	204.0	1.0	.	93
CMIP	80790	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	81736275	81736275	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_198390	exon17	c.1944+1G>A	.	TCCACAGTGAGTT	.	722.0	368.0	934.0	2.0	.	.
CMTM1	113540	hgsc.bcm.edu;broad.mit.edu	37	16	66600574	66600575	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CMTM1	NM_181268	exon1	c.158_159insC	p.H53fs	GGAAGCACCCCGC	.	139.0	10.0	209.0	0.0	.	90
CNTLN	54875	broad.mit.edu;ucsc.edu	37	9	17457520	17457520	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CNTLN	NM_017738	exon19	c.3115-2A>G	.	AAAAAAAGAAGCT	.	81.0	5.0	81.0	0.0	.	91
COL14A1	7373	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	121326235	121326235	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL14A1	NM_021110	exon38	c.G4520A	p.G1507E	CTCAAGGACCAAG	.	204.0	86.0	263.0	1.0	.	543
COL7A1	1294	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	48608550	48608550	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL7A1	NM_000094	exon93	c.G7148A	p.G2383D	GGAGGGCCAGGAG	.	99.0	24.0	125.0	0.0	.	160
CPEB3	22849	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	10	93999727	93999727	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CPEB3	NM_014912	exon2	c.C381T	p.I127I	TGGGGTGATCCCC	.	71.0	18.0	76.0	0.0	.	90
CPNE5	57699	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	36710124	36710124	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CPNE5	NM_020939	exon21	c.1703delC	p.P568fs	GCGGGTGGGGGAC	.	93.0	23.0	111.0	0.0	.	91
CTBP1	1487	bcgsc.ca;mdanderson.org	37	4	1206151	1206151	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CTBP1	NM_001328	exon9	c.C1200T	p.I400I	GGGGACGATACCT	.	57.0	11.0	92.0	2.0	.	91
CUBN	8029	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	17169924	17169924	+	Splice_Site	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CUBN	NM_001081	exon4	c.253-1G>C	.	CTGGATCTAATTT	.	104.0	23.0	104.0	0.0	.	166
CYFIP2	26999	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	156714055	156714055	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYFIP2	NM_001037332	exon3	c.A145G	p.R49G	GAGGACAGGAATG	.	182.0	104.0	102.0	0.0	.	22
CYLC1	1538	hgsc.bcm.edu;broad.mit.edu	37	X	83128980	83128981	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	CYLC1,NS,malignant_melanoma,0	CYLC1	NM_021118	exon4	c.1264_1265insA	p.E422fs	AAAGATGAAAAAA	.	149.0	10.0	136.0	0.0	.	112
CYLC2	1539	hgsc.bcm.edu;broad.mit.edu	37	9	105767323	105767324	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYLC2	NM_001340	exon5	c.410_411insA	p.G137fs	AACAAGGAAAAAA	.	208.0	13.0	244.0	0.0	.	91
CYP2A7	1549	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	41387943	41387943	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYP2A7	NM_000764	exon1	c.T173C	p.I58T	TTCATGATGGAGT	.	375.0	179.0	409.0	1.0	.	93
DCAF5	8816	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	69584924	69584924	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DCAF5	NM_003861	exon4	c.A467G	p.N156S	AAAATGTTGTCAT	.	90.0	16.0	125.0	0.0	.	91
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	155157446	155157447	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DCHS2	NM_017639	exon25	c.6992_6993del	p.2331_2331del	TATGGTAGAGGAA	.	227.0	0.0	191.0	0.0	.	94
DDN	23109	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	49391730	49391730	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DDN	NM_015086	exon2	c.G929C	p.G310A	CCCTTGCCGGGCT	.	100.0	16.0	101.0	0.0	.	90
DGKG	1608	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	185969660	185969660	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DGKG	NM_001346	exon19	c.G1649A	p.S550N	AAGGGGCTCTGCT	.	145.0	28.0	220.0	0.0	.	714
DLAT	1737	broad.mit.edu;bcgsc.ca	37	11	111896425	111896426	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DLAT	NM_001931	exon1	c.229_230insT	p.L77fs	CTGCAGCTTTTGG	.	93.0	9.0	114.0	0.0	.	226
DLK2	65989	hgsc.bcm.edu;broad.mit.edu	37	6	43418412	43418413	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DLK2	NM_206539	exon6	c.1017_1018insC	p.P339fs	GGGTCCAGGGGGG	.	143.0	11.0	182.0	0.0	.	68
DNAH2	146754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	7701533	7701533	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH2	NM_020877	exon53	c.C8289T	p.I2763I	GGGTATCGGGGGC	.	46.0	30.0	86.0	0.0	.	102
DNAH5	1767	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	13727745	13727745	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH5	NM_001369	exon70	c.G11904A	p.M3968I	TTTCCACATTTTC	.	354.0	118.0	320.0	0.0	.	182
DNAH6	1768	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	2	84774640	84774640	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH6	NM_001370	exon7	c.C1090T	p.R364X	GAATTTCGAAATG	.	358.0	149.0	353.0	1.0	.	69
DOT1L	84444	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	2202716	2202716	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DOT1L	NM_032482	exon9	c.A725G	p.N242S	TGAATAATTTTGC	.	288.0	198.0	346.0	0.0	.	132
DPM2	8818	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	130699764	130699764	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DPM2	NM_003863	exon2	c.C42T	p.V14V	AACGGCGACGAGG	.	129.0	59.0	147.0	1.0	.	90
DPY19L1	23333	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	35050986	35050986	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DPY19L1	NM_015283	exon5	c.C407T	p.T136M	GTAACCGTCCAAC	.	367.0	69.0	364.0	0.0	.	68
DRD5	1816	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	4	9784569	9784569	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DRD5	NM_000798	exon1	c.G916A	p.V306M	GTCTTCGTGTGTT	.	49.0	8.0	66.0	0.0	.	91
DYNC1LI2	1783	broad.mit.edu;bcgsc.ca	37	16	66761590	66761591	+	Splice_Site	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DYNC1LI2	NM_006141	exon12	c.1261+1->A	.	TACATACTTTTGA	.	65.0	7.0	80.0	0.0	.	93
EBLN2	55096	hgsc.bcm.edu;broad.mit.edu	37	3	73111508	73111509	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_018029	exon1	c.276_277insC	p.E92fs	ATTGGAACCCCAA	.	148.0	11.0	151.0	0.0	.	.
EBLN2	55096	hgsc.bcm.edu;broad.mit.edu	37	3	73111541	73111542	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_018029	exon1	c.309_310insA	p.I103fs	GGACATTAAAAAA	.	195.0	13.0	231.0	0.0	.	.
