Normal	Chrom	Pos	Ref	Alt	Gene	Transcript	RNA	CDS	Protein	Type	Effect	CancerGene	Description	DRIVER_CATEGORY	Age	pCR_vs_RD	PreTxTumorSizeClinOrRad	Tumor_size_surgery(cm)	Grade	group	Ki67_biopsy	NumPosLn	ANTHRACYCLINE	TAXANE	geneRef	DEPTH_PD12334a	TUM_PILEUP_MUTS_PD12334a	Pileup_MtAlpct_PD12334a	ID.2	DEPTH_PD12334c	TUM_PILEUP_MUTS_PD12334c	Pileup_MtAlpct_PD12334c	ID.3	DEPTH_PD12334d	TUM_PILEUP_MUTS_PD12334d	Pileup_MtAlpct_PD12334d	ID.4	DEPTH_PD12334e	TUM_PILEUP_MUTS_PD12334e	Pileup_MtAlpct_PD12334e	ID.5	DEPTH_PD12334f	TUM_PILEUP_MUTS_PD12334f	Pileup_MtAlpct_PD12334f	ID.6	DEPTH_PD12334g	TUM_PILEUP_MUTS_PD12334g	Pileup_MtAlpct_PD12334g	ID.7	DEPTH_PD12334h	TUM_PILEUP_MUTS_PD12334h	Pileup_MtAlpct_PD12334h	ID.8	DEPTH_PD12334i	TUM_PILEUP_MUTS_PD12334i	Pileup_MtAlpct_PD12334i
PD12334b	6	157505472	C	A	ARID1B	CCDS5251.1	r.3551c>a	c.3399C>A	p.A1133A	Sub	silent	2	SILENT	SILENT	50	pS	2.5	2.5	3	3	40	4	YES	YES	ARID1B:p.A1133A	90	0	0	6:157505472	87	0	0	6:157505472	121	0	0	6:157505472	92	0	0	6:157505472	119	0	0	6:157505472	211	0	0	6:157505472	132	0	0	6:157505472	624	35	5.6
PD12334b	10	123274774	A	G	FGFR2	CCDS7620.2	r.1739u>c	c.1147T>C	p.C383R	Sub	missense	2	ONCOGENIC_OTHER_GENE	ONCOGENIC	50	pS	2.5	2.5	3	3	40	4	YES	YES	FGFR2:p.C383R	385	78	20.3	10:123274774	223	45	20.2	10:123274774	353	64	18.1	10:123274774	305	41	13.4	10:123274774	425	87	20.5	10:123274774	570	152	26.7	10:123274774	427	78	18.3	10:123274774	808	52	6.4
PD12334b	1	206651147	G	C	IKBKE	CCDS30996.1	r.1130g>c	c.757G>C	p.E253Q	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	IKBKE:p.E253Q	218	39	17.9	1:206651147	397	71	17.9	1:206651147	362	61	16.9	1:206651147	269	28	10.4	1:206651147	268	52	19.4	1:206651147	528	88	16.7	1:206651147	341	66	19.4	1:206651147	1499	50	3.3
PD12334b	6	32168666	T	G	NOTCH4	CCDS34420.1	r.4396a>c	c.4257A>C	p.G1419G	Sub	silent	3	SILENT	SILENT	50	pS	2.5	2.5	3	3	40	4	YES	YES	NOTCH4:p.G1419G	21	6	28.6	6:32168666	30	11	36.7	6:32168666	34	18	52.9	6:32168666	15	3	20	6:32168666	25	8	32	6:32168666	68	20	29.4	6:32168666	32	10	31.2	6:32168666	150	38	25.3
PD12334b	6	157469818	G	C	ARID1B	CCDS5251.1	r.2551g>c	c.2399G>C	p.G800A	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	ARID1B:p.G800A	182	0	0	6:157469818	201	0	0	6:157469818	242	0	0	6:157469818	193	0	0	6:157469818	208	0	0	6:157469818	370	0	0	6:157469818	234	0	0	6:157469818	1196	63	5.3
PD12334b	12	112926291	T	G	PTPN11	CCDS9163.1	r.1622u>g	c.1424T>G	p.L475R	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	PTPN11:p.L475R	267	25	9.4	12:112926291	157	0	0	12:112926291	153	0	0	12:112926291	247	0	0	12:112926291	258	0	0	12:112926291	311	0	0	12:112926291	300	0	0	12:112926291	376	0	0
