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	TranscriptID	Exon	ChromChange	AAChange	COSMIC_Codon	COSMIC_Gene	Drug_Target
PSD	5662	broad.mit.edu	36	10	104165844	104165845	+	Frame_Shift_Ins	INS	-	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_002779	exon3	c.677_678insC	p.R226fs	.	.	.
SVIL	6840	broad.mit.edu	36	10	29862172	29862172	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_021738	exon8	c.C1130T	p.A377V	.	.	.
ARHGAP12	94134	broad.mit.edu	36	10	32136748	32136748	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_018287	exon20	c.G2385A	p.E795E	.	.	.
PCDH15	65217	broad.mit.edu	36	10	55747135	55747135	+	Missense_Mutation	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001142767	exon7	c.G667T	p.D223Y	.	.	.
TET1	80312	broad.mit.edu	36	10	70102791	70102791	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_030625	exon8	c.C4807T	p.P1603S	.	.	.
USP54	159195	broad.mit.edu	36	10	74971500	74971500	+	Missense_Mutation	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_152586	exon6	c.A575G	p.N192S	.	.	.
NRBF2	29982	broad.mit.edu	36	10	64583536	64583537	+	Frame_Shift_Del	DEL	AC	-	-	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	AC	AC	AC	-	AC	AC	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_030759	exon4	c.416_417del	p.139_139del	.	.	.
ARAP1	116985	broad.mit.edu	36	11	72102885	72102886	+	Frame_Shift_Ins	INS	-	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001040118	exon4	c.639_640insC	p.P213fs	.	.	.
MLL	4297	broad.mit.edu	36	11	117876997	117876997	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_005933	exon25	c.G6235A	p.V2079I	.	.	.
PHLDB1	23187	broad.mit.edu	36	11	117990497	117990497	+	Missense_Mutation	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001144758	exon3	c.A74G	p.D25G	.	.	.
NUP160	23279	broad.mit.edu	36	11	47786553	47786553	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_015231	exon18	c.C2346T	p.C782C	.	.	.
FRMD8	83786	broad.mit.edu	36	11	64913508	64913508	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_031904	exon3	c.C186T	p.R62R	.	.	.
KSR2	283455	broad.mit.edu	36	12	116683537	116683537	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_173598	exon4	c.C561T	p.P187P	.	.	.
RERG	85004	broad.mit.edu	36	12	15261677	15261677	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_032918	exon2	c.C14T	p.A5V	.	.	.
LRTM2	654429	broad.mit.edu	36	12	1814102	1814102	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001039029	exon5	c.C1067T	p.P356L	.	.	.
KRAS	3845	broad.mit.edu	36	12	25289552	25289552	+	Missense_Mutation	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_004985	exon2	c.G34T	p.G12C	 KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,+1 	.	.
BICD1	636	broad.mit.edu	36	12	32372554	32372554	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001003398	exon5	c.G1898A	p.R633Q	.	.	.
MLL2	8085	broad.mit.edu	36	12	47720488	47720488	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_003482	exon31	c.C7332T	p.F2444F	.	.	.
KRT72	140807	broad.mit.edu	36	12	51267851	51267851	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001146226	exon6	c.G1015A	p.A339T	.	.	.
DNAJC14	85406	broad.mit.edu	36	12	54508644	54508644	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_032364	exon2	c.C66T	p.L22L	.	.	.
NAV3	89795	broad.mit.edu	36	12	77066825	77066825	+	Missense_Mutation	SNP	G	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_014903	exon22	c.G4780T	p.A1594S	.	.	.
OTX2	5015	broad.mit.edu	36	14	56340801	56340802	+	Frame_Shift_Ins	INS	-	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	-	-					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_021728	exon4	c.131_132insC	p.R44fs	.	.	.
AHNAK2	113146	broad.mit.edu	36	14	104481217	104481218	+	Missense_Mutation	DNP	CA	TG	TG	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	CA	CA					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_138420	exon7	c.11615_11616CA	.	.	.	.
OR4K14	122740	broad.mit.edu	36	14	19552921	19552921	+	Missense_Mutation	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001004712	exon1	c.A272G	p.K91R	.	.	.
LRFN5	145581	broad.mit.edu	36	14	41430824	41430824	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_152447	exon4	c.C2007T	p.N669N	.	.	.