ELF1	1997	hgsc.bcm.edu;broad.mit.edu	37	13	41507921	41507922	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ELF1	NM_172373	exon9	c.1500_1501insG	p.G500fs	GGCAGGGCCCAAG	.	179.0	11.0	207.0	0.0	.	227
ELN	2006	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	7	73459566	73459566	+	Missense_Mutation	SNP	G	G	T	rs139718810	alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ELN	NM_001081753	exon10	c.G499T	p.G167C	TTCCCCGGTGTGG	.	59.0	21.0	48.0	0.0	G|1.000;A|0.000	95
EPG5	57724	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	18	43458391	43458391	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EPG5	NM_020964	exon34	c.A5892G	p.V1964V	AATGATTACTGAA	.	113.0	12.0	80.0	0.0	.	580
ERAP1	51752	hgsc.bcm.edu;broad.mit.edu	37	5	96132948	96132949	+	In_Frame_Ins	INS	-	-	TCATCTTCA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERAP1	NM_001198541	exon4	c.728_729insTGAAGATGA	p.S243delinsMKMS	TAGGTGCTCATCT	.	239.0	20.0	281.0	0.0	.	70
ERI2	112479	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	20810230	20810230	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERI2	NM_001142725	exon9	c.A892G	p.I298V	CACAAATTGACTT	.	605.0	189.0	427.0	0.0	.	153
ERMAP	114625	hgsc.bcm.edu;broad.mit.edu	37	1	43304572	43304573	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERMAP	NM_018538	exon7	c.617_618insA	p.G206fs	TTTTAGGAAAACT	.	182.0	12.0	186.0	0.0	.	91
ESCO1	114799	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	18	19112484	19112484	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ESCO1	NM_052911	exon11	c.C2325T	p.F775F	CATGCTGAATACC	.	229.0	155.0	285.0	0.0	.	90
ETV3L	440695	hgsc.bcm.edu;broad.mit.edu	37	1	157067713	157067714	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ETV3L	NM_001004341	exon4	c.554_555insC	p.R185fs	GGCCCTCGGGGGG	.	184.0	11.0	169.0	0.0	.	228
EVPL	2125	broad.mit.edu;bcgsc.ca	37	17	74003866	74003867	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EVPL	NM_001988	exon22	c.5420_5421insC	p.Q1807fs	GTGCTCTGGGGGG	.	131.0	13.0	133.0	0.0	.	93
EZH1	2145	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	40871173	40871173	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EZH1	NM_001991	exon8	c.A717G	p.A239A	GGCAATTGCACTG	.	325.0	45.0	266.0	0.0	.	229
F13A1	2162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	6145912	6145912	+	Silent	SNP	G	G	A	rs200672690		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	F13A1	NM_000129	exon15	c.C2139T	p.D713D	CAGGGAGTCACTG	.	144.0	61.0	171.0	0.0	G|0.999;A|0.001	519
F8	2157	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	154158684	154158684	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	F8	NM_000132	exon14	c.G3381C	p.W1127C	TTGTATCCACCTT	.	165.0	28.0	149.0	0.0	.	182
FADS6	283985	broad.mit.edu;mdanderson.org	37	17	72889516	72889516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FADS6	NM_178128	exon1	c.G178A	p.A60T	GCAAGGCGAAGAG	.	32.0	6.0	25.0	0.0	.	22
FAM107B	83641	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	14563197	14563197	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM107B	NM_031453	exon5	c.G913T	p.E305X	AGGACTCCTGGGC	.	140.0	30.0	200.0	0.0	.	156
FAM160A2	84067	hgsc.bcm.edu;broad.mit.edu	37	11	6238840	6238841	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM160A2	NM_032127	exon9	c.2018_2019insG	p.E673fs	AGCAGTTCCCCAG	.	157.0	11.0	297.0	0.0	.	92
FANCD2	2177	hgsc.bcm.edu;bcgsc.ca	37	3	10108913	10108913	+	Missense_Mutation	SNP	G	G	T	rs80258959	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FANCD2	NM_001018115	exon26	c.G2406T	p.Q802H	CTGCCAGGAAACA	.	114.0	12.0	109.0	0.0	G|0.990;T|0.010	229
FANCD2	2177	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	10108898	10108898	+	Silent	SNP	A	A	G	rs77246387	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FANCD2	NM_001018115	exon26	c.A2391G	p.V797V	GATTGTAAATGCC	.	106.0	13.0	96.0	0.0	A|0.909;G|0.091	229
FGD3	89846	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	95796931	95796931	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FGD3	NM_001083536	exon17	c.C1894T	p.P632S	TCAGATCCCCAGG	.	73.0	22.0	112.0	0.0	.	228
FGD4	121512	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	32760995	32760995	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FGD4	NM_139241	exon8	c.G1098A	p.L366L	GAAATTGCCTCCT	.	328.0	107.0	344.0	0.0	.	229
FILIP1L	11259	hgsc.bcm.edu;broad.mit.edu	37	3	99568989	99568990	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FILIP1L	NM_001042459	exon5	c.1531_1532insA	p.L511fs	TCTTTAATTTTTC	.	232.0	15.0	276.0	0.0	.	45
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu	37	2	186673386	186673387	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FSIP2	NM_173651	exon17	c.19620_19621insA	p.P6540fs	CTTTCCTAAAAAA	.	167.0	12.0	132.0	0.0	.	90
FUBP1	8880	hgsc.bcm.edu;ucsc.edu	37	1	78429797	78429797	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FUBP1	NM_003902	exon12	c.C991T	p.R331X	GACATCGGTCTGG	.	602.0	219.0	645.0	0.0	.	227
GLA	2717	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	100655664	100655678	+	In_Frame_Del	DEL	GGCCACATATAAAGA	GGCCACATATAAAGA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGCCACATATAAAGA	GGCCACATATAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GLA	NM_000169	exon4	c.615_629del	p.205_210del	TGAAAGGGCCACA	.	111.0	11.0	115.0	0.0	.	130
GLI2	2736	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	121726367	121726367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GLI2	NM_005270	exon5	c.G721A	p.A241T	TCAGACGCCAGCC	.	94.0	13.0	132.0	0.0	.	954
GP6	51206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	55539031	55539040	+	Frame_Shift_Del	DEL	GCTGTGGGCG	GCTGTGGGCG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GCTGTGGGCG	GCTGTGGGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GP6	NM_016363	exon4	c.516_525del	p.172_175del	GGTTCCGCTGTGG	.	82.0	11.0	109.0	0.0	.	92
GRINA	2907	broad.mit.edu;bcgsc.ca	37	8	145065553	145065554	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GRINA	NM_001009184	exon2	c.162_163insC	p.Q54fs	CGGTCAGCCAGGG	.	79.0	8.0	85.0	0.0	.	90
GUCY1A2	2977	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	106810544	106810544	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GUCY1A2	NM_000855	exon4	c.C848A	p.P283Q	TTGCCTGGGTTTG	.	94.0	22.0	118.0	0.0	.	589
GUF1	60558	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	44692732	44692732	+	Splice_Site	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GUF1	NM_021927	exon12	c.1336-2A>T	.	ATTTTTAGGAACA	.	240.0	103.0	248.0	0.0	.	91
HCN3	57657	hgsc.bcm.edu;bcgsc.ca	37	1	155255629	155255629	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HCN3	NM_020897	exon6	c.C1351A	p.P451T	TTCCAGCCGGGGG	.	401.0	36.0	184.0	0.0	.	154
HECW2	57520	hgsc.bcm.edu;bcgsc.ca	37	2	197183465	197183465	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HECW2	NM_020760	exon9	c.G2149C	p.D717H	CTTCATCCTCCCC	.	127.0	9.0	163.0	0.0	.	668
HEPHL1	341208	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	93822053	93822053	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HEPHL1	NM_001098672	exon12	c.C2213A	p.A738D	ACATCGCCGCTGA	.	83.0	17.0	106.0	0.0	.	71
HEPHL1	341208	ucsc.edu;bcgsc.ca	37	11	93822054	93822054	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HEPHL1	NM_001098672	exon12	c.C2214A	p.A738A	CATCGCCGCTGAA	.	83.0	17.0	106.0	1.0	.	71
HFM1	164045	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	91742607	91742607	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HFM1	NM_001017975	exon31	c.G3404C	p.S1135T	TTTTTGCTGGCAG	.	292.0	90.0	294.0	0.0	.	112
HFM1	164045	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	91742600	91742600	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HFM1	NM_001017975	exon31	c.3411delA	p.K1137fs	CCCAGGTTTTTTG	.	317.0	77.0	317.0	0.0	.	112
