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_PD9852a	TUM_PILEUP_MUTS_PD9852a	Pileup_MtAlpct_PD9852a	ID.2	DEPTH_PD9852c	TUM_PILEUP_MUTS_PD9852c	Pileup_MtAlpct_PD9852c	ID.3	DEPTH_PD9852d	TUM_PILEUP_MUTS_PD9852d	Pileup_MtAlpct_PD9852d	ID.4	DEPTH_PD9852e	TUM_PILEUP_MUTS_PD9852e	Pileup_MtAlpct_PD9852e	ID.5	DEPTH_PD9852g	TUM_PILEUP_MUTS_PD9852g	Pileup_MtAlpct_PD9852g	ID.6	DEPTH_PD9852h	TUM_PILEUP_MUTS_PD9852h	Pileup_MtAlpct_PD9852h	ID.7	DEPTH_PD9852i	TUM_PILEUP_MUTS_PD9852i	Pileup_MtAlpct_PD9852i
PD9852b	3	134920419	T	C	EPHB1	CCDS46921.1	r.2604u>c	c.2234T>C	p.L745P	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	EPHB1:p.L745P	248	54	21.8	3:134920419	251	76	30.3	3:134920419	221	41	18.6	3:134920419	253	81	32	3:134920419	194	37	19.1	3:134920419	300	60	20	3:134920419	186	43	23.1
PD9852b	6	160511040	C	T	IGF2R	CCDS5273.1	r.6708c>u	c.6560C>T	p.A2187V	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	IGF2R:p.A2187V	259	0	0	6:160511040	219	0	0	6:160511040	189	0	0	6:160511040	192	0	0	6:160511040	195	15	7.7	6:160511040	298	0	0	6:160511040	190	1	0.5
PD9852b	12	420130	T	A	KDM5A	CCDS41736.1	r.3500a>u	c.3137A>T	p.Q1046L	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	KDM5A:p.Q1046L	227	19	8.4	12:420130	167	32	19.2	12:420130	219	24	11	12:420130	180	33	18.3	12:420130	188	17	9	12:420130	259	26	10	12:420130	159	22	13.8
PD9852b	2	39515316	C	T	MAP4K3	CCDS1803.1	r.1745g>a	c.1420G>A	p.V474I	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	MAP4K3:p.V474I	241	0	0	2:39515316	266	0	0	2:39515316	178	0	0	2:39515316	217	0	0	2:39515316	203	0	0	2:39515316	284	9	3.2	2:39515316	176	14	8
PD9852b	20	46277813	C	T	NCOA3	CCDS13407.1	r.3802c>u	c.3611C>T	p.A1204V	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	NCOA3:p.A1204V	192	26	13.5	20:46277813	163	29	17.8	20:46277813	175	18	10.3	20:46277813	180	28	15.6	20:46277813	201	12	6	20:46277813	230	8	3.5	20:46277813	170	3	1.8
PD9852b	3	178952085	A	G	PIK3CA	CCDS43171.1	r.3297a>g	c.3140A>G	p.H1047R	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	75	pS	4	4	3	1	32	0	YES	YES	PIK3CA:p.H1047R	203	52	25.6	3:178952085	294	132	44.9	3:178952085	200	58	29	3:178952085	236	68	28.8	3:178952085	243	45	18.5	3:178952085	138	29	21	3:178952085	182	50	27.5
PD9852b	6	106552889	G	A	PRDM1	CCDS5054.2	r.1088g>a	c.854G>A	p.R285K	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	75	pS	4	4	3	1	32	0	YES	YES	PRDM1:p.R285K	407	1	0.2	6:106552889	294	0	0	6:106552889	289	26	9	6:106552889	292	0	0	6:106552889	280	1	0.4	6:106552889	419	0	0	6:106552889	282	0	0
PD9852b	17	7578437	G	A	TP53	CCDS11118.1	r.683c>u	c.493C>T	p.Q165*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	75	pS	4	4	3	1	32	0	YES	YES	TP53:p.Q165*	151	47	31.1	17:7578437	103	45	43.7	17:7578437	87	25	28.7	17:7578437	93	36	38.7	17:7578437	112	32	28.6	17:7578437	156	41	26.3	17:7578437	117	32	27.4