Table 2 Gene-based P-values from joint analysis of LoF variants with exome-wide significance, overall breast cancer risk in estrogen receptor-positive and estrogen receptor-negative breast cancers

From: Whole exome sequencing identifies FANCM as a susceptibility gene for estrogen-receptor-negative breast cancer in Hispanic/Latina women

Gene

Chr

Overall

ER + 

ER−

BRCA1a

17

2.3 × 10−10

0.03

4.4 × 10−16

BRCA2a

13

8.4 × 10−10

3.3 × 10−4

8.0 × 10−15

FANCM

14

9.8 × 10−3

0.11

4.1 × 10−7

PALB2

16

1.8 × 10−8

1.3 × 10−5

5.9 × 10−5

  1. P-values are from gene-based SKAT-O analyses. Bold P-values indicate Bonferroni corrected statistical significance, adjusting for multiple comparisons in a two-sided test at an alpha threshold of 0.05/20,000 = 2.5 × 10−6. Overall breast cancer analyses included N = 8614 (4264 cases and 4350 controls). Estrogen receptor-positive analyses included N = 6444 independent samples (2094 cases and 4350 controls). Estrogen receptor-analyses included H = 5063 independent samples (713 cases and 4350 controls).
  2. Chr chromosome; ER estrogen receptor; LoF loss of function.
  3. aDiscovery participants were selected for being BRCA1/2 negative (see section “Methods”), replication results are presented for BRCA1/2.
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