BRCAness digitalMLPA profiling predicts benefit of intensified platinum-based chemotherapy in triple-negative and luminal-type breast cancer

Lips, Esther H.; Benard-Slagter, Anne; Opdam, Mark; Scheerman, Caroline E.; Wesseling, Jelle; Hogervorst, Frans B. L.; Linn, Sabine C.; Savola, Suvi; Nederlof, Petra M.

doi:10.1186/s13058-020-01313-7

Table 1 Patient and sample characteristics

From: BRCAness digitalMLPA profiling predicts benefit of intensified platinum-based chemotherapy in triple-negative and luminal-type breast cancer

A. Series 1 for development of the BRCA1 classifier
	Training set		Validation set
	N	%	N	%
Material type
Fresh frozen	27	38	24	34
FFPE	44	62	46	66
ER status
ER neg	48	68	48	69
ER pos	21	30	21	30
Unknown	2	3	1	1
HER status
HER2 neg	24	34	21	30
HER2 pos	4	6	3	4
Unknown	43	61	56	66
Array-based BRCA1-like classification
Non-BRCA1-like	30	42	28	40
BRCA1-like	41	58	42	60
Mutation status
BRCA1mut	8	11	8	11
BRCA2mut	2	3	3	4
Unknown	61	86	59	84
BRCA1 promoter methylation
Non-methylated	39	55	36	51
BRCA1-methylated	14	20	12	17
Unknown	18	25	22	31
B. Series 2 for development of the BRCA2 classifier
	Training set		Validation set
	N	%	N	%
Material type
Fresh frozen	21	38	21	38
FFPE	34	62	35	63
ER status
ER neg	13	24	16	29
ER pos	40	73	38	68
Unknown	2	4	2	4
HER status
HER2 neg	20	36	20	36
HER2 pos	5	9	4	7
Unknown	30	55	32	57
Array-based BRCA2-like classification
Non-BRCA2-like	30	55	28	50
BRCA2-like	25	46	28	50
Mutation status
BRCA1mut	1	13	1	13
BRCA2mut	7	88	7	88
Unknown	47		48
C. Series 3 for assessing treatment prediction power
	FEC	HD-CTC	Total	pvalue
	n(%)	n(%)	n(%)
Age
< 40	17 (32%)	20 (29%)	37 (30%)	0.84
> 40	36 (68%)	49 (71%)	85 (70%)
ER status
Neg	21 (40%)	22 (32%)	43 (35%)	0.45
Pos	32 (60%)	47 (68%)	79 (65%)
PR status
Neg	30 (57%)	28 (41%)	58 (48%)	0.10
Pos	23 (43%)	41 (59%)	64 (52%)
pT-stage
1	6 (11%)	16 (23%)	22 (18%)	0.03
2	37 (70%)	49 (71%)	86 (70%)
3	10 (19%)	4 (6%)	14 (11%)
Grade
I	6 (12%)	13 (21%)	19 (17%)	0.17
II	16 (31%)	25 (40%)	41 (35%)
III	29 (57%)	25 (40%)	54 (47%)
No. of positive lymph nodes
< 10	34 (64%)	47 (68%)	81 (66%)	0.70
≥ 10	19 (36%)	22 (32%)	41 (34%)
Array-based BRCA1-like classification
Non-BRCA1-like	39 (74%)	56 (81%)	95 (78%)	0.38
BRCA1-like	14 (26%)	13 (19%)	27 (22%)
Array-based BRCA2-like classification
Non-BRCA2-like	40 (75%)	53 (77%)	93 (76%)	1.00
BRCA2-like	13 (23%)	16 (23%)	29 (24%)
D. Clinical variables in patients included in the digitalMLPA analysis and in the total HER2-negative trial population
	digitalMLPA tested,n(%)	digitalMLPA not tested,n(%)	pvalue
n	122	500
Age (median (SD))	44.00 (6.96)	44.67 (6.12)	0.28
Treatment
CONV	53 (43.4)	249 (49.8)	0.25
HD	69 (56.6)	251 (50.2)
ER status
Negative (< 10%)	43 (35.2)	106 (21.2)	< 0.01
Positive (≥ 10%)	79 (64.8)	393 (78.6)
NA	0 (0.0)	1 (0.2)
PR status
Negative (< 10%)	58 (47.5)	170 (34.0)	0.01
Positive (≥ 10%)	64 (52.5)	319 (63.8)
NA	0 (0.0)	11 (2.2)
pT-stage
1	22 (18.0)	129 (25.8)	0.05
2	86 (70.5)	290 (58.0)
3	14 (11.5)	79 (15.8)
NA	0 (0.0)	2 (0.4)
Grade
Grade I	19 (15.6)	121 (24.2)	0.05
Grade II	41 (33.6)	192 (38.4)
Grade III	54 (44.3)	176 (35.2)
NA	8 (6.6)	11 (2.2)
No. of positive lymph nodes
LN < 10	81 (66.4)	324 (64.8)	0.82
LN ≥ 10	41 (33.6)	176 (35.2)
Array-based BRCA1-like classification
Non-BRCA1-like	95 (77.9)	115 (23.0)	0.05
BRCA1-like	27 (22.1)	16 (3.2)
NA	0 (0.0)	369 (73.8)
Array-based BRCA2-like classification
Non-BRCA2-like	93 (76.2)	105 (21.0)	0.27
BRCA2-like	29 (23.8)	22 (4.4)
NA	0 (0.0)	373 (74.6)

FFPE formalin-fixed, parafin-embedded, ER estrogen-receptor, PR progesterone receptor, pT-stage pathological Tumor size, FEC 5-fluorouracil-epirubicin-cyclophosphamide, HD-CTC high-dose cyclophosphamide-thiotepa-carboplatin, CONV conventional dose 5-fluorouracil-epirubicin-cyclophosphamide, HD high-dose cyclophosphamide-thiotepa-carboplatin, NA not available

Back to article page

ISSN: 1465-542X

Contact us

Submission enquiries: journalsubmissions@springernature.com

Breast Cancer Research

Contact us