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. 2018 Nov 13;144(8):1962–1974. doi: 10.1002/ijc.31921

Table 3.

Analyses by hormone receptor status and restricted to pseudo‐incident cases, for the 7 genes associated with BC (P ≤ 0.05)

Any variant LoF Likely deleterious MV
Gene Analysis1 Case carriers OR2 (95%CI) p‐Value Case carriers OR2 (95%CI) p‐Value Case carriers OR2 (95%CI) p‐Value
ATM ER positive 47 2.1 (1.4, 3.3) 0.001 9 17.7 (2.2, 140) 0.006 38 1.7 (1.1, 2.8) 0.02
ER negative 8 2.1 (0.9, 4.5) 0.07 2 20.8 (1.9, 232) 0.01 6 1.6 (0.7, 3.8) 0.31
PR positive 38 2.1 (1.3, 3.4) 0.001 9 22.0 (2.8, 174) 0.003 29 1.6 (1.0, 2.7) 0.06
PR negative 12 1.7 (0.9, 3.4) 0.10 2 10.9 (1.0, 120) 0.05 10 1.5 (0.7, 3.0) 0.27
HER2 positive 3 1.3 (0.4, 4.2) 0.70 0 ‐ ‐ 3 1.3 (0.4, 4.3) 0.68
HER2 negative 24 1.8 (1.1, 3.1) 0.02 6 19.2 (2.3, 160) 0.006 18 1.4 (0.8, 2.5) 0.27
Pseudo‐incident cases3 41 1.9 (1.2, 2.9) 0.006 8 15.6 (1.9, 125) 0.01 33 1.5 (1.0, 2.5) 0.08
CHEK2 ER positive 39 3.5 (2.1, 6.0) 0.000004 16 7.9 (2.6, 23.9) 0.0003 23 2.5 (1.3, 4.7) 0.004
ER negative 3 1.3 (0.4, 4.5) 0.64 1 2.5 (0.3, 22.2) 0.42 2 1.1 (0.2, 4.8) 0.91
PR positive 35 3.9 (2.2, 6.7) 0.000001 17 10.5 (3.5, 31.3) 0.00003 18 2.4 (1.2, 4.7) 0.01
PR negative 6 1.6 (0.7, 4.1) 0.29 0 ‐ ‐ 6 2.0 (0.8, 5.2) 0.14
HER2 positive 5 3.8 (1.4, 10.4) 0.009 1 4.3 (0.5, 39.1) 0.2 4 3.7 (1.2, 11.3) 0.02
HER2 negative 27 4.1 (2.3, 7.3) 0.000002 11 9.0 (2.8, 28.4) 0.0002 16 3.0 (1.5, 6.0) 0.002
Pseudo‐incident cases3 37 3.3 (1.9, 5.6) 0.00001 12 5.9 (1.9, 18.4) 0.002 25 2.7 (1.5, 5.0) 0.001
FANCI ER positive 9 0.7 (0.3, 1.6) 0.44 3 4.7 (0.5, 46.3) 0.19 6 0.5 (0.2, 1.3) 0.17
ER negative 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
PR positive 8 0.9 (0.4, 1.9) 0.70 2 4.7 (0.4, 52.0) 0.21 6 0.7 (0.3, 1.7) 0.39
PR negative 1 0.2 (0.0, 1.8) 0.17 1 4.3 (0.2, 79.5) 0.33 0 ‐ ‐
HER2 positive 1 0.7 (0.1, 5.4) 0.75 1 15.1 (0.7, 319) 0.09 0 ‐ ‐
HER2 negative 3 0.4 (0.1, 1.4) 0.20 0 ‐ ‐ 3 0.4 (0.1, 1.5) 0.19
Pseudo‐incident cases3 6 0.5 (0.2, 1.2) 0.11 2 2.8 (0.2, 32.8) 0.42 4 0.4 (0.1, 1.0) 0.06
MAST1 ER positive 8 1.8 (0.7, 5.0) 0.23 0 ‐ ‐ 8 2.1 (0.8, 5.9) 0.15
ER negative 3 3.8 (1.0, 14.4) 0.05 0 ‐ ‐ 3 4.3 (1.1, 16.8) 0.04