HGSNAT	138050	broad.mit.edu;bcgsc.ca	37	8	43002098	43002099	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HGSNAT	NM_152419	exon2	c.126_127insA	p.D42fs	CTTAGACAAAAAA	.	82.0	9.0	100.0	0.0	.	68
HIST1H2BM	8342	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	27782957	27782957	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIST1H2BM	NM_003521	exon1	c.C136G	p.L46V	AAGGTGCTGAAGC	.	192.0	76.0	266.0	0.0	.	131
HIST1H4D	8360	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	26189253	26189253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIST1H4D	NM_003539	exon1	c.C52T	p.R18C	GGTGACGCTTGGC	.	75.0	30.0	64.0	0.0	.	68
HIVEP2	3097	hgsc.bcm.edu;broad.mit.edu	37	6	143094744	143094745	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIVEP2	NM_006734	exon5	c.1132_1133insA	p.G378fs	CTTGTCCTTTTTT	.	299.0	18.0	284.0	0.0	.	95
HOXC10	3226	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	54382990	54382990	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HOXC10	NM_017409	exon2	c.G789A	p.L263L	TTGGCTGACAGCA	.	200.0	25.0	220.0	0.0	.	91
HOXC8	3224	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	54404963	54404963	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HOXC8	NM_022658	exon2	c.G527C	p.R176P	TGACACGAAAACG	.	116.0	20.0	105.0	0.0	.	91
HSPB2	3316	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	111784239	111784239	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSPB2	NM_001541	exon2	c.G169A	p.G57R	CCAGCTGGGGAGG	.	50.0	10.0	54.0	0.0	.	659
IL17C	27189	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	88705412	88705412	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IL17C	NM_013278	exon2	c.G30A	p.L10L	GTTTCTGACCTGG	.	142.0	23.0	185.0	0.0	.	90
IL6R	3570	hgsc.bcm.edu;broad.mit.edu	37	1	154437759	154437760	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IL6R	NM_000565	exon10	c.1310_1311insG	p.L437fs	GCAGCCTGGGGTC	.	172.0	11.0	158.0	0.0	.	229
IPO7	10527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	9463685	9463693	+	In_Frame_Del	DEL	AACAAAGAA	AACAAAGAA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AACAAAGAA	AACAAAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IPO7	NM_006391	exon24	c.2960_2968del	p.987_990del	ATGAAGAACAAAG	.	314.0	0.0	361.0	0.0	.	271
ITGAV	3685	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	187540361	187540361	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ITGAV	NM_002210	exon27	c.G2737T	p.V913F	AAGATTGTCTGCC	.	291.0	88.0	253.0	0.0	.	653
JAG2	3714	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	14	105609430	105609430	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	JAG2	NM_002226	exon26	c.C3319T	p.R1107C	GCTTGCGTGTCCA	.	14.0	7.0	27.0	0.0	.	846
JAK2	3717	hgsc.bcm.edu;broad.mit.edu	37	9	5069192	5069193	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	JAK2	NM_004972	exon11	c.1497_1498insC	p.C499fs	ATGCTGTCCCCCA	.	178.0	12.0	195.0	0.0	.	75307
KAT6B	23522	hgsc.bcm.edu;broad.mit.edu	37	10	76735587	76735588	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_012330	exon8	c.1492_1493insC	p.T498fs	CCCCCAACCCCCA	.	118.0	10.0	130.0	0.0	.	.
KBTBD13	390594	broad.mit.edu;bcgsc.ca;mdanderson.org	37	15	65369217	65369217	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001101362	exon1	c.C64T	p.R22C	GCCGACCGCGCCC	.	25.0	14.0	21.0	0.0	.	.
KCNH2	3757	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	7	150671893	150671893	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNH2	NM_000238	exon2	c.G213T	p.G71G	GCGCGGCCCGTGC	.	61.0	17.0	21.0	0.0	.	94
KCNN3	3782	hgsc.bcm.edu;broad.mit.edu	37	1	154842187	154842188	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNN3	NM_001204087	exon1	c.254_255insC	p.L85fs	TGAGACAGGGGAT	.	149.0	10.0	66.0	0.0	.	91
KCTD4	386618	hgsc.bcm.edu;broad.mit.edu	37	13	45768382	45768383	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCTD4	NM_198404	exon2	c.321_322insA	p.N107fs	AAGTTGATTTTCT	.	175.0	11.0	241.0	0.0	.	90
KDR	3791	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	55976873	55976873	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KDR	NM_002253	exon8	c.C1039T	p.R347C	TGACACGCTCCCC	.	268.0	113.0	333.0	0.0	.	2298
KIAA1147	57189	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	141362636	141362636	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1147	NM_001080392	exon9	c.A1188C	p.Q396H	GTTGTTTTGTTCT	.	118.0	39.0	99.0	0.0	.	69
KIAA1614	57710	broad.mit.edu;bcgsc.ca	37	1	180904976	180904977	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1614	NM_020950	exon5	c.1931_1932insC	p.S644fs	GCAGCAGCCCGCG	.	77.0	9.0	60.0	0.0	.	26
KIAA1755	85449	hgsc.bcm.edu;broad.mit.edu	37	20	36869926	36869927	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1755	NM_001029864	exon3	c.607_608insG	p.P203fs	GAAGGGGCCCCCA	.	181.0	11.0	198.0	0.0	.	95
KLHL10	317719	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	40004434	40004434	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KLHL10	NM_152467	exon5	c.A1702C	p.S568R	GCTCTGAGCTGCT	.	387.0	200.0	270.0	0.0	.	227
KLHL11	55175	hgsc.bcm.edu;bcgsc.ca	37	17	40010740	40010740	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KLHL11	NM_018143	exon2	c.G1379A	p.G460E	CCATGTCCTCCAA	.	498.0	45.0	350.0	0.0	.	90
KNTC1	9735	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	123097712	123097712	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KNTC1	NM_014708	exon54	c.T5676G	p.C1892W	TCAGTGTCTCTTC	.	177.0	63.0	158.0	0.0	.	543
KRT78	196374	broad.mit.edu;bcgsc.ca	37	12	53242576	53242577	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KRT78	NM_173352	exon1	c.139_140insG	p.C47fs	CCAGGCACCCCCC	.	79.0	8.0	96.0	0.0	.	188
KRTAP5-1	387264	hgsc.bcm.edu;broad.mit.edu	37	11	1605983	1605984	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KRTAP5-1	NM_001005922	exon1	c.497_498insG	p.A166fs	CCACAGGCCCCCT	.	135.0	11.0	248.0	0.0	.	44
LAMA3	3909	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	21331052	21331052	+	Silent	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LAMA3	NM_001127717	exon5	c.G855T	p.R285R	TCGGCGGGTGAGT	.	111.0	28.0	161.0	0.0	.	100
LAMB4	22798	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	107763585	107763585	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LAMB4	NM_007356	exon2	c.T25C	p.L9L	GGTGCAAAAAAAG	.	147.0	60.0	147.0	0.0	.	140
LARP7	51574	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	113568542	113568542	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LARP7	NM_001267039	exon9	c.A855T	p.K285N	GAAAAAACGGGAC	.	248.0	120.0	273.0	0.0	.	93
LCE1C	353133	hgsc.bcm.edu;broad.mit.edu	37	1	152777757	152777758	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LCE1C	NM_178351	exon2	c.198_199insG	p.G66fs	GCAGCATCCCCCA	.	161.0	12.0	150.0	0.0	.	90
LRP11	84918	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	150174142	150174142	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LRP11	NM_032832	exon2	c.G768A	p.M256I	TACCTTCATGTCC	.	146.0	57.0	199.0	0.0	.	90
MC5R	4161	ucsc.edu;bcgsc.ca;mdanderson.org	37	18	13826422	13826422	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MC5R	NM_005913	exon1	c.G658A	p.A220T	CGGATCGCGGCTC	.	138.0	42.0	214.0	1.0	.	526
MED12L	116931	broad.mit.edu;bcgsc.ca	37	3	151148162	151148163	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MED12L	NM_053002	exon42	c.6379_6380insT	p.L2127fs	AAGCAGCTTTCCA	.	72.0	7.0	94.0	0.0	.	576
MEF2A	4205	broad.mit.edu;bcgsc.ca	37	15	100252792	100252792	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MEF2A	NM_005587	exon11	c.G1316T	p.R439L	AGCCCCGACAGGA	.	36.0	7.0	51.0	0.0	.	455
MFF	56947	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	228220420	228220420	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MFF	NM_020194	exon10	c.C840T	p.T280T	TACAACCATTGAA	.	372.0	127.0	350.0	0.0	.	153
MIR122	406906	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	56118310	56118312	+	RNA	DEL	AGC	AGC	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	TTCCTTAGCAGAG	.	71.0	39.0	133.0	0.0	.	.