PD12334b	4	55144092	C	A	PDGFRA	CCDS3495.1	r.2252c>a	c.1921C>A	p.L641I	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	PDGFRA:p.L641I	347	0	0	4:55144092	224	0	0	4:55144092	262	0	0	4:55144092	296	0	0	4:55144092	344	0	0	4:55144092	283	0	0	4:55144092	338	0	0	4:55144092	303	20	6.6
PD12334b	16	3777993	G	T	CREBBP	CCDS10509.1	r.7860c>a	c.7055C>A	p.P2352Q	Sub	missense	2	UNKOWN_OTHER	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	CREBBP:p.P2352Q	93	0	0	16:3777993	138	0	0	16:3777993	145	0	0	16:3777993	133	0	0	16:3777993	114	0	0	16:3777993	235	0	0	16:3777993	142	0	0	16:3777993	736	104	14.1
PD12334b	19	42798812	T	A	CIC	CCDS12601.1	r.4424u>a	c.4384T>A	p.S1462T	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	CIC:p.S1462T	239	1	0.4	19:42798812	449	119	26.5	19:42798812	493	0	0	19:42798812	366	0	0	19:42798812	277	0	0	19:42798812	547	1	0.2	19:42798812	368	0	0	19:42798812	1768	0	0
PD12334b	7	106508551	C	A	PIK3CG	CCDS5739.1	r.855c>a	c.545C>A	p.T182N	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	PIK3CG:p.T182N	347	65	18.7	7:106508551	723	146	20.2	7:106508551	629	154	24.5	7:106508551	515	59	11.5	7:106508551	404	94	23.3	7:106508551	754	148	19.6	7:106508551	471	64	13.6	7:106508551	1749	122	7
PD12334b	19	7143057	G	A	INSR	CCDS12176.1	r.2421c>u	c.2312C>T	p.T771M	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	INSR:p.T771M	84	23	27.4	19:7143057	146	38	26	19:7143057	143	37	25.9	19:7143057	102	26	25.5	19:7143057	90	31	34.4	19:7143057	208	65	31.2	19:7143057	118	33	28	19:7143057	688	139	20.2
PD12334b	15	41796818	C	T	LTK	CCDS10077.1	r.2292g>a	c.2141G>A	p.W714*	Sub	nonsense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	LTK:p.W714*	135	25	18.5	15:41796818	114	25	21.9	15:41796818	165	43	26.1	15:41796818	161	38	23.6	15:41796818	158	31	19.6	15:41796818	286	59	20.6	15:41796818	191	43	22.5	15:41796818	952	194	20.4
PD12334b	12	112892431	T	C	PTPN11	CCDS9163.1	r.787u>c	c.589T>C	p.Y197H	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	50	pS	2.5	2.5	3	3	40	4	YES	YES	PTPN11:p.Y197H	304	79	26	12:112892431	191	57	29.8	12:112892431	181	59	32.6	12:112892431	286	77	26.9	12:112892431	298	60	20.1	12:112892431	185	42	22.7	12:112892431	244	34	13.9	12:112892431	121	23	19
PD12334b	15	88679839	G	A	NTRK3	CCDS32322.1	r.786c>u	c.624C>T	p.D208D	Sub	silent	1	SILENT	SILENT	50	pS	2.5	2.5	3	3	40	4	YES	YES	NTRK3:p.D208D	113	0	0	15:88679839	81	0	0	15:88679839	111	0	0	15:88679839	128	0	0	15:88679839	139	0	0	15:88679839	185	0	0	15:88679839	157	0	0	15:88679839	480	31	6.5
PD12334b	3	178952085	A	G	PIK3CA	CCDS43171.1	r.3297a>g	c.3140A>G	p.H1047R	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	50	pS	2.5	2.5	3	3	40	4	YES	YES	PIK3CA:p.H1047R	229	0	0	3:178952085	160	0	0	3:178952085	190	0	0	3:178952085	197	0	0	3:178952085	284	2	0.7	3:178952085	121	0	0	3:178952085	214	10	4.7	3:178952085	76	1	1.3