Table 4 Copy number variations stratified by BRCA status

From: Mutational profiling of familial male breast cancers reveals similarities with luminal A female breast cancer with rare TP53 mutations

		Gains				Losses
Gene	Chromosome position	All cases (%)	*BRCA1* (%)	*BRCA2* (%)	BRCAX (%)	All cases (%)	*BRCA1* (%)	*BRCA2* (%)	BRCAX (%)
NRAS	1p13.2	2.3	0.0	0.0	4.0	29.5	0.0	31.3	32.0
MPL	1p34	20.5	33.3	25.0	16.0	4.5	0.0	0.0	8.0
ALK	2p23	2.3	0.0	0.0	4.0	20.5	0.0	18.8	24.0
IDH1	2q33.3	15.9	33.3	12.5	16.0	9.1	0.0	18.8	4.0
ERBB4	2q33.3–q34	6.8	0.0	6.3	8.0	20.5	33.3	12.5	24.0
CTNNB1	3p21	25.0	0.0	31.3	24.0	9.1	33.3	6.3	8.0
MLH1	3p21.3	18.2	33.3	18.8	16.0	0.0	0.0	0.0	0.0
VHL	3p25.3	6.8	0.0	12.5	4.0	6.8	0.0	0.0	12.0
PIK3CA	3q26.3	6.8	0.0	12.5	4.0	15.9	0.0	12.5	20.0
FGFR3	4p16.3	18.2	0.0	31.3	12.0	15.9	0.0	12.5	20.0
RP11-530I17.1	4q11–q12	0.0	0.0	0.0	0.0	11.4	0.0	12.5	12.0
KDR	4q11–q12	0.0	0.0	0.0	0.0	13.6	0.0	18.8	12.0
KIT	4q11–q12	0.0	0.0	0.0	0.0	29.5	0.0	25.0	36.0
FIP1L1	4q12	2.3	0.0	6.3	0.0	29.5	0.0	25.0	36.0
PDGFRA	4q12	2.3	0.0	6.3	0.0	29.5	0.0	25.0	36.0
FBXW7	4q31.3	6.8	0.0	12.5	4.0	27.3	0.0	31.3	28.0
APC	5q21–q22	2.3	0.0%	6.3	0.0	29.5	0.0	37.5	28.0
CTC-554D6.1	5q22.2	2.3	0.0	6.3	0.0	29.5	0.0	37.5	28.0
CSF1R	5q32	13.6	0.0	18.8	12.0	6.8	0.0	6.3	8.0
NPM1	5q35.1	0.0	0.0	0.0	0.0	6.8	0.0	0.0	12.0
EGFR	7p12	0.0	0.0	0.0	0.0	22.7	0.0	18.8	28.0
RP5-1091E12.1	7p12	6.8	0.0	6.3	8.0	13.6	0.0	18.8	12.0
MET	7q31	2.3	0.0	6.3	0.0	27.3	0.0	25.0	32.0
RP11-286H14.8	7q32	4.5	0.0	6.3	4.0	25.0	0.0	31.3	24.0
SMO	7q32.1	2.3	0.0	6.3	0.0	18.2	0.0	18.8	20.0
BRAF	7q34	9.1	33.3	6.3	8.0	20.5	0.0	18.8	24.0
FGFR1	8p12	18.2	0.0	12.5	24.0	11.4	0.0	6.3	16.0
RP11-350N15.4	8p12	13.6	0.0	6.3	20.0	11.4	0.0	6.3	16.0
CDKN2A	9p21	4.5	0.0	0.0	7.7	4.5	0.0	20.0	0.0
GNAQ	9q21	2.3	0.0	0.0	4.0	36.4	0.0	37.5	40.0
MTAP	9p21	2.3	0.0	0.0	4.0	2.3	0.0	20.0	0.0
JAK2	9p24	4.5	0.0	6.3	4.0	25.0	33.3	25.0	24.0
ABL1	9q34.1	0.0	0.0	0.0	0.0	47.7	66.7	43.8	48.0
RET	10q11.2	4.5	0.0	12.5	0.0	15.9	0.0	6.3	24.0
PTEN	10q23.2	2.3	0.0	6.3	0.0	27.3	0.0	31.3	28.0
FGFR2	10q26	6.8	0.0	6.3	8.0	13.6	0.0	12.5	16.0
HRAS	11p15.5	15.9	0.0	37.5*	4.0	4.5	0.0	6.3	4.0
ATM	11q22–q23	2.3	0.0	6.3	0.0	34.1	66.7	31.3	32.0
C11orf65	11q22.3	2.3	33.3	0.0	0.0	38.6	66.7	37.5	36.0
KRAS	12p12.1	0.0	0.0	0.0	0.0	27.3	0.0	31.3	28.0
PTPN11	12q24.1	2.3	0.0	0.0	4.0	11.4	0.0	6.3	16.0
HNF1A	12q24.2	11.4	0.0	6.3	16.0	25.0	0.0	25.0	28.0
FLT3	13q12	6.8	33.3	6.3	4.0	15.9	0.0	6.3	24.0
RB1	13q12	0.0	0.0	0.0	0.0	25.0	0.0	43.8**	16.0
AKT1	14q32.32	9.1	0.0	12.5	8.0	6.8	0.0	6.3	8.0
CDH1	16q22.1	6.8	0.0	6.3	8.0	13.6	0.0	18.8	12.0
ERBB2	17q12	9.1	33.3	6.3	8.0	4.5	0.0	0.0	8.0
TP53	17q13.1	0.0	0.0	0.0	0.0	15.9	0.0	12.5	20.0
SMAD4	18q21.1	0.0	0.0	0.0	0.0	22.7	33.3	25.0	20.0
JAK3	19p13.1	2.3	0.0	6.3	0.0	18.2	0.0	12.5	24.0
NOTCH1	19p13.2–p13.1	9.1	0.0	12.5	8.0	22.7	66.7	18.8	20.0
STK11	19p13.3	9.1	0.0	25.0***	0.0	9.1	0.0	12.5	8.0
GNA11	19p13.3	2.3	0.0	0.0	4.0	20.5	0.0	25.0	20.0
SRC	20q12–q13	11.4	0.0	12.5	12.0	13.6	33.3	12.5	12.0
GNAS	20q13.3	34.1	0.0	50.0	28.0	4.5	0.0	0.0	8.0
SMARCB1	22q11.23	6.8	0.0	18.8***	0.0	20.5	0.0	12.5	28.0

*P=0.0061; **P=0.0270; ***P=0.0134; ****P=0.0423. Light grey=30–40% frequency; medium grey=40–50% frequency; dark grey=>50% frequency.

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Table 4 Copy number variations stratified by BRCA status

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