MIR92B	693235	hgsc.bcm.edu;broad.mit.edu	37	1	155165011	155165012	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	AGTGTTGTTTTTT	.	263.0	17.0	46.0	0.0	.	.
MLEC	9761	broad.mit.edu;bcgsc.ca	37	12	121134204	121134205	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MLEC	NM_014730	exon5	c.735_736insA	p.L245fs	TAATCTCAAAAAA	.	68.0	7.0	83.0	0.0	.	91
MLL2	8085	hgsc.bcm.edu;broad.mit.edu	37	12	49425625	49425626	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MLL2	NM_003482	exon39	c.12863_12864insC	p.R4288fs	GGGAGCCGGGGTG	.	165.0	11.0	239.0	0.0	.	612
MSLN	10232	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	812697	812697	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MSLN	NM_005823	exon3	c.C17G	p.A6G	CAACGGCTCGACC	.	159.0	29.0	131.0	0.0	.	91
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11303173	11303173	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MTOR	NM_004958	exon9	c.T1410C	p.H470H	TTACTTATGGGCG	.	40.0	24.0	67.0	0.0	.	1439
MYL4	4635	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	45299202	45299202	+	Silent	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYL4	NM_001002841	exon5	c.G468C	p.R156R	GCTTCGGCACGTC	.	167.0	83.0	144.0	0.0	.	92
MYO10	4651	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	16701663	16701663	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYO10	NM_012334	exon25	c.C2841T	p.F947F	CTCGTCGAAATTG	.	83.0	33.0	114.0	0.0	.	3
MYPN	84665	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	69881741	69881741	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYPN	NM_001256267	exon3	c.G546T	p.K182N	CCACAAGAGTAAA	.	85.0	22.0	111.0	0.0	.	95
NANOGNB	360030	hgsc.bcm.edu;broad.mit.edu	37	12	7922711	7922712	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145465	exon2	c.235_236insA	p.E79fs	AAAGAAGAAAAAA	.	163.0	10.0	156.0	0.0	.	.
NAPA	8775	hgsc.bcm.edu;broad.mit.edu	37	19	47995348	47995349	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NAPA	NM_003827	exon8	c.590_591insC	p.L197fs	TTGAGGAGGGGGC	.	158.0	13.0	145.0	0.0	.	90
NBAS	51594	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	15519748	15519748	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NBAS	NM_015909	exon30	c.G3568T	p.D1190Y	AGCTATCAGTGAG	.	334.0	44.0	337.0	0.0	.	94
NCOA1	8648	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	2	24991260	24991260	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NCOA1	NM_003743	exon21	c.A4326T	p.X1442Y	TGAATAACCACTT	.	81.0	17.0	102.0	0.0	.	228
NELFE	7936	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	31921602	31921602	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_002904	exon10	c.G949C	p.G317R	GGGTCCCGTTGAG	.	327.0	65.0	251.0	0.0	.	.
NFATC3	4775	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	16	68224766	68224766	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NFATC3	NM_173163	exon9	c.G2194C	p.D732H	TCCTCTGATTCAG	.	185.0	14.0	217.0	0.0	.	92
NGF	4803	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	115829018	115829018	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NGF	NM_002506	exon3	c.C399T	p.F133F	CACCGAGAATTCG	.	144.0	60.0	158.0	0.0	.	1083
NLGN1	22871	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	173998709	173998709	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLGN1	NM_014932	exon7	c.C2088T	p.A696A	TGCAGCCCTGTAC	.	121.0	56.0	142.0	0.0	.	231
NLRP1	22861	hgsc.bcm.edu;broad.mit.edu	37	17	5462267	5462268	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLRP1	NM_014922	exon4	c.1749_1750insA	p.K583fs	AAGGGTCTTTTTT	.	158.0	11.0	219.0	0.0	.	274
NLRP2	55655	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	55508705	55508705	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLRP2	NM_017852	exon12	c.C2900G	p.P967R	CCATCCCTCCGTT	.	319.0	96.0	313.0	0.0	.	120
NT5C1B-RDH14	100526794	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	18736770	18736770	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001199103	exon9	c.G1640A	p.R547H	AAGCGGCGGGCTA	.	187.0	33.0	146.0	0.0	.	.
NUDT17	200035	hgsc.bcm.edu;broad.mit.edu	37	1	145587383	145587384	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NUDT17	NM_001012758	exon6	c.697_698insC	p.G233fs	GAAGTCCGGGTGT	.	127.0	10.0	97.0	0.0	.	90
NXPH1	30010	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	8791057	8791057	+	Silent	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NXPH1	NM_152745	exon3	c.T474A	p.T158T	TTCAACTGGTCAA	.	144.0	41.0	128.0	0.0	.	69
OR10A2	341276	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	6891840	6891840	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR10A2	NM_001004460	exon1	c.G855T	p.K285N	GGTGAAGAATGCC	.	127.0	43.0	202.0	0.0	.	113
OR10A7	121364	broad.mit.edu;bcgsc.ca	37	12	55614789	55614810	+	Frame_Shift_Del	DEL	GAGAGAAACTCATCTAAGATAT	GAGAGAAACTCATCTAAGATAT	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GAGAGAAACTCATCTAAGATAT	GAGAGAAACTCATCTAAGATAT	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR10A7	NM_001005280	wholegene			TTTTTAGAGAGAA	.	243.0	0.0	227.0	0.0	.	72
OR2A12	346525	hgsc.bcm.edu;broad.mit.edu	37	7	143792820	143792821	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2A12	NM_001004135	exon1	c.620_621insG	p.V207fs	TCTTAGTGGGGCC	.	143.0	11.0	133.0	0.0	.	92
OR2B11	127623	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	247614658	247614658	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2B11	NM_001004492	exon1	c.C627A	p.F209L	CACGAAGAAGGCC	.	111.0	34.0	93.0	0.0	.	69
OR2C1	4993	hgsc.bcm.edu;bcgsc.ca	37	16	3406154	3406154	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2C1	NM_012368	exon1	c.G214A	p.A72T	GACCTTGCTTTCG	.	520.0	34.0	292.0	0.0	.	69
OR5D13	390142	hgsc.bcm.edu;ucsc.edu	37	11	55541187	55541187	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR5D13	NM_001001967	exon1	c.A274T	p.R92X	GAATACAGAACCA	.	525.0	110.0	638.0	0.0	.	71
OR5D16	390144	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	55606431	55606431	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR5D16	NM_001005496	exon1	c.C204A	p.L68L	CCACCTCTCCTTT	.	407.0	89.0	511.0	0.0	.	73
OR6C4	341418	hgsc.bcm.edu;broad.mit.edu	37	12	55945306	55945307	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6C4	NM_001005494	exon1	c.296_297insT	p.Y99fs	CTCAGTATTTTTT	.	218.0	18.0	206.0	0.0	.	68
OR6S1	341799	broad.mit.edu;bcgsc.ca	37	14	21109759	21109760	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6S1	NM_001001968	exon1	c.92_93insT	p.S31fs	AACACAGAAAATA	.	74.0	8.0	103.0	0.0	.	70
OR6X1	390260	hgsc.bcm.edu;broad.mit.edu	37	11	123624382	123624383	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6X1	NM_001005188	exon1	c.845_846insC	p.L282fs	TTCAGAAGGGGGG	.	144.0	10.0	168.0	0.0	.	71
ORC1	4998	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	52859445	52859445	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ORC1	NM_004153	exon6	c.C752A	p.T251N	CATGAAGTCTGCT	.	104.0	39.0	70.0	0.0	.	206
OTP	23440	ucsc.edu;bcgsc.ca;mdanderson.org	37	5	76932769	76932769	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OTP	NM_032109	exon2	c.G324C	p.R108R	GCGCGTCCGGTGG	.	97.0	14.0	111.0	1.0	.	69
PA2G4	5036	bcgsc.ca;mdanderson.org	37	12	56500791	56500791	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PA2G4	NM_006191	exon3	c.A235G	p.S79G	CCCACCAGCATTT	.	300.0	42.0	316.0	1.0	.	68
PANK4	55229	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	2452651	2452651	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PANK4	NM_018216	exon3	c.G311C	p.C104S	TCCAGGCAGGCTT	.	312.0	54.0	299.0	0.0	.	158
PARD3	56288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	34400172	34400172	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PARD3	NM_019619	exon25	c.G3996A	p.V1332V	GGGGGGCACATCT	.	101.0	53.0	150.0	0.0	.	92
PCDH15	65217	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	10	56128943	56128943	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCDH15	NM_001142763	exon6	c.G426A	p.V142V	GTCTCTCACCACT	.	136.0	24.0	162.0	0.0	.	193
PCDHGA10	56106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140793274	140793274	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_032090	exon1	c.C532T	p.P178S	CTCAGCCCCAATA	.	72.0	13.0	72.0	0.0	.	.
