Table 3. Open in new tab Case-control...

Gene	ER+/HER2-	ER+/HER2+	ER-/HER2+	TNBC
ATM	136	13 197	1.0	2.65 (2.17 to 3.21)	44	2892	1.5	3.99 (2.88 to 5.40)	16	1321	1.2	3.21 (1.86 to 5.13)	11	5204	0.2	0.57 (0.29 to 0.98)
BARD1	18	12 280	0.2	1.53 (0.9 to 2.46)	7	2703	0.3	2.74 (1.15 to 5.49)	3	1229	0.2	2.60 (0.64 to 6.93)	44	4824	0.9	9.76 (6.77 to 13.87)
BRCA1	134	16 935	0.8	3.66 (2.95 to 4.53)	24	3778	0.6	3.00 (1.92 to 4.48)	23	1697	1.4	6.56 (4.14 to 9.88)	370	6723	5.5	28.62 (24.16 to 34)
BRCA2	307	16 935	1.8	5.96 (5.09 to 6.98)	58	3778	1.5	5.05 (3.77 to 6.64)	21	1697	1.2	4.08 (2.54 to 6.2)	164	6723	2.4	8.16 (6.73 to 9.86)
BRIP1	35	12 322	0.3	1.38 (0.95 to 1.94)	6	2708	0.2	1.08 (0.43 to 2.23)	1	1233	0.1	0.40 (0.02 to 1.76)	21	4832	0.4	2.09 (1.30 to 3.20)
CDH1	20	16 537	0.1	8.51 (4.36 to 17.04)	2	3699	0.1	3.84 (0.60 to 13.68)	1	1658	0.1	4.29 (0.24 to 21.26)	4	6569	0.1	4.46 (1.26 to 12.43)
CHEK2	221	13 190	1.7	2.35 (2.02 to 2.73)	68	2889	2.4	3.48 (2.68 to 4.44)	12	1320	0.9	1.37 (0.73 to 2.31)	15	5189	0.3	0.45 (0.26 to 0.72)
MSH6	17	7605	0.2	2.25 (1.30 to 3.66)	5	1570	0.3	3.23 (1.14 to 7.14)	1	722	0.1	1.41 (0.08 to 6.32)	7	2726	0.3	2.66 (1.12 to 5.33)
NBN	32	12 280	0.3	1.81 (1.22 to 2.62)	6	2703	0.2	1.57 (0.62 to 3.26)	1	1229	0.1	0.58 (0.03 to 2.59)	10	4824	0.2	1.48 (0.73 to 2.66)
NF1	10	12 089	0.1	2.36 (1.11 to 4.56)	5	2654	0.2	5.38 (1.85 to 12.5)	1	1205	0.1	2.35 (0.13 to 10.83)	10	4750	0.2	5.68 (2.68 to 10.94)
PALB2	119	14 004	0.9	5.15 (4.07 to 6.5)	19	3084	0.6	3.74 (2.25 to 5.86)	8	1390	0.6	3.49 (1.57 to 6.64)	73	5530	1.3	7.88 (5.96 to 10.32)
PTEN	13	16 975	0.1	10.35 (4.32 to 26.55)	2	3786	0.1	6.76 (1.02 to 26.9)	2	1702	0.1	14.46 (2.19 to 57.05)	2	6727	0.0	3.64 (0.55 to 14.31)
RAD51C	17	12 322	0.1	1.60 (0.92 to 2.61)	2	2708	0.1	0.87 (0.14 to 2.75)	3	1233	0.2	2.94 (0.72 to 7.84)	17	4832	0.4	4.56 (2.61 to 7.50)
RAD51D	6	12 131	0.1	1.14 (0.43 to 2.46)	1	2659	0.0	0.86 (0.05 to 3.92)	1	1209	0.1	1.91 (0.11 to 8.74)	8	4758	0.2	4.14 (1.80 to 8.35)
TP53	16	17 004	0.1	3.45 (1.83 to 6.28)	12	3793	0.3	11.95 (5.84 to 23.0)	10	1704	0.6	22.71 (10.45 to 45.49)	5	6746	0.1	2.95 (1.00 to 7.04)
Total Freq (%)		7.6				8.4					7.0				12.5

Gene

ER+/HER2-

ER+/HER2+

ER-/HER2+

TNBC

No. mut

No. tested

Freq (%)

