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_PD9772a3	TUM_PILEUP_MUTS_PD9772a3	Pileup_MtAlpct_PD9772a3	ID.2	DEPTH_PD9772c	TUM_PILEUP_MUTS_PD9772c	Pileup_MtAlpct_PD9772c	ID.3	DEPTH_PD9772d	TUM_PILEUP_MUTS_PD9772d	Pileup_MtAlpct_PD9772d
PD9772b	5	112175087	G	C	APC	CCDS4107.1	r.4176g>c	c.3796G>C	p.D1266H	Sub	missense	1	UNKNOWN_BCA_GENE	UNKNOWN	46	pCR	3.7	0	3	1	95	0	YES	YES	APC:p.D1266H	68	0	0	5:112175087	36	2	5.6	5:112175087	48	8	16.7
PD9772b	16	343528	C	A	AXIN1	CCDS10405.1	r.2518g>u	c.2146G>T	p.E716*	Sub	nonsense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	pCR	3.7	0	3	1	95	0	YES	YES	AXIN1:p.E716*	46	37	80.4	16:343528	24	16	66.7	16:343528	39	23	59
PD9772b	7	27148184	G	A	HOXA3	CCDS5404.1	r.882c>u	c.682C>T	p.L228L	Sub	silent	3	SILENT	SILENT	46	pCR	3.7	0	3	1	95	0	YES	YES	HOXA3:p.L228L	110	64	58.2	7:27148184	93	38	40.9	7:27148184	108	36	33.3
PD9772b	3	10084343	T	G	FANCD2	CCDS2595.1	r.977u>g	c.884T>G	p.L295R	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	pCR	3.7	0	3	1	95	0	YES	YES	FANCD2:p.L295R	63	47	74.6	3:10084343	46	32	69.6	3:10084343	85	52	61.2
PD9772b	5	180057561	C	T	FLT4	CCDS4457.1	r.473g>a	c.394G>A	p.V132M	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	pCR	3.7	0	3	1	95	0	YES	YES	FLT4:p.V132M	51	0	0	5:180057561	15	4	26.7	5:180057561	25	1	4
PD9772b	11	108115649	G	T	ATM	CCDS31669.1	r.1182g>u	c.797G>T	p.W266L	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	46	pCR	3.7	0	3	1	95	0	YES	YES	ATM:p.W266L	60	38	63.3	11:108115649	26	8	30.8	11:108115649	51	25	49
PD9772b	17	7578263	G	A	TP53	CCDS11118.1	r.776c>u	c.586C>T	p.R196*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	46	pCR	3.7	0	3	1	95	0	YES	YES	TP53:p.R196*	250	210	84	17:7578263	146	103	70.5	17:7578263	182	110	60.4