PCDHGC3	5098	hgsc.bcm.edu;bcgsc.ca	37	5	140855947	140855947	+	Silent	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCDHGC3	NM_032402	exon1	c.G264C	p.V88V	GTTTGTGAACGAC	.	175.0	27.0	168.0	0.0	.	24
PCNT	5116	hgsc.bcm.edu;broad.mit.edu	37	21	47819683	47819684	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCNT	NM_006031	exon25	c.4764_4765insA	p.Q1588fs	AAAACAGAAAAAC	.	207.0	13.0	237.0	0.0	.	141
PCNXL2	80003	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	233137318	233137318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCNXL2	NM_014801	exon29	c.G5062A	p.A1688T	CTGGAGCTACAAC	.	354.0	89.0	313.0	1.0	.	91
PDLIM2	64236	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	8	22438952	22438952	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PDLIM2	NM_021630	exon3	c.A904G	p.I302V	GTGGCCATCAACG	.	82.0	25.0	261.0	0.0	.	90
PGAM1	5223	broad.mit.edu;bcgsc.ca	37	10	99190813	99190814	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PGAM1	NM_002629	exon3	c.516_517insC	p.V172fs	AATAGTTCCCCAG	.	262.0	11.0	340.0	0.0	.	226
PI4KAP2	375133	hgsc.bcm.edu;broad.mit.edu	37	22	21838338	21838339	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PI4KAP2	.	.	.	.	ATCAAACCCCCGC	.	138.0	12.0	115.0	0.0	.	68
PIAS4	51588	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	19	4037690	4037690	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PIAS4	NM_015897	exon11	c.C1350T	p.G450G	TGGCGGCGGCCCG	.	68.0	37.0	33.0	0.0	.	659
PIK3CA	5290	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	bycluster	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	PIK3CA,bladder,carcinoma,0	PIK3CA	NM_006218	exon10	c.G1633A	p.E545K	ATCACTGAGCAGG	.	460.0	90.0	497.0	1.0	.	27752
PJA1	64219	hgsc.bcm.edu;broad.mit.edu	37	X	68382256	68382257	+	Nonsense_Mutation	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PJA1	NM_145119	exon2	c.826_827insT	p.D276_T277delinsX	CAGTATCAAAAAA	.	152.0	11.0	127.0	0.0	.	130
PLCG1	5335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	39794969	39794969	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLCG1	NM_182811	exon17	c.C1935T	p.R645R	CCTGCGCTGTAAT	.	95.0	18.0	119.0	0.0	.	911
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu	37	3	155200477	155200478	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLCH1	NM_001130960	exon23	c.3362_3363insA	p.S1121fs	AAGATGCTTTTCC	.	183.0	11.0	210.0	0.0	.	151
PLEKHA4	57664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	49364948	49364948	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA4	NM_001161354	exon4	c.A194G	p.D65G	GAGCTGTCCTGGG	.	77.0	29.0	68.0	0.0	.	227
PLEKHA5	54477	hgsc.bcm.edu;broad.mit.edu	37	12	19427544	19427545	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA5	NM_001256470	exon11	c.940_941insA	p.Q314fs	AACAATCAAAAAA	.	145.0	10.0	133.0	0.0	.	227
PLEKHA8P1	51054	hgsc.bcm.edu;broad.mit.edu	37	12	45567240	45567241	+	RNA	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA8P1	.	.	.	.	TTCTGTCAAAAAT	.	163.0	10.0	180.0	0.0	.	226
POGZ	23126	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	151413427	151413427	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	POGZ	NM_145796	exon3	c.T260G	p.V87G	AGTGTGACAAGAG	.	459.0	50.0	404.0	1.0	.	93
POT1	25913	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	124464094	124464094	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	POT1	NM_015450	exon19	c.A1827G	p.S609S	ATTGTATGACTTG	.	304.0	114.0	262.0	0.0	.	227
PRDX2	7001	hgsc.bcm.edu;broad.mit.edu	37	19	12911099	12911100	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRDX2	NM_005809	exon4	c.272_273insC	p.I91fs	TCTTTCCGGGGGG	.	184.0	11.0	212.0	0.0	.	90
PRNP	5621	broad.mit.edu;bcgsc.ca	37	20	4680180	4680181	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRNP	NM_001080121	exon2	c.314_315insA	p.P105fs	GTAAGCCAAAAAC	.	68.0	7.0	84.0	0.0	.	514
PRPF39	55015	hgsc.bcm.edu;broad.mit.edu	37	14	45564691	45564692	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRPF39	NM_017922	exon2	c.249_250insT	p.K83fs	TGAAAAATTTTGG	.	166.0	10.0	176.0	0.0	.	70
PRPF40A	55660	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	153529052	153529052	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRPF40A	NM_017892	exon13	c.T1291A	p.S431T	ACTTTGATCTTGC	.	259.0	89.0	247.0	0.0	.	68
PTEN	5728	hgsc.bcm.edu;broad.mit.edu	37	10	89720665	89720666	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	PTEN,NS,carcinoma,+2	PTEN	NM_000314	exon8	c.816_817insT	p.H272fs	GTTTCACTTTTGG	.	218.0	16.0	139.0	0.0	.	17735
PTK6	5753	ucsc.edu;mdanderson.org	37	20	62162199	62162199	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTK6	NM_005975	exon6	c.C914A	p.S305X	TTCTGCGACTCCA	.	236.0	39.0	219.0	1.0	.	419
PTPN12	5782	broad.mit.edu;bcgsc.ca	37	7	77247882	77247883	+	Frame_Shift_Ins	INS	-	-	GT	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTPN12	NM_002835	exon12	c.1025_1026insGT	p.S342fs	CCCGCAGGTATTG	.	71.0	7.0	66.0	0.0	.	228
PTPN21	11099	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	14	88938677	88938677	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTPN21	NM_007039	exon15	c.C2782T	p.Q928X	CATCTTGGAATCG	.	284.0	51.0	358.0	0.0	.	230
PXDN	7837	broad.mit.edu;bcgsc.ca	37	2	1652251	1652251	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PXDN	NM_012293	exon17	c.G3301A	p.A1101T	AGAAAGCTTTGTG	.	34.0	6.0	73.0	0.0	.	166
PYGM	5837	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	64517976	64517976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PYGM	NM_005609	exon17	c.G2049A	p.M683I	GTTGAGCATGAAC	.	138.0	24.0	177.0	0.0	.	92
R3HDM1	23518	bcgsc.ca;mdanderson.org	37	2	136409526	136409526	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	R3HDM1	NM_015361	exon17	c.G1847C	p.G616A	CTGCTGGATATCC	.	176.0	34.0	184.0	0.0	.	91
RABGGTA	5875	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	24738189	24738189	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_004581	exon7	c.G726A	p.Q242Q	TGCATCCTGGGGG	.	128.0	29.0	150.0	0.0	.	.