ESR2	2100	broad.mit.edu	36	14	63797213	63797213	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001437	exon5	c.G659A	p.R220Q	.	.	.
HERC2	8924	broad.mit.edu	36	15	26152419	26152419	+	Missense_Mutation	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_004667	exon28	c.A4337G	p.K1446R	.	.	.
TP53BP1	7158	broad.mit.edu	36	15	41492702	41492702	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_005657	exon24	c.G5197A	p.A1733T	.	.	.
TLN2	83660	broad.mit.edu	36	15	60884852	60884852	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_015059	exon48	c.G6478A	p.V2160M	.	.	.
HERC2	8924	broad.mit.edu	36	15	26117219	26117221	+	In_Frame_Del	DEL	AGA	-	-	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	AGA	AGA					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_004667	exon50	c.7909_7911del	p.2637_2637del	.	.	.
TSC2	7249	broad.mit.edu	36	16	2046718	2046718	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001114382	exon8	c.G721A	p.V241I	.	.	.
DHX58	79132	broad.mit.edu	36	17	37509245	37509245	+	Missense_Mutation	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A	A	A	A	A	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_024119	exon12	c.T1661C	p.L554P	.	.	.
CDC27	996	broad.mit.edu	36	17	42589724	42589724	+	Silent	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001114091	exon6	c.A501G	p.T167T	.	.	.
RNF213	57674	broad.mit.edu	36	17	75928609	75928609	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_020914	exon27	c.C5994T	p.F1998F	.	.	.
GUCY2D	3000	broad.mit.edu	36	17	7856545	7856545	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_000180	exon10	c.G2009A	p.R670Q	.	.	.
SMCHD1	23347	broad.mit.edu	36	18	2664059	2664059	+	Missense_Mutation	SNP	A	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_015295	exon5	c.A553C	p.N185H	.	.	.
SMAD2	4087	broad.mit.edu	36	18	43622209	43622209	+	Nonsense_Mutation	SNP	G	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001135937	exon10	c.C1301G	p.S434X	.	.	.
DSEL	92126	broad.mit.edu	36	18	63331939	63331939	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_032160	exon2	c.G917A	p.R306H	.	.	.
RIT2	6014	broad.mit.edu	36	18	38577518	38577522	+	Frame_Shift_Del	DEL	TTCTC	-	-	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	TTCTC	TTCTC	TTCTC	-	TTCTC	TTCTC	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_002930	exon5	c.588_592del	p.196_198del	.	.	.
WDR88	126248	broad.mit.edu	36	19	38358157	38358157	+	Missense_Mutation	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_173479	exon11	c.A1258G	p.R420G	.	.	.
SIGLEC7	27036	broad.mit.edu	36	19	56339743	56339743	+	Silent	SNP	C	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_014385	exon2	c.C702G	p.L234L	.	.	.
COL11A1	1301	broad.mit.edu	36	1	103252735	103252735	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001854	exon13	c.C1492T	p.R498C	.	.	.
FAM5B	57795	broad.mit.edu	36	1	175516318	175516318	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_021165	exon8	c.C1383T	p.G461G	.	.	.
RYR2	6262	broad.mit.edu	36	1	235736664	235736664	+	Missense_Mutation	SNP	G	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001035	exon23	c.G2645T	p.R882I	.	.	.
PGBD2	267002	broad.mit.edu	36	1	247177602	247177602	+	Nonsense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_170725	exon3	c.C196T	p.R66X	.	.	.
ZMYM6	9204	broad.mit.edu	36	1	35247077	35247077	+	Nonsense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_007167	exon11	c.C1528T	p.R510X	.	.	.
ZMYM6	9204	broad.mit.edu	36	1	35248763	35248763	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_007167	exon10	c.G1364A	p.G455D	.	.	.
RSPO1	284654	broad.mit.edu	36	1	37852151	37852151	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001038633	exon7	c.C437T	p.A146V	.	.	.
MED8	112950	broad.mit.edu	36	1	43625139	43625139	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_052877	exon4	c.C388T	p.R130C	.	.	.
TNNI3K	51086	broad.mit.edu	36	1	74782222	74782222	+	Nonsense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_015978	exon25	c.C2476T	p.R826X	.	.	.
MACROD2	140733	broad.mit.edu	36	20	15158668	15158668	+	Silent	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_080676	exon6	c.A501G	p.S167S	.	.	.
