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_PD12335a	TUM_PILEUP_MUTS_PD12335a	Pileup_MtAlpct_PD12335a	ID.2	DEPTH_PD12335c	TUM_PILEUP_MUTS_PD12335c	Pileup_MtAlpct_PD12335c	ID.3	DEPTH_PD12335d	TUM_PILEUP_MUTS_PD12335d	Pileup_MtAlpct_PD12335d	ID.4	DEPTH_PD12335e	TUM_PILEUP_MUTS_PD12335e	Pileup_MtAlpct_PD12335e	ID.5	DEPTH_PD12335f	TUM_PILEUP_MUTS_PD12335f	Pileup_MtAlpct_PD12335f	ID.6	DEPTH_PD12335g	TUM_PILEUP_MUTS_PD12335g	Pileup_MtAlpct_PD12335g	ID.7	DEPTH_PD12335h	TUM_PILEUP_MUTS_PD12335h	Pileup_MtAlpct_PD12335h	ID.8	DEPTH_PD12335i	TUM_PILEUP_MUTS_PD12335i	Pileup_MtAlpct_PD12335i
PD12335b	17	37673790	C	G	CDK12	CCDS11337.1	r.3255c>g	c.2944C>G	p.L982V	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	CDK12:p.L982V	463	15	3.2	17:37673790	1309	53	4	17:37673790	738	30	4.1	17:37673790	748	23	3.1	17:37673790	2922	112	3.8	17:37673790	951	32	3.4	17:37673790	2122	87	4.1	17:37673790	1367	52	3.8
PD12335b	4	55561905	A	C	KIT	CCDS3496.1	r.392a>c	c.295A>C	p.N99H	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	KIT:p.N99H	137	2	1.5	4:55561905	487	0	0	4:55561905	260	7	2.7	4:55561905	432	0	0	4:55561905	719	49	6.8	4:55561905	199	9	4.5	4:55561905	524	32	6.1	4:55561905	271	8	3
PD12335b	X	41203516	C	T	DDX3X	CCDS43931.1	r.1744c>u	c.889C>T	p.P297S	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	DDX3X:p.P297S	62	0	0	X:41203516	208	0	0	X:41203516	116	0	0	X:41203516	152	0	0	X:41203516	454	38	8.4	X:41203516	148	0	0	X:41203516	265	11	4.2	X:41203516	176	0	0
PD12335b	1	27058045	C	T	ARID1A	CCDS285.1	r.2124c>u	c.1753C>T	p.Q585*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	80	pS	4	4	2	2	29	NA	NO	NO	ARID1A:p.Q585*	412	96	23.3	1:27058045	583	122	20.9	1:27058045	614	193	31.4	1:27058045	638	156	24.5	1:27058045	494	113	22.9	1:27058045	637	129	20.3	1:27058045	531	181	34.1	1:27058045	403	82	20.3
PD12335b	5	180038409	G	A	FLT4	CCDS4457.1	r.3687c>u	c.3608C>T	p.S1203F	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	FLT4:p.S1203F	267	10	3.7	5:180038409	158	13	8.2	5:180038409	205	0	0	5:180038409	172	11	6.4	5:180038409	147	0	0	5:180038409	300	0	0	5:180038409	154	0	0	5:180038409	140	0	0
PD12335b	11	76257223	C	T	C11orf30	CCDS8244.1	r.3799c>u	c.3656C>T	p.S1219F	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	C11orf30:p.S1219F	99	14	14.1	11:76257223	366	42	11.5	11:76257223	161	19	11.8	11:76257223	346	29	8.4	11:76257223	612	47	7.7	11:76257223	184	18	9.8	11:76257223	458	58	12.7	11:76257223	257	34	13.2
PD12335b	20	62161484	G	T	PTK6	CCDS13524.1	r.1143c>a	c.1115C>A	p.S372Y	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	PTK6:p.S372Y	502	19	3.8	20:62161484	527	31	5.9	20:62161484	645	28	4.3	20:62161484	571	37	6.5	20:62161484	469	1	0.2	20:62161484	634	0	0	20:62161484	566	0	0	20:62161484	391	0	0
PD12335b	6	160500662	C	T	IGF2R	CCDS5273.1	r.5677c>u	c.5529C>T	p.V1843V	Sub	silent	3	SILENT	SILENT	80	pS	4	4	2	2	29	NA	NO	NO	IGF2R:p.V1843V	194	11	5.7	6:160500662	360	27	7.5	6:160500662	370	21	5.7	6:160500662	430	48	11.2	6:160500662	338	25	7.4	6:160500662	386	28	7.3	6:160500662	391	31	7.9	6:160500662	233	20	8.6
PD12335b	9	80409396	C	A	GNAQ	CCDS6658.1	r.941g>u	c.718G>T	p.V240L	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	80	pS	4	4	2	2	29	NA	NO	NO	GNAQ:p.V240L	34	5	14.7	9:80409396	58	14	24.1	9:80409396	62	19	30.6	9:80409396	28	2	7.1	9:80409396	73	8	11	9:80409396	78	12	15.4	9:80409396	149	36	24.2	9:80409396	150	25	16.7