PR positive 5 1.2 (0.4, 3.9) 0.79 0 ‐ ‐ 5 1.7 (0.5, 5.3) 0.38
PR negative 4 3.0 (0.9, 10.0) 0.08 0 ‐ ‐ 4 3.4 (1.0, 11.9) 0.05
HER2 positive 2 4.2 (0.9, 20.0) 0.08 0 ‐ ‐ 2 4.7 (1.0, 23.1) 0.06
HER2 negative 2 0.8 (0.2, 3.7) 0.75 0 ‐ ‐ 2 0.9 (0.2, 4.3) 0.89
Pseudo‐incident cases3 8 1.9 (0.7, 5.0) 0.20 0 ‐ ‐ 8 2.1 (0.8, 6.0) 0.14
PALB2 ER positive 21 4.6 (2.1, 10.1) 0.0002 8 5.4 (1.4, 20.4) 0.01 13 4.2 (1.6, 11.1) 0.004
ER negative 1 1.1 (0.1, 8.8) 0.93 0 ‐ ‐ 1 1.6 (0.2, 13.7) 0.65
PR positive 14 3.7 (1.6, 8.7) 0.002 3 2.4 (0.5, 11.9) 0.29 11 4.4 (1.6, 11.9) 0.004
PR negative 7 4.9 (1.8, 13.4) 0.002 5 11.1 (2.6, 47.4) 0.001 2 2.0 (0.4, 10.0) 0.40
HER2 positive 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
HER2 negative 13 4.7 (2.0, 11.1) 0.0004 3 3.4 (0.7, 16.7) 0.14 10 5.3 (1.9, 14.8) 0.001
Pseudo‐incident cases3 15 3.2 (1.4, 7.3) 0.007 5 3.2 (0.8, 13.6) 0.11 10 3.1 (1.1, 8.7) 0.03
POLH ER positive 4 0.6 (0.2, 1.8) 0.30 1 ‐ ‐ 3 0.4 (0.1, 1.5) 0.19
ER negative 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
PR positive 4 0.7 (0.2, 2.2) 0.60 1 ‐ ‐ 3 0.5 (0.2, 1.9) 0.34
PR negative 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
HER2 positive 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
HER2 negative 1 0.2 (0.0, 1.8) 0.20 1 ‐ ‐ 0 ‐ ‐
Pseudo‐incident cases3 1 0.1 (0.0, 1.1) 0.06 0 ‐ ‐ 1 0.1 (0.0, 1.1) 0.06
RTEL1 ER positive 5 0.5 (0.2, 1.2) 0.12 0 ‐ ‐ 5 0.5 (0.2, 1.2) 0.12
ER negative 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
PR positive 5 0.6 (0.2, 1.5) 0.30 0 ‐ ‐ 5 0.6 (0.2, 1.5) 0.27
PR negative 0 ‐ ‐ 0 ‐ ‐ 0 ‐ ‐
HER2 positive 2 1.4 (0.3, 6.6) 0.61 0 ‐ ‐ 2 1.5 (0.3, 6.6) 0.61
HER2 negative 2 0.3 (0.1, 1.3) 0.10 0 ‐ ‐ 2 0.3 (0.1, 1.3) 0.10
Pseudo‐incident cases3 7 0.6 (0.3, 1.5) 0.30 0 ‐ ‐ 7 0.6 (0.3, 1.5) 0.31

Abbreviations: ER, estrogen receptor; PR, progesterone receptor; HER2, HER2 gene amplification.

1

ER, PR and HER2 status were available for 788 (67%), 742 (63%), and 475 (40%) of sequenced GENESIS cases.

2

Reference group: noncarriers of a variant in the tested gene; adjusting for ethnicity and age at inclusion.

3

Cases diagnosed with BC less than 5 years before enrollment in GENESIS (N = 663).