CHD6	84181	broad.mit.edu	36	20	39549739	39549739	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_032221	exon14	c.G1981A	p.D661N	.	.	.
CSTF1	1477	broad.mit.edu	36	20	54407616	54407616	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001033521	exon5	c.G832A	p.V278I	.	.	.
KRTAP6-2	337967	broad.mit.edu	36	21	30892921	30892921	+	Missense_Mutation	SNP	G	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_181604	exon1	c.C144A	p.F48L	.	.	.
CRYBB3	1417	broad.mit.edu	36	22	23928691	23928691	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_004076	exon3	c.G126A	p.S42S	.	.	.
PKDREJ	10343	broad.mit.edu	36	22	45037158	45037158	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_006071	exon1	c.C726T	p.N242N	.	.	.
ABCB6	10058	broad.mit.edu	36	2	219786263	219786264	+	Missense_Mutation	DNP	AA	GG	GG	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	AA	AA					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_005689	exon12	c.1748_1749CC	.	.	.	.
C2orf28	51374	broad.mit.edu	36	2	27291715	27291715	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_080592	exon3	c.C409T	p.L137L	.	.	.
PCYOX1	51449	broad.mit.edu	36	2	70340043	70340043	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_016297	exon2	c.C160T	p.R54W	.	.	.
PIK3CA	5290	broad.mit.edu	36	3	180434779	180434779	+	Missense_Mutation	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_006218	exon21	c.A3140G	p.H1047R	 PIK3CA,breast,NS,Substitution - Missense,0 	.	.
TPRG1	285386	broad.mit.edu	36	3	190439351	190439351	+	Silent	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_198485	exon4	c.C438A	p.I146I	.	.	.
TP63	8626	broad.mit.edu	36	3	191069098	191069098	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001114980	exon6	c.G746A	p.R249Q	.	.	.
GP5	2814	broad.mit.edu	36	3	195600208	195600208	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_004488	exon2	c.C93T	p.D31D	.	.	.
CTNNB1	1499	broad.mit.edu	36	3	41241693	41241693	+	Missense_Mutation	SNP	C	A	A	rs5743392	byHapMap	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001098210	exon4	c.C486A	p.D162E	.	.	.
ZNF167	55888	broad.mit.edu	36	3	44587308	44587308	+	Nonsense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_018651	exon6	c.C1702T	p.R568X	.	.	.
FOXP1	27086	broad.mit.edu	36	3	71104507	71104507	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_032682	exon18	c.G1541A	p.R514H	.	.	.
OR5AC2	81050	broad.mit.edu	36	3	99289298	99289298	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_054106	exon1	c.G592A	p.A198T	.	.	.
SCD5	79966	broad.mit.edu	36	4	83821008	83821008	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001037582	exon3	c.C445T	p.R149W	.	.	.
PCDHA3	56145	broad.mit.edu	36	5	140162261	140162261	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_031497	exon1	c.C1295T	p.S432L	.	.	.
PCDHA13	56136	broad.mit.edu	36	5	140242813	140242813	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_031865	exon1	c.C776T	p.T259I	.	.	.
RANBP17	64901	broad.mit.edu	36	5	170284034	170284034	+	Missense_Mutation	SNP	T	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_022897	exon12	c.T1343G	p.V448G	.	.	.
CDC20B	166979	broad.mit.edu	36	5	54458911	54458911	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001170402	exon8	c.G920A	p.R307Q	.	.	.
ZNF366	167465	broad.mit.edu	36	5	71792870	71792870	+	Silent	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_152625	exon2	c.C210T	p.V70V	.	.	.
LPA	4018	broad.mit.edu	36	6	160888899	160888899	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_005577	exon33	c.C5216T	p.T1739M	.	.	.
MLLT4	4301	broad.mit.edu	36	6	168095438	168095438	+	Missense_Mutation	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T	T	T	T	T	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001040000	exon29	c.T4534C	p.S1512P	.	.	.
MUC17	140453	broad.mit.edu	36	7	100464673	100464673	+	Missense_Mutation	SNP	G	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001040105	exon3	c.G3256T	p.A1086S	.	.	.
DOCK4	9732	broad.mit.edu	36	7	111249670	111249670	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_014705	exon27	c.C2914T	p.R972C	.	.	.
EPHA1	2041	broad.mit.edu	36	7	142805961	142805961	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_005232	exon6	c.G1191A	p.R397R	.	.	.