OR (95% CI)

No. mut

No. tested

Freq (%)

OR (95% CI)

No. mut

No. tested

Freq (%)

OR (95% CI)

No. mut

No.tested

Freq (%)

OR (95% CI)

ATM

136

13 197

1.0

2.65 (2.17 to 3.21)

2892

1.5

3.99 (2.88 to 5.40)

1321

1.2

3.21 (1.86 to 5.13)

5204

0.2

0.57 (0.29 to 0.98)

BARD1

12 280

0.2

1.53 (0.9 to 2.46)

2703

0.3

2.74 (1.15 to 5.49)

1229

0.2

2.60 (0.64 to 6.93)

4824

0.9

9.76 (6.77 to 13.87)

BRCA1

134

16 935

0.8

3.66 (2.95 to 4.53)

3778

0.6

3.00 (1.92 to 4.48)

1697

1.4

6.56 (4.14 to 9.88)

370

6723

5.5

28.62 (24.16 to 34)

BRCA2

307

16 935

1.8

5.96 (5.09 to 6.98)

3778

1.5

5.05 (3.77 to 6.64)

1697

1.2

4.08 (2.54 to 6.2)

164

6723

2.4

8.16 (6.73 to 9.86)

BRIP1

12 322

0.3

1.38 (0.95 to 1.94)

2708

0.2

1.08 (0.43 to 2.23)

1233

0.1

0.40 (0.02 to 1.76)

4832

0.4

2.09 (1.30 to 3.20)

CDH1

16 537

0.1

8.51 (4.36 to 17.04)

3699

0.1

3.84 (0.60 to 13.68)

1658

0.1

4.29 (0.24 to 21.26)

6569

0.1

4.46 (1.26 to 12.43)

CHEK2

221

13 190

1.7

2.35 (2.02 to 2.73)

2889

2.4

3.48 (2.68 to 4.44)

1320

0.9

1.37 (0.73 to 2.31)

5189

0.3

0.45 (0.26 to 0.72)

MSH6

7605

0.2

2.25 (1.30 to 3.66)

1570

0.3

3.23 (1.14 to 7.14)

722

0.1

1.41 (0.08 to 6.32)

2726

0.3

2.66 (1.12 to 5.33)

NBN

12 280

0.3

1.81 (1.22 to 2.62)

2703

0.2

1.57 (0.62 to 3.26)

1229

0.1

0.58 (0.03 to 2.59)

4824

0.2

1.48 (0.73 to 2.66)

NF1

12 089

0.1

2.36 (1.11 to 4.56)

2654

0.2

5.38 (1.85 to 12.5)

1205

0.1

2.35 (0.13 to 10.83)

4750

0.2

5.68 (2.68 to 10.94)

PALB2

119

14 004

0.9

5.15 (4.07 to 6.5)

3084

0.6

3.74 (2.25 to 5.86)

1390

0.6

3.49 (1.57 to 6.64)

5530

1.3

7.88 (5.96 to 10.32)

PTEN

16 975

0.1

10.35 (4.32 to 26.55)

3786

0.1

6.76 (1.02 to 26.9)

1702

0.1

14.46 (2.19 to 57.05)

6727

0.0

3.64 (0.55 to 14.31)

RAD51C

12 322

0.1

1.60 (0.92 to 2.61)

2708

0.1

0.87 (0.14 to 2.75)

1233

0.2

2.94 (0.72 to 7.84)

4832

0.4

4.56 (2.61 to 7.50)

RAD51D

12 131

0.1

1.14 (0.43 to 2.46)

2659

0.0

0.86 (0.05 to 3.92)

1209

0.1

1.91 (0.11 to 8.74)

4758

0.2

4.14 (1.80 to 8.35)

TP53

17 004

0.1

3.45 (1.83 to 6.28)

3793

0.3

11.95 (5.84 to 23.0)

1704

0.6

22.71 (10.45 to 45.49)

6746

0.1

2.95 (1.00 to 7.04)

Total Freq (%)