RAD50	10111	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	5	131924503	131924503	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD50	NM_005732	exon8	c.G1176T	p.Q392H	AAGACAGATTAAA	.	524.0	47.0	400.0	0.0	.	229
RAD51	5888	hgsc.bcm.edu;broad.mit.edu	37	15	41022163	41022164	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD51	NM_001164269	exon9	c.890_891insA	p.S297fs	ATGCATCAACAAC	.	164.0	10.0	185.0	0.0	.	563
RAD52	5893	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	1023279	1023279	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD52	NM_134424	exon11	c.G976C	p.E326Q	TGTCTTCAAGAGT	.	125.0	18.0	144.0	0.0	.	227
RANBP9	10048	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	13657454	13657454	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RANBP9	NM_005493	exon4	c.C791G	p.S264C	CCAGAAGAACAAA	.	211.0	23.0	223.0	0.0	.	414
RAPGEF1	2889	hgsc.bcm.edu;broad.mit.edu	37	9	134501450	134501451	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAPGEF1	NM_198679	exon10	c.1564_1565insC	p.Y522fs	GCGCGTAGGGGAC	.	157.0	10.0	199.0	0.0	.	849
RBL2	5934	hgsc.bcm.edu;broad.mit.edu	37	16	53513829	53513830	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RBL2	NM_005611	exon19	c.2807_2808insA	p.R936fs	GGAAAAGAAAAAG	.	151.0	10.0	269.0	0.0	.	841
RBMXL3	139804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	114426299	114426299	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145346	exon1	c.C2295T	p.D765D	CCATGACAGTTCC	.	50.0	36.0	113.0	0.0	.	.
RGS4	5999	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	163039295	163039295	+	Silent	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RGS4	NM_001102445	exon2	c.T312A	p.G104G	TGCAGGTCTGCCG	.	146.0	23.0	140.0	0.0	.	652
RGS7	6000	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	240976967	240976967	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RGS7	NM_002924	exon13	c.T907G	p.S303A	GGTTAGAAGGGTC	.	148.0	71.0	105.0	0.0	.	232
RIMS3	9783	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	41092203	41092203	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RIMS3	NM_014747	exon8	c.C913T	p.P305S	ATGAGGGGCTGGT	.	51.0	9.0	82.0	0.0	.	90
RING1	6015	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	33177781	33177781	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	RING1,NS,carcinoma,0	RING1	NM_002931	exon4	c.T329G	p.I110S	CTAAGATCTATCC	.	132.0	39.0	102.0	0.0	.	159
RNASEH2A	10535	broad.mit.edu;bcgsc.ca	37	19	12918138	12918139	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNASEH2A	NM_006397	exon3	c.318_319insG	p.L106fs	CATGCTTGGGCGG	.	69.0	7.0	75.0	0.0	.	524
RNF166	115992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	88766049	88766049	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF166	NM_178841	exon3	c.C404A	p.P135H	GATGTGGGCACCA	.	94.0	52.0	135.0	0.0	.	226
RNF26	79102	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	11	119206969	119206969	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF26	NM_032015	exon1	c.G1137C	p.K379N	GAAGAAGTGTGTC	.	61.0	9.0	82.0	0.0	.	227
RNF44	22838	hgsc.bcm.edu;bcgsc.ca	37	5	175957958	175957958	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF44	NM_014901	exon5	c.C530A	p.S177Y	TCACTGGAGATGA	.	76.0	20.0	70.0	0.0	.	658
RNU6-71	100873774	hgsc.bcm.edu;broad.mit.edu	37	6	56472828	56472829	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	GAAATAATTTTTT	.	191.0	14.0	153.0	0.0	.	.
RP1	6101	hgsc.bcm.edu;broad.mit.edu	37	8	55542461	55542462	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RP1	NM_006269	exon4	c.6019_6020insA	p.Q2007fs	AGAAAACAAAAAA	.	188.0	13.0	208.0	0.0	.	102
RPL10A	4736	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	35437288	35437288	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RPL10A	NM_007104	exon4	c.A292C	p.K98Q	AATAAAAAACTGG	.	72.0	23.0	71.0	0.0	.	91
RPL36A-HNRNPH2	0	hgsc.bcm.edu;broad.mit.edu	37	X	100646804	100646805	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001199973	exon3	c.279_280insA	p.R93fs	TTTCCGGAAAAAG	.	153.0	10.0	196.0	0.0	.	.
RRP12	23223	hgsc.bcm.edu;broad.mit.edu	37	10	99116875	99116876	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RRP12	NM_015179	exon34	c.3870_3871insA	p.N1290fs	TCTGCGGTTTTTG	.	118.0	11.0	104.0	0.0	.	92
RTEL1	51750	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	62326478	62326478	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RTEL1	NM_032957	exon33	c.C3475G	p.L1159V	ACAGACCTGACCG	.	44.0	6.0	43.0	0.0	.	44
RXFP3	51289	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	33937720	33937720	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RXFP3	NM_016568	exon1	c.G875A	p.R292H	TGGTGCGCTTCAT	.	151.0	67.0	117.0	0.0	.	91
RXFP4	339403	hgsc.bcm.edu;broad.mit.edu	37	1	155912224	155912225	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RXFP4	NM_181885	exon1	c.724_725insG	p.R242fs	GACAGCAGGGTCG	.	158.0	10.0	149.0	0.0	.	90
RYR2	6262	ucsc.edu;bcgsc.ca	37	1	237433796	237433796	+	Splice_Site	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RYR2	NM_001035	exon2	c.49-1G>C	.	TTTGCAGGATGAT	.	525.0	63.0	438.0	1.0	.	158
SAMD15	161394	hgsc.bcm.edu;broad.mit.edu	37	14	77844867	77844868	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SAMD15	NM_001010860	exon1	c.1106_1107insG	p.E369fs	CAAATGAGAAAAA	.	215.0	18.0	222.0	0.0	.	90
SCAP	22937	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	3	47476584	47476584	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SCAP	NM_012235	exon3	c.G166T	p.E56X	TGAATTCCACAGG	.	108.0	24.0	167.0	0.0	.	91
SCIN	85477	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	12666376	12666376	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SCIN	NM_001112706	exon8	c.G1149T	p.Q383H	TCCGCAGATGGCA	.	296.0	105.0	269.0	0.0	.	24
SENP3	26168	hgsc.bcm.edu;ucsc.edu	37	17	7470288	7470288	+	Missense_Mutation	SNP	A	A	G	rs76586164		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SENP3	NM_015670	exon8	c.A1307G	p.K436R	TACCAAAGGGTTA	.	209.0	20.0	405.0	0.0	A|0.500;G|0.500	659
SENP6	26054	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	6	76386875	76386875	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SENP6	NM_015571	exon14	c.C1751G	p.P584R	AAATTCCCTTTGA	.	514.0	162.0	399.0	1.0	.	660