DGKB	1607	broad.mit.edu	36	7	14344748	14344748	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_145695	exon22	c.G2042A	p.R681Q	.	.	.
RAMP3	10268	broad.mit.edu	36	7	45189507	45189507	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_005856	exon3	c.C418T	p.R140C	.	.	.
ADCY1	107	broad.mit.edu	36	7	45598968	45598968	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_021116	exon2	c.C725T	p.A242V	.	.	.
ABCA13	154664	broad.mit.edu	36	7	48283137	48283137	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_152701	exon15	c.G3165A	p.P1055P	.	.	.
SAMD9L	219285	broad.mit.edu	36	7	92599385	92599385	+	Missense_Mutation	SNP	T	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_152703	exon5	c.A3836T	p.K1279I	.	.	.
TFPI2	7980	broad.mit.edu	36	7	93357421	93357421	+	Missense_Mutation	SNP	A	G	G	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	A	A					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_006528	exon2	c.T235C	p.W79R	.	.	.
MYOM2	9172	broad.mit.edu	36	8	1992977	1992977	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_003970	exon4	c.G368A	p.R123H	.	.	.
WRN	7486	broad.mit.edu	36	8	31097326	31097326	+	Missense_Mutation	SNP	G	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_000553	exon21	c.G2474C	p.G825A	.	.	.
NRG1	3084	broad.mit.edu	36	8	32705131	32705131	+	De_novo_Start_OutOfFrame	SNP	T	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_013957	exon6	c.T625A	p.L209M	.	.	.
ADAM32	203102	broad.mit.edu	36	8	39126528	39126528	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_145004	exon5	c.C338T	p.T113M	.	.	.
RP1	6101	broad.mit.edu	36	8	55703340	55703341	+	Missense_Mutation	DNP	GG	TT	TT	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	GG	GG					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_006269	exon4	c.4345_4346TT	.	.	.	.
CERCAM	51148	broad.mit.edu	36	9	130237812	130237812	+	Missense_Mutation	SNP	T	C	C	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	T	T					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_016174	exon12	c.T1595C	p.L532P	.	.	.
BEX4	56271	broad.mit.edu	36	X	102357776	102357776	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001080425	exon3	c.C39T	p.N13N	.	.	.
NRK	203447	broad.mit.edu	36	X	105048278	105048278	+	Missense_Mutation	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_198465	exon16	c.C2470A	p.Q824K	.	.	.
COL4A5	1287	broad.mit.edu	36	X	107785253	107785253	+	Missense_Mutation	SNP	G	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_000495	exon37	c.G3283T	p.G1095C	.	.	.
IRS4	8471	broad.mit.edu	36	X	107865057	107865057	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_003604	exon1	c.G1174A	p.E392K	.	.	.
MOSPD2	158747	broad.mit.edu	36	X	14801737	14801737	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_152581	exon2	c.C15T	p.H5H	.	.	.
CXorf23	256643	broad.mit.edu	36	X	19863916	19863916	+	Missense_Mutation	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_198279	exon9	c.G1795T	p.D599Y	.	.	.
NR0B1	190	broad.mit.edu	36	X	30237078	30237078	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_000475	exon1	c.G324A	p.S108S	.	.	.
FAM47C	442444	broad.mit.edu	36	X	36937788	36937788	+	Missense_Mutation	SNP	C	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001013736	exon1	c.C1384A	p.L462I	.	.	.
PHF8	23133	broad.mit.edu	36	X	54030313	54030313	+	Missense_Mutation	SNP	G	A	A	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	NM_001184898	exon16	c.C1918T	p.R640W	.	.	.
NAP1L3	4675	broad.mit.edu	36	X	92813568	92813568	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_004538	exon1	c.G1392A	p.E464E	.	.	.
PCDH19	57526	broad.mit.edu	36	X	99549397	99549397	+	Silent	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C					Unknown	Unknown	Somatic	Phase_I	Capture				Illumina HiSeq	NM_001105243	exon1	c.G855A	p.T285T	.	.	.
SSX6	280657	broad.mit.edu	36	X	47855617	47855617	+	Missense_Mutation	SNP	C	T	T	novel	unknown	TCGA-AA-3696-01A-01W-0900-09	TCGA-AA-3696-10A-01W-0900-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	.	.	.	.	.	.	.