7.6

8.4

7.0

12.5

Gene	ER+/HER2-	ER+/HER2+	ER-/HER2+	TNBC
ATM	136	13 197	1.0	2.65 (2.17 to 3.21)	44	2892	1.5	3.99 (2.88 to 5.40)	16	1321	1.2	3.21 (1.86 to 5.13)	11	5204	0.2	0.57 (0.29 to 0.98)
BARD1	18	12 280	0.2	1.53 (0.9 to 2.46)	7	2703	0.3	2.74 (1.15 to 5.49)	3	1229	0.2	2.60 (0.64 to 6.93)	44	4824	0.9	9.76 (6.77 to 13.87)
BRCA1	134	16 935	0.8	3.66 (2.95 to 4.53)	24	3778	0.6	3.00 (1.92 to 4.48)	23	1697	1.4	6.56 (4.14 to 9.88)	370	6723	5.5	28.62 (24.16 to 34)
BRCA2	307	16 935	1.8	5.96 (5.09 to 6.98)	58	3778	1.5	5.05 (3.77 to 6.64)	21	1697	1.2	4.08 (2.54 to 6.2)	164	6723	2.4	8.16 (6.73 to 9.86)
BRIP1	35	12 322	0.3	1.38 (0.95 to 1.94)	6	2708	0.2	1.08 (0.43 to 2.23)	1	1233	0.1	0.40 (0.02 to 1.76)	21	4832	0.4	2.09 (1.30 to 3.20)
CDH1	20	16 537	0.1	8.51 (4.36 to 17.04)	2	3699	0.1	3.84 (0.60 to 13.68)	1	1658	0.1	4.29 (0.24 to 21.26)	4	6569	0.1	4.46 (1.26 to 12.43)
CHEK2	221	13 190	1.7	2.35 (2.02 to 2.73)	68	2889	2.4	3.48 (2.68 to 4.44)	12	1320	0.9	1.37 (0.73 to 2.31)	15	5189	0.3	0.45 (0.26 to 0.72)
MSH6	17	7605	0.2	2.25 (1.30 to 3.66)	5	1570	0.3	3.23 (1.14 to 7.14)	1	722	0.1	1.41 (0.08 to 6.32)	7	2726	0.3	2.66 (1.12 to 5.33)
NBN	32	12 280	0.3	1.81 (1.22 to 2.62)	6	2703	0.2	1.57 (0.62 to 3.26)	1	1229	0.1	0.58 (0.03 to 2.59)	10	4824	0.2	1.48 (0.73 to 2.66)
NF1	10	12 089	0.1	2.36 (1.11 to 4.56)	5	2654	0.2	5.38 (1.85 to 12.5)	1	1205	0.1	2.35 (0.13 to 10.83)	10	4750	0.2	5.68 (2.68 to 10.94)
PALB2	119	14 004	0.9	5.15 (4.07 to 6.5)	19	3084	0.6	3.74 (2.25 to 5.86)	8	1390	0.6	3.49 (1.57 to 6.64)	73	5530	1.3	7.88 (5.96 to 10.32)
PTEN	13	16 975	0.1	10.35 (4.32 to 26.55)	2	3786	0.1	6.76 (1.02 to 26.9)	2	1702	0.1	14.46 (2.19 to 57.05)	2	6727	0.0	3.64 (0.55 to 14.31)
RAD51C	17	12 322	0.1	1.60 (0.92 to 2.61)	2	2708	0.1	0.87 (0.14 to 2.75)	3	1233	0.2	2.94 (0.72 to 7.84)	17	4832	0.4	4.56 (2.61 to 7.50)
RAD51D	6	12 131	0.1	1.14 (0.43 to 2.46)	1	2659	0.0	0.86 (0.05 to 3.92)	1	1209	0.1	1.91 (0.11 to 8.74)	8	4758	0.2	4.14 (1.80 to 8.35)
TP53	16	17 004	0.1	3.45 (1.83 to 6.28)	12	3793	0.3	11.95 (5.84 to 23.0)	10	1704	0.6	22.71 (10.45 to 45.49)	5	6746	0.1	2.95 (1.00 to 7.04)
Total Freq (%)		7.6				8.4					7.0				12.5

Table 3.

