Breast Cancer Survival Analysis (Morra A et al 2021)
- The summary results from this paper can be downloaded here.
In downloading the data, you are accepting the terms and conditions as set out below.
These results files provide summary survival association statistics for the analyses described in Morra et al (Breast Cancer Res, 2021). Summary survival association statistics are provided for overall breast cancer, and for the following patient subgroups: a) younger than age 40 years at diagnosis; b) diagnosed with grade 3 tumours; c) diagnosed with estrogen receptor positive (ER+) tumours, who received endocrine therapy (any kind); d) diagnosed with ER-negative (ER-) tumours, who received chemotherapy (any kind); e) diagnosed with tumours that were ER+ or progesterone receptor-positive (PR+), and human epidermal growth factor receptor 2-negative (HER2-); f) diagnosed with ER+ or PR+, and HER2- tumours, who received chemotherapy (any kind); g) diagnosed with ER+ or PR+, and HER2- tumours, who did not receive chemotherapy; h) diagnosed with ER+ or PR+, and HER2+ tumours; i) diagnosed with ER- and PR- and HER2+ tumours; j) diagnosed with ER- and PR- and HER2- tumours; k) who received Tamoxifen; l) who received an aromatase inhibitor; m) who received a Cyclophosphamide Methotrexate Fluorouracil (CMF)-like chemotherapy regimen; n) who received Taxanes; o) who received anthracyclines.
Additional results files are provided with the summary survival association statistics for the extra GWAS analyses performed in the following patient subgroups, which are not part of the above mentioned publication: 1) patients diagnosed with tumours of size ≤ 2 cm; 2) patients diagnosed with tumours of size > 2 cm and ≤ 5 cm; 3) patients diagnosed with tumours of size > 5 cm; 4) patients diagnosed with lymph node negative tumours; 5) patients diagnosed with lymph node positive tumours; 6) patients diagnosed with TNM stage 1 tumours; 7) patients diagnosed with TNM stage 2 tumours; 8) patients diagnosed with TNM stage 3 tumours.
Description of field names in the results files are also included in the download.
Acknowledgements
You are free to use make use of this resource in publications.
If you do so, please cite Morra et al (Breast Cancer Res, 2021) and please acknowledge the following:
BCAC is funded by Cancer Research UK [C1287/A16563], the European Union's Horizon 2020 Research and Innovation Programme (grant numbers 634935 and 633784 for BRIDGES and B-CAST respectively), and by the European Community´s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). The EU Horizon 2020 Research and Innovation Programme funding source had no role in study design, data collection, data analysis, data interpretation or writing of the report.
Genotyping of the OncoArray was funded by the NIH Grant U19 CA148065, and Cancer Research UK Grant C1287/A16563 and the PERSPECTIVE project supported by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research (grant GPH-129344) and, the Ministère de l’Économie, Science et Innovation du Québec through Genome Québec and the PSRSIIRI-701 grant, and the Quebec Breast Cancer Foundation. Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defence (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, and Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. The DRIVE Consortium was funded by U19 CA148065.
Disclaimer Use of Survival Estimates
The summary estimates for the association between germline variants and survival are based on BCAC iCOGS and Oncoarray data as published in: Morra A and Schmidt MK et al Breast Cancer Res 2021 (PMCID: PMC8371820), and are for women of European ancestry only. Please refer to this paper when using these survival summary results. The estimates were based on follow-up data available at the time of the analyses (BCAC version 12) and on imputed genotype data using either the 1000 Genomes Project or the Haplotype Reference Consortium data set as a reference, choosing for each genetic variant the reference panel with the best imputation quality (r2) for that specific variant. The alternative allele frequencies provided in the results files are the estimated alternative allele frequency of the iCOGS and OncoArray datasets, which are based on the total set