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_PD9770a	TUM_PILEUP_MUTS_PD9770a	Pileup_MtAlpct_PD9770a	ID.2	DEPTH_PD9770c	TUM_PILEUP_MUTS_PD9770c	Pileup_MtAlpct_PD9770c	ID.3	DEPTH_PD9770d	TUM_PILEUP_MUTS_PD9770d	Pileup_MtAlpct_PD9770d	ID.4	DEPTH_PD9770e	TUM_PILEUP_MUTS_PD9770e	Pileup_MtAlpct_PD9770e	ID.5	DEPTH_PD9770e2	TUM_PILEUP_MUTS_PD9770e2	Pileup_MtAlpct_PD9770e2	ID.6	DEPTH_PD9770f	TUM_PILEUP_MUTS_PD9770f	Pileup_MtAlpct_PD9770f
PD9770b	3	178952085	A	G	PIK3CA	CCDS43171.1	r.3297a>g	c.3140A>G	p.H1047R	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	62	RD	3.1	1.7	2	1	40	1	YES	YES	PIK3CA:p.H1047R	79	18	22.8	3:178952085	20	7	35	3:178952085	14	1	7.1	3:178952085	25	3	12	3:178952085	37	15	40.5	3:178952085	25	1	4
PD9770b	1	120496303	C	A	NOTCH2	CCDS908.1	r.2448g>u	c.2228G>T	p.C743F	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	62	RD	3.1	1.7	2	1	40	1	YES	YES	NOTCH2:p.C743F	81	0	0	1:120496303	22	0	0	1:120496303	9	0	0	1:120496303	28	0	0	1:120496303	50	0	0	1:120496303	31	4	12.9
PD9770b	20	31017154	A	T	ASXL1	CCDS13201.1	r.909a>u	c.485A>T	p.K162M	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	62	RD	3.1	1.7	2	1	40	1	YES	YES	ASXL1:p.K162M	102	19	18.6	20:31017154	29	7	24.1	20:31017154	39	10	25.6	20:31017154	53	10	18.9	20:31017154	51	14	27.5	20:31017154	45	5	11.1
PD9770b	19	15285015	G	T	NOTCH3	CCDS12326.1	r.4676c>a	c.4600C>A	p.R1534R	Sub	silent	3	SILENT	SILENT	62	RD	3.1	1.7	2	1	40	1	YES	YES	NOTCH3:p.R1534R	62	0	0	19:15285015	84	0	0	19:15285015	51	0	0	19:15285015	12	0	0	19:15285015	15	0	0	19:15285015	31	4	12.9
PD9770b	19	33792828	G	A	CEBPA	ENST00000498907	r.643c>u	c.493C>T	p.R165C	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	62	RD	3.1	1.7	2	1	40	1	YES	YES	CEBPA:p.R165C	15	0	0	19:33792828	64	0	0	19:33792828	35	0	0	19:33792828	0	0	NA	19:33792828	7	4	57.1	19:33792828	10	0	0
PD9770b	1	154951221	C	T	CKS1B	CCDS1077.1	r.255c>u	c.208C>T	p.R70W	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	62	RD	3.1	1.7	2	1	40	1	YES	YES	CKS1B:p.R70W	87	22	25.3	1:154951221	24	10	41.7	1:154951221	19	8	42.1	1:154951221	87	24	27.6	1:154951221	69	38	55.1	1:154951221	62	13	21
PD9770b	17	7577022	G	A	TP53	CCDS11118.1	r.1106c>u	c.916C>T	p.R306*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	62	RD	3.1	1.7	2	1	40	1	YES	YES	TP53:p.R306*	122	41	33.6	17:7577022	28	16	57.1	17:7577022	45	13	28.9	17:7577022	26	4	15.4	17:7577022	39	21	53.8	17:7577022	47	7	14.9