SFSWAP	6433	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	132204080	132204080	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SFSWAP	NM_001261411	exon4	c.A602T	p.E201V	ACGTGGAGTTGGT	.	362.0	81.0	215.0	0.0	.	91
SGSM2	9905	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	2282729	2282729	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SGSM2	NM_014853	exon24	c.G3071A	p.R1024H	CAGAACGTGCTGA	.	126.0	19.0	161.0	1.0	.	68
SHOX2	6474	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	3	157823590	157823590	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SHOX2	NM_003030	exon1	c.G224T	p.G75V	CCTCCTCCGCCTC	.	19.0	13.0	21.0	0.0	.	90
SIDT2	51092	ucsc.edu;bcgsc.ca;mdanderson.org	37	11	117053474	117053474	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SIDT2	NM_001040455	exon6	c.C654T	p.F218F	AGCCTTCATCGGC	.	108.0	25.0	136.0	2.0	.	90
SLC22A8	9376	broad.mit.edu;bcgsc.ca	37	11	62767298	62767299	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC22A8	NM_001184732	exon4	c.454_455insC	p.I152fs	TCAGGATGGGCCT	.	77.0	9.0	103.0	0.0	.	93
SLC25A3	5250	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	98991699	98991699	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC25A3	NM_005888	exon4	c.T348C	p.V116V	TGGTGTTCGTGGT	.	458.0	172.0	410.0	0.0	.	90
SLC38A10	124565	hgsc.bcm.edu;broad.mit.edu	37	17	79226065	79226066	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC38A10	NM_001037984	exon13	c.1875_1876insA	p.K625fs	CTTGGCCTTTTCC	.	132.0	12.0	114.0	0.0	.	70
SLCO1B1	10599	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	21329794	21329794	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLCO1B1	NM_006446	exon5	c.A444G	p.L148L	AATTTTATCACTC	.	266.0	80.0	274.0	0.0	.	97
SMARCA4	6597	bcgsc.ca;mdanderson.org	37	19	11098360	11098360	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMARCA4	NM_003072	exon6	c.C878T	p.A293V	ATGCTGCTGCCCC	.	186.0	58.0	212.0	1.0	.	1523
SMNDC1	10285	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	112053908	112053908	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMNDC1	NM_005871	exon6	c.A717G	p.X239X	TTCTGATTATTGA	.	132.0	54.0	159.0	0.0	.	91
SNX18	112574	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	53815183	53815183	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SNX18	NM_052870	exon1	c.G1401A	p.V467V	GAAGGTGGGCCAG	.	60.0	19.0	85.0	1.0	.	226
SOX14	8403	hgsc.bcm.edu;bcgsc.ca	37	3	137483875	137483875	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SOX14	NM_004189	exon1	c.C249G	p.P83P	CAAGCCCAAGAAC	.	131.0	9.0	159.0	0.0	.	90
SPAG9	9043	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	49075937	49075937	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPAG9	NM_001130528	exon15	c.A1706C	p.K569T	TCAGGCTTCTTAG	.	386.0	47.0	288.0	0.0	.	659
SPATA2L	124044	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	89764069	89764069	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPATA2L	NM_152339	exon3	c.G948C	p.L316L	CCTACTCAGCTCA	.	91.0	18.0	65.0	0.0	.	90
SPATA31C1	441452	bcgsc.ca;mdanderson.org	37	9	90536519	90536519	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145124	exon4	c.G1697A	p.G566E	ACTCAGGAAGTGA	.	114.0	25.0	164.0	1.0	.	.
SPEF2	79925	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	35807028	35807028	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPEF2	NM_024867	exon35	c.C5230A	p.L1744I	AGCCACCTAAAGA	.	325.0	116.0	369.0	0.0	.	26
SRCRB4D	136853	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	76029631	76029631	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SRCRB4D	NM_080744	exon4	c.C447G	p.H149Q	CTCGTAGTGAAAG	.	147.0	51.0	184.0	0.0	.	91
SRL	6345	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	4242512	4242512	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SRL	NM_001098814	exon6	c.A1064T	p.K355M	TTGTCCTTGTAAG	.	263.0	43.0	233.0	0.0	.	73
SSTR3	6753	hgsc.bcm.edu;bcgsc.ca	37	22	37602710	37602710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SSTR3	NM_001051	exon2	c.C1133T	p.T378M	GGCTGCGTGATCT	.	82.0	5.0	104.0	0.0	.	522
ST18	9705	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	53092714	53092714	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ST18	NM_014682	exon9	c.G245T	p.G82V	AAGGGGCCATCGT	.	260.0	47.0	354.0	0.0	.	95
ST8SIA6	338596	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	17365101	17365101	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ST8SIA6	NM_001004470	exon7	c.A691T	p.N231Y	CAAGATTTGTTTT	.	266.0	62.0	354.0	0.0	.	91
STK31	56164	hgsc.bcm.edu;broad.mit.edu	37	7	23775340	23775341	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STK31	NM_001260505	exon7	c.667_668insA	p.E223fs	TGTGAGGAAAAAA	.	141.0	12.0	121.0	0.0	.	338
STON1-GTF2A1L	286749	hgsc.bcm.edu;broad.mit.edu	37	2	48809580	48809581	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STON1-GTF2A1L	NM_001198593	exon2	c.1808_1809insG	p.L603fs	CATGTCTGGGGAG	.	164.0	11.0	151.0	0.0	.	27
STOX2	56977	broad.mit.edu;bcgsc.ca	37	4	184931964	184931965	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STOX2	NM_020225	exon3	c.1973_1974insA	p.P658fs	AGTCACCAAAAGG	.	74.0	9.0	68.0	0.0	.	22
SUPT6H	6830	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	27001353	27001353	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SUPT6H	NM_003170	exon3	c.G162T	p.L54F	CAACTTGAAAGGC	.	284.0	31.0	192.0	0.0	.	93
SVOPL	136306	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	138312995	138312996	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SVOPL	NM_001139456	exon10	c.977_978insG	p.D326fs	CCTGAGTCCCCCC	.	131.0	13.0	139.0	0.0	.	68
SWAP70	23075	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	9769515	9769515	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SWAP70	NM_015055	exon10	c.G1466A	p.R489H	ATCAGCGTGTCCT	.	96.0	17.0	125.0	0.0	.	228
SYNE4	163183	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	19	36496296	36496296	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001039876	exon6	c.G911A	p.G304D	CCGAGGCCAGACT	.	197.0	32.0	172.0	0.0	.	.
TCEB3CL2	100506888	broad.mit.edu;bcgsc.ca	37	18	44543597	44543598	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001242907	exon1	c.775_776insG	p.P259fs	TTTTCGGCCCGGC	.	217.0	14.0	250.0	0.0	.	.
