Table 2. Effect estimates and standard errors for gene expression suggestively (p-value < 1.0x10-04) associated with breast cancer risk in a meta-analysis of the Up for a Challenge and UK Biobank datasets.
| # SNPs in | Imputation | U4C | UK Biobank | Meta-analysis | |||||
|---|---|---|---|---|---|---|---|---|---|
| Gene | Locationa | Prediction | Qualityb | Beta (SE) | p-value | Beta (SE) | p-value | Beta (SE) | p-value |
| Breast Tissue Gene Expression | |||||||||
| RCCD1 | 15q26.1 | 24 | 0.16 | -0.11 (0.038) | 5.8x10-03 | -0.24 (0.057) | 2.6x10-05 | -0.15 (0.032) | 3.6x10-06 |
| DHODH | 16q22.2 | 7 | 0.026 | -0.52 (0.12) | 2.4x10-05 | -0.29 (0.15) | 0.056 | -0.43 (0.095) | 7.1x10-06 |
| ANKLE1 | 19p13.11 | 6 | 0.081 | 0.19 (0.093) | 0.044 | 0.43 (0.12) | 1.9x10-04 | 0.28 (0.072) | 9.3x10-05 |
| Whole Blood Gene Expression | |||||||||
| RCCD1 | 15q26.1 | 20 | 0.35 | -0.074 (0.026) | 4.7x10-03 | -0.14 (0.039) | 2.7x10-04 | -0.095 (0.022) | 1.2x10-05 |
| ACAP1 | 17p13.1 | 19 | 0.39 | 0.098 (0.037) | 7.9x10-03 | 0.11 (0.033) | 7.9x10-04 | 0.11 (0.025) | 1.9x10-05 |
| LRRC25 | 19p13.11 | 33 | 0.35 | 0.086 (0.029) | 2.7x10-03 | 0.094 (0.034) | 6.5x10-03 | 0.089 (0.022) | 5.2x10-05 |
Abbreviations: SE: standard error; SNP: single nucleotide polymorphism; U4C: Up for a Challenge
a According to human reference genome GRCh37/hg19
b r2 estimate derived from 10 fold cross-validation of true gene expression and predicted gene expression