Table 1 Frequency of CNVs and overlapping genes in breast cancer cases and controls
Genomic feature | Total count | Mean frequency | Difference in means | Case/control ratio | P value | |||
|---|---|---|---|---|---|---|---|---|
Cases (n = 200) | Controls (n = 293) | Cases | Controls | Case - controls | 95% CI | |||
CNVs | ||||||||
All | 5109 | 6133 | 25.6 | 20.9 | 4.6 | 3.2, 6.0 | 1.2 | 2e-10 |
Deletions | 3622 | 3644 | 18.1 | 12.4 | 5.7 | 4.4, 7.0 | 1.5 | 2e-16 |
Gains | 1487 | 2489 | 7.4 | 8.5 | -1.1 | -1.9, -0.3 | 0.9 | 0.01 |
CNVs overlapping genes | ||||||||
All | 1734 | 2069 | 8.7 | 7.1 | 1.6 | 0.9, 2.4 | 1.2 | 3e-05 |
Deletions | 1048 | 956 | 5.2 | 3.3 | 2.0 | 1.4, 2.6 | 1.6 | 4e-10 |
Gains | 686 | 1113 | 3.4 | 3.8 | -0.4 | -0.8, 0.1 | 0.9 | 0.1 |
Genes overlapping CNVs | ||||||||
All | 2816 | 3501 | 14.1 | 12.0 | 2.1 | 0.5, 3.8 | 1.2 | 0.01 |
Deletions | 1450 | 1368 | 7.3 | 4.7 | 2.6 | 1.7, 3.5 | 1.6 | 2e-08 |
Gains | 1366 | 2133 | 6.8 | 7.3 | -0.5 | -1.8, 0.9 | 0.9 | 0.5 |