Open in new tab

Case-control association analysis of mutations and breast cancer clinical pathology subtypes*

Gene	ER+/HER2-				ER+/HER2+				ER-/HER2+				TNBC
Gene	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No.tested	Freq (%)	OR (95% CI)
ATM	136	13 197	1.0	2.65 (2.17 to 3.21)	44	2892	1.5	3.99 (2.88 to 5.40)	16	1321	1.2	3.21 (1.86 to 5.13)	11	5204	0.2	0.57 (0.29 to 0.98)
BARD1	18	12 280	0.2	1.53 (0.9 to 2.46)	7	2703	0.3	2.74 (1.15 to 5.49)	3	1229	0.2	2.60 (0.64 to 6.93)	44	4824	0.9	9.76 (6.77 to 13.87)
BRCA1	134	16 935	0.8	3.66 (2.95 to 4.53)	24	3778	0.6	3.00 (1.92 to 4.48)	23	1697	1.4	6.56 (4.14 to 9.88)	370	6723	5.5	28.62 (24.16 to 34)
BRCA2	307	16 935	1.8	5.96 (5.09 to 6.98)	58	3778	1.5	5.05 (3.77 to 6.64)	21	1697	1.2	4.08 (2.54 to 6.2)	164	6723	2.4	8.16 (6.73 to 9.86)
BRIP1	35	12 322	0.3	1.38 (0.95 to 1.94)	6	2708	0.2	1.08 (0.43 to 2.23)	1	1233	0.1	0.40 (0.02 to 1.76)	21	4832	0.4	2.09 (1.30 to 3.20)
CDH1	20	16 537	0.1	8.51 (4.36 to 17.04)	2	3699	0.1	3.84 (0.60 to 13.68)	1	1658	0.1	4.29 (0.24 to 21.26)	4	6569	0.1	4.46 (1.26 to 12.43)
CHEK2	221	13 190	1.7	2.35 (2.02 to 2.73)	68	2889	2.4	3.48 (2.68 to 4.44)	12	1320	0.9	1.37 (0.73 to 2.31)	15	5189	0.3	0.45 (0.26 to 0.72)
MSH6	17	7605	0.2	2.25 (1.30 to 3.66)	5	1570	0.3	3.23 (1.14 to 7.14)	1	722	0.1	1.41 (0.08 to 6.32)	7	2726	0.3	2.66 (1.12 to 5.33)
NBN	32	12 280	0.3	1.81 (1.22 to 2.62)	6	2703	0.2	1.57 (0.62 to 3.26)	1	1229	0.1	0.58 (0.03 to 2.59)	10	4824	0.2	1.48 (0.73 to 2.66)
NF1	10	12 089	0.1	2.36 (1.11 to 4.56)	5	2654	0.2	5.38 (1.85 to 12.5)	1	1205	0.1	2.35 (0.13 to 10.83)	10	4750	0.2	5.68 (2.68 to 10.94)
PALB2	119	14 004	0.9	5.15 (4.07 to 6.5)	19	3084	0.6	3.74 (2.25 to 5.86)	8	1390	0.6	3.49 (1.57 to 6.64)	73	5530	1.3	7.88 (5.96 to 10.32)
PTEN	13	16 975	0.1	10.35 (4.32 to 26.55)	2	3786	0.1	6.76 (1.02 to 26.9)	2	1702	0.1	14.46 (2.19 to 57.05)	2	6727	0.0	3.64 (0.55 to 14.31)
RAD51C	17	12 322	0.1	1.60 (0.92 to 2.61)	2	2708	0.1	0.87 (0.14 to 2.75)	3	1233	0.2	2.94 (0.72 to 7.84)	17	4832	0.4	4.56 (2.61 to 7.50)
RAD51D	6	12 131	0.1	1.14 (0.43 to 2.46)	1	2659	0.0	0.86 (0.05 to 3.92)	1	1209	0.1	1.91 (0.11 to 8.74)	8	4758	0.2	4.14 (1.80 to 8.35)
TP53	16	17 004	0.1	3.45 (1.83 to 6.28)	12	3793	0.3	11.95 (5.84 to 23.0)	10	1704	0.6	22.71 (10.45 to 45.49)	5	6746	0.1	2.95 (1.00 to 7.04)
Total Freq (%)			7.6				8.4				7.0				12.5

