Table 2 Association of Average Mutant Allele Frequencies at baseline (T0) with patient and tumor characteristics.

Clinical characteristics			Patients, n (%)	Average MAF at baseline for all variants (%)	p value
Patients	Age, years	≤ 50	15 (58)	1.89	0.2010
	Age, years	> 50	11 (42)	3.90	0.2010
	BRCA 1/2 mutated^a	Positive	4 (57)	1.76	0.0245
	BRCA 1/2 mutated^a	Negative	3 (43)	0.34	0.0245
Pre-NAC (Neoadjuvant chemotherapy) tumor	cT	1–2	21 (81)	1.05	0.0127
	cT	3–4	5 (19)	11.65	0.0127
	cN	0	13 (50)	1.10	0.0216
	cN	1–3	13 (50)	4.78	0.0216
	Stage	I	1 (4)	0.01	Only 1 value
		II	19 (73)	1.15	0.0167
		III	4 (22)	9.73	0.0167
	Grade	1	0 (0)		No value
		2	5 (19)	0.42	0.0019
		3	21 (81)	3.30	0.0019
	Histological type^b	Ductal	25 (89)	3.00	0.0842
	Histological type^b	Lobular	3 (11)	13.26	0.0842
Treatment	NAC drugs regimen	Only taxane	4 (15)	0.51	0.2392
		AT	17 (65)	3.94
		TA	3 (12)	0.80
		Other	2 (8)	4.39
Post-NAC tumor^c	pN	Negative	17 (68)	1.15	0.0207
	pN	Positive	8 (32)	6.24	0.0207
	Residual tumor size (cm)	0	9 (36)	0.64	0.0626
		≤ 2	4 (16)	1.39
		> 2	12 (48)	4.69
	RCB	0	8 (31)	0.69	0.0065
		≥ 1	18 (69)	3.57	0.0065
		0–1	11 (42)	0.96	0.0146
		2–3	15 (58)	3.90	0.0146

Average MAF of all 117 gene variants according to different patient characteristics (age, BRCA1/2 status), pre-neoadjuvant chemotherapy (pre-NAC) tumor characteristics (cT, cN, stage, grade, and histology), treatment (NAC), or post-NAC tumor characteristics (pN, residual tumor size, RCB score). Stage (cT, cN and stage) is according to the AJCC 8th edition. NAC drug regimens were classified as only taxanes, anthracycline before (AT) or after (TA) taxanes, or other regimens. Average MAF is compared with a two-tailed Student’s t test when there were 2 independent groups and with an analysis of variance (ANOVA) test when there were more than 2. Italic is added when there are not enough values to do the calculation and there are no p values < 0.05.
^aBRCA1/2 status: unknown data for 19, so we have n = 7.
^b2 patients had lobular and ductal breast cancer, so we have n = 28.
^cOne patient had no surgery due to the development of metastatic disease, so we have n = 25 at the surgery for pN and residual tumor size. This patient was assigned an RCB score = 3.

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