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_PD14753a	TUM_PILEUP_MUTS_PD14753a	Pileup_MtAlpct_PD14753a	ID.2	DEPTH_PD14753c	TUM_PILEUP_MUTS_PD14753c	Pileup_MtAlpct_PD14753c	ID.3	DEPTH_PD14753d	TUM_PILEUP_MUTS_PD14753d	Pileup_MtAlpct_PD14753d	ID.4	DEPTH_PD14753e	TUM_PILEUP_MUTS_PD14753e	Pileup_MtAlpct_PD14753e	ID.5	DEPTH_PD14753f	TUM_PILEUP_MUTS_PD14753f	Pileup_MtAlpct_PD14753f
PD14753b	12	46245891	G	A	ARID2	CCDS31783.1	r.4113g>a	c.3985G>A	p.E1329K	Sub	missense	1	UNKNOWN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	ARID2:p.E1329K	95	7	7.4	12:46245891	129	0	0	12:46245891	277	69	24.9	12:46245891	291	1	0.3	12:46245891	209	0	0
PD14753b	X	44966779	G	C	KDM6A	CCDS14265.1	r.4044g>c	c.4003G>C	p.E1335Q	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	KDM6A:p.E1335Q	73	0	0	X:44966779	83	0	0	X:44966779	141	15	10.6	X:44966779	73	0	0	X:44966779	153	0	0
PD14753b	3	10083320	G	C	FANCD2	CCDS2595.1	r.802g>c	c.709G>C	p.E237Q	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	FANCD2:p.E237Q	125	13	10.4	3:10083320	217	31	14.3	3:10083320	274	25	9.1	3:10083320	349	0	0	3:10083320	375	0	0
PD14753b	7	2969691	C	T	CARD11	CCDS5336.2	r.1992g>a	c.1588G>A	p.E530K	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	CARD11:p.E530K	182	18	9.9	7:2969691	182	7	3.8	7:2969691	225	7	3.1	7:2969691	202	0	0	7:2969691	206	1	0.5
PD14753b	19	40317610	C	T	DYRK1B	CCDS12543.1	r.1393g>a	c.1113G>A	p.G371G	Sub	silent	3	SILENT	SILENT	46	RD	2.3	0.6	3	3	70	0	YES	YES	DYRK1B:p.G371G	30	0	0	19:40317610	22	1	4.5	19:40317610	54	6	11.1	19:40317610	36	0	0	19:40317610	48	0	0
PD14753b	12	53876419	C	A	MAP3K12	CCDS8860.1	r.2167g>u	c.2069G>T	p.G690V	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	MAP3K12:p.G690V	112	32	28.6	12:53876419	99	35	35.4	12:53876419	210	60	28.6	12:53876419	147	1	0.7	12:53876419	171	0	0
PD14753b	6	117709118	T	C	ROS1	CCDS5116.1	r.2038a>g	c.1839A>G	p.K613K	Sub	silent	3	SILENT	SILENT	46	RD	2.3	0.6	3	3	70	0	YES	YES	ROS1:p.K613K	111	0	0	6:117709118	159	0	0	6:117709118	213	0	0	6:117709118	416	0	0	6:117709118	442	109	24.7
PD14753b	4	55948737	G	A	KDR	CCDS3497.1	r.4024c>u	c.3728C>T	p.P1243L	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	KDR:p.P1243L	108	17	15.7	4:55948737	148	27	18.2	4:55948737	211	43	20.4	4:55948737	307	0	0	4:55948737	267	0	0
PD14753b	6	160517504	C	G	IGF2R	CCDS5273.1	r.6837c>g	c.6689C>G	p.S2230C	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	IGF2R:p.S2230C	146	0	0	6:160517504	193	0	0	6:160517504	312	34	10.9	6:160517504	276	0	0	6:160517504	255	0	0
PD14753b	9	87342605	C	G	NTRK2	CCDS6671.1	r.1828c>g	c.890C>G	p.S297*	Sub	nonsense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	NTRK2:p.S297*	113	6	5.3	9:87342605	136	0	0	9:87342605	235	28	11.9	9:87342605	275	0	0	9:87342605	313	0	0
PD14753b	6	135515561	C	G	MYB	CCDS47481.1	r.1110c>g	c.911C>G	p.S304*	Sub	nonsense	1	UNKNOWN_EFFECT_BCA_GENE	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	MYB:p.S304*	85	5	5.9	6:135515561	104	7	6.7	6:135515561	253	0	0	6:135515561	384	0	0	6:135515561	303	0	0
PD14753b	13	32972638	G	T	BRCA2	CCDS9344.1	r.10221g>u	c.9988G>T	p.E3330*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	46	RD	2.3	0.6	3	3	70	0	YES	YES	BRCA2:p.E3330*	106	19	17.9	13:32972638	121	29	24	13:32972638	231	47	20.3	13:32972638	141	0	0	13:32972638	256	0	0
PD14753b	17	7577538	C	T	TP53	CCDS11118.1	r.933g>a	c.743G>A	p.R248Q	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	46	RD	2.3	0.6	3	3	70	0	YES	YES	TP53:p.R248Q	145	35	24.1	17:7577538	164	36	22	17:7577538	247	64	25.9	17:7577538	282	266	94.3	17:7577538	212	96	45.3
PD14753b	7	151859945	C	G	MLL3	CCDS5931.1	r.10936g>c	c.10717G>C	p.D3573H	Sub	missense	1	UNKNOWN_BCA	UNKNOWN	46	RD	2.3	0.6	3	3	70	0	YES	YES	MLL3:p.D3573H	153	42	27.5	7:151859945	185	63	34.1	7:151859945	320	116	36.2	7:151859945	544	0	0	7:151859945	364	0	0