Gene	ER+/HER2-				ER+/HER2+				ER-/HER2+				TNBC
Gene	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No. tested	Freq (%)	OR (95% CI)	No. mut	No.tested	Freq (%)	OR (95% CI)
ATM	136	13 197	1.0	2.65 (2.17 to 3.21)	44	2892	1.5	3.99 (2.88 to 5.40)	16	1321	1.2	3.21 (1.86 to 5.13)	11	5204	0.2	0.57 (0.29 to 0.98)
BARD1	18	12 280	0.2	1.53 (0.9 to 2.46)	7	2703	0.3	2.74 (1.15 to 5.49)	3	1229	0.2	2.60 (0.64 to 6.93)	44	4824	0.9	9.76 (6.77 to 13.87)
BRCA1	134	16 935	0.8	3.66 (2.95 to 4.53)	24	3778	0.6	3.00 (1.92 to 4.48)	23	1697	1.4	6.56 (4.14 to 9.88)	370	6723	5.5	28.62 (24.16 to 34)
BRCA2	307	16 935	1.8	5.96 (5.09 to 6.98)	58	3778	1.5	5.05 (3.77 to 6.64)	21	1697	1.2	4.08 (2.54 to 6.2)	164	6723	2.4	8.16 (6.73 to 9.86)
BRIP1	35	12 322	0.3	1.38 (0.95 to 1.94)	6	2708	0.2	1.08 (0.43 to 2.23)	1	1233	0.1	0.40 (0.02 to 1.76)	21	4832	0.4	2.09 (1.30 to 3.20)
CDH1	20	16 537	0.1	8.51 (4.36 to 17.04)	2	3699	0.1	3.84 (0.60 to 13.68)	1	1658	0.1	4.29 (0.24 to 21.26)	4	6569	0.1	4.46 (1.26 to 12.43)
CHEK2	221	13 190	1.7	2.35 (2.02 to 2.73)	68	2889	2.4	3.48 (2.68 to 4.44)	12	1320	0.9	1.37 (0.73 to 2.31)	15	5189	0.3	0.45 (0.26 to 0.72)
MSH6	17	7605	0.2	2.25 (1.30 to 3.66)	5	1570	0.3	3.23 (1.14 to 7.14)	1	722	0.1	1.41 (0.08 to 6.32)	7	2726	0.3	2.66 (1.12 to 5.33)
NBN	32	12 280	0.3	1.81 (1.22 to 2.62)	6	2703	0.2	1.57 (0.62 to 3.26)	1	1229	0.1	0.58 (0.03 to 2.59)	10	4824	0.2	1.48 (0.73 to 2.66)
NF1	10	12 089	0.1	2.36 (1.11 to 4.56)	5	2654	0.2	5.38 (1.85 to 12.5)	1	1205	0.1	2.35 (0.13 to 10.83)	10	4750	0.2	5.68 (2.68 to 10.94)
PALB2	119	14 004	0.9	5.15 (4.07 to 6.5)	19	3084	0.6	3.74 (2.25 to 5.86)	8	1390	0.6	3.49 (1.57 to 6.64)	73	5530	1.3	7.88 (5.96 to 10.32)
PTEN	13	16 975	0.1	10.35 (4.32 to 26.55)	2	3786	0.1	6.76 (1.02 to 26.9)	2	1702	0.1	14.46 (2.19 to 57.05)	2	6727	0.0	3.64 (0.55 to 14.31)
RAD51C	17	12 322	0.1	1.60 (0.92 to 2.61)	2	2708	0.1	0.87 (0.14 to 2.75)	3	1233	0.2	2.94 (0.72 to 7.84)	17	4832	0.4	4.56 (2.61 to 7.50)
RAD51D	6	12 131	0.1	1.14 (0.43 to 2.46)	1	2659	0.0	0.86 (0.05 to 3.92)	1	1209	0.1	1.91 (0.11 to 8.74)	8	4758	0.2	4.14 (1.80 to 8.35)
TP53	16	17 004	0.1	3.45 (1.83 to 6.28)	12	3793	0.3	11.95 (5.84 to 23.0)	10	1704	0.6	22.71 (10.45 to 45.49)	5	6746	0.1	2.95 (1.00 to 7.04)
Total Freq (%)			7.6				8.4				7.0				12.5

Logistic regression by comparing each gene mutation frequency with Genome Aggregation Database reference controls, weighted by race and ethnicity (large genomic rearrangement variants were excluded). CI = confidence interval; ER = estrogen receptor; Freq = frequency; mut = mutations; OR = odds ratio; TNBC = triple-negative breast cancer (ER-/PR-/HER2-).

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