TCF7L1	83439	broad.mit.edu;bcgsc.ca	37	2	85536234	85536235	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TCF7L1	NM_031283	exon12	c.1416_1417insG	p.H472fs	CTCCCACGGGAGC	.	78.0	8.0	109.0	0.0	.	585
TERF1	7013	hgsc.bcm.edu;broad.mit.edu	37	8	73951354	73951355	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TERF1	NM_017489	exon9	c.1043_1044insA	p.T348fs	TAGGTACAAAAAA	.	135.0	11.0	102.0	0.0	.	228
THRAP3	9967	hgsc.bcm.edu;broad.mit.edu	37	1	36755000	36755001	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	THRAP3	NM_005119	exon5	c.1380_1381insA	p.N460fs	TGCAAACAAAAAC	.	128.0	10.0	126.0	0.0	.	663
TMED9	54732	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	177019352	177019354	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMED9	NM_017510	exon1	c.137_139del	p.46_47del	AGACGGAGAAGAA	.	250.0	0.0	285.0	0.0	.	90
TMEM125	128218	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	43738869	43738869	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMEM125	NM_144626	exon4	c.C476T	p.S159L	TGGGCTCGCTTTT	.	378.0	84.0	416.0	2.0	.	153
TMEM186	25880	hgsc.bcm.edu;bcgsc.ca	37	16	8890210	8890210	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMEM186	NM_015421	exon2	c.C241G	p.L81V	CTGTCAGGGCAGT	.	123.0	8.0	129.0	0.0	.	91
TMPRSS4	56649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	117979580	117979580	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMPRSS4	NM_019894	exon7	c.C552T	p.L184L	CTGTCTCTCAGGC	.	76.0	40.0	107.0	0.0	.	90
TPRX1	284355	hgsc.bcm.edu;broad.mit.edu	37	19	48305271	48305272	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TPRX1	NM_198479	exon2	c.997_998insC	p.L333fs	GCCATAAGGGGGC	.	160.0	11.0	122.0	0.0	.	90
TRANK1	9881	broad.mit.edu;bcgsc.ca	37	3	36899168	36899169	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRANK1	NM_014831	exon12	c.1913_1914insC	p.Q638fs	GAACCCTGGGACT	.	60.0	7.0	115.0	0.0	.	24
TRIOBP	11078	broad.mit.edu;bcgsc.ca	37	22	38130525	38130526	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRIOBP	NM_001039141	exon9	c.4182_4183insC	p.L1394fs	CCCGCTGCCCCCC	.	99.0	10.0	85.0	0.0	.	136
TSHR	7253	hgsc.bcm.edu;broad.mit.edu	37	14	81609512	81609513	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TSHR	NM_000369	exon10	c.1110_1111insA	p.L370fs	GGAGCTCAAAAAC	.	188.0	12.0	213.0	0.0	.	1650
TTC1	7265	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	159437629	159437629	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTC1	NM_003314	exon2	c.C94G	p.P32A	GGCCCTCCAGTTC	.	97.0	38.0	87.0	0.0	.	91
TTC27	55622	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	33012108	33012108	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTC27	NM_017735	exon16	c.G1890T	p.Q630H	CTGGCAGATTTGG	.	153.0	23.0	187.0	0.0	.	90
TTC40	54777	hgsc.bcm.edu;broad.mit.edu	37	10	134726617	134726618	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001200049	exon18	c.2266_2267insG	p.R756fs	TCTGCCGCCCGGC	.	126.0	10.0	166.0	0.0	.	.
TTN	7273	broad.mit.edu;bcgsc.ca	37	2	179511798	179511799	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTN	NM_001267550	exon215	c.40215_40216insC	p.P13405fs	TTCAACAGGGGGA	.	162.0	18.0	138.0	0.0	.	636
TUBA3C	7278	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	19751669	19751669	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TUBA3C	NM_006001	exon4	c.C454G	p.L152V	TGAGCAGAGATGC	.	358.0	78.0	570.0	0.0	.	95
UMODL1	89766	broad.mit.edu;mdanderson.org	37	21	43529800	43529800	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UMODL1	NM_173568	exon10	c.G1648A	p.A550T	GGCCGGGCCTGTG	.	17.0	7.0	15.0	0.0	.	93
UNKL	64718	hgsc.bcm.edu;broad.mit.edu	37	16	1417771	1417772	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UNKL	NM_001193388	exon13	c.1674_1675insC	p.P558fs	AGAGGATGGGGGG	.	185.0	11.0	196.0	0.0	.	90
USP31	57478	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	23093878	23093878	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	USP31	NM_020718	exon12	c.C1831G	p.L611V	GGGCAAGCTGAAA	.	168.0	30.0	133.0	0.0	.	663
UTP20	27340	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	101711355	101711355	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UTP20	NM_014503	exon22	c.C2652T	p.A884A	ACCTGCCGCAGGA	.	141.0	32.0	138.0	0.0	.	155
VCX	26609	hgsc.bcm.edu;bcgsc.ca	37	X	7811709	7811709	+	Silent	SNP	G	G	C	rs139507263	byfrequency;alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VCX	NM_013452	exon3	c.G273C	p.P91P	GCCGCCGGAGGAG	.	84.0	28.0	81.0	0.0	G|0.999;A|0.001	22
VWDE	221806	ucsc.edu;bcgsc.ca;mdanderson.org	37	7	12397021	12397021	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VWDE	NM_001135924	exon17	c.A3395G	p.D1132G	CCAGAGTCCAACG	.	151.0	43.0	142.0	1.0	.	68
WDR44	54521	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	117528110	117528110	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDR44	NM_001184965	exon5	c.G919T	p.A307S	GATTTGGCAAGTG	.	148.0	105.0	190.0	0.0	.	133
WDTC1	23038	hgsc.bcm.edu;broad.mit.edu	37	1	27622887	27622888	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDTC1	NM_015023	exon10	c.944_945insG	p.S315fs	ACTCCTCGGGGGG	.	237.0	17.0	415.0	0.0	.	91
WNT6	7475	broad.mit.edu;bcgsc.ca	37	2	219735805	219735814	+	Frame_Shift_Del	DEL	GGCTGGCCGG	GGCTGGCCGG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGCTGGCCGG	GGCTGGCCGG	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WNT6	NM_006522	exon2	c.137_146del	p.46_49del	CACGGCGGCTGGC	.	61.0	7.0	73.0	0.0	.	564
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu	37	2	168104502	168104503	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	XIRP2	NM_152381	exon9	c.6600_6601insA	p.K2200fs	TATAAAGAAAAAG	.	172.0	11.0	153.0	0.0	.	104
XPO4	64328	ucsc.edu;bcgsc.ca;mdanderson.org	37	13	21418016	21418016	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	XPO4	NM_022459	exon5	c.G466C	p.A156P	AACAGGCCAGAGT	.	62.0	11.0	79.0	0.0	.	272
ZBTB39	9880	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	57397205	57397205	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZBTB39	NM_014830	exon2	c.G1497A	p.T499T	GGACAGCGTGTGC	.	63.0	14.0	63.0	0.0	.	135
ZBTB49	166793	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	4303971	4303971	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZBTB49	NM_145291	exon3	c.A408G	p.L136L	GTCTCTACAAAGC	.	98.0	48.0	114.0	0.0	.	92
ZEB2	9839	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	145187479	145187479	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZEB2	NM_001171653	exon3	c.C188G	p.A63G	ACACTAGCTGGAC	.	252.0	97.0	282.0	0.0	.	297
ZFYVE16	9765	ucsc.edu;mdanderson.org	37	5	79739077	79739077	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZFYVE16	NM_001105251	exon6	c.C2555G	p.S852X	CAGTCTCAGCACT	.	418.0	51.0	352.0	1.0	.	90
ZFYVE20	64145	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	15126258	15126258	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZFYVE20	NM_022340	exon8	c.C582T	p.I194I	AAGGCTGATGAGC	.	125.0	65.0	142.0	0.0	.	92
ZNF20	7568	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	12243428	12243428	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF20	NM_021143	exon4	c.G1573C	p.E525Q	TTCTTTCATGTTC	.	192.0	64.0	145.0	0.0	.	22
ZNF521	25925	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	22804595	22804595	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF521	NM_015461	exon4	c.G3287A	p.C1096Y	TTCACGCAGCCGG	.	104.0	75.0	135.0	0.0	.	275
ZP4	57829	hgsc.bcm.edu;bcgsc.ca	37	1	238053180	238053180	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZP4	NM_021186	exon3	c.T387C	p.P129P	ATCCATAGGACAC	.	174.0	40.0	141.0	0.0	.	93
RTTN	25914	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	18	67794863	67794864	+	Missense_Mutation	DNP	CC	CC	AA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	p.R1086I	AACTTCCCTGTGG	.	71.0	55.0	93.0	0.0	.	.
NPSR1	387129	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	34888201	34888202	+	Missense_Mutation	DNP	CC	CC	AA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	p.NL317KM	TCAGAACCTGCCA	.	225.0	85.0	265.0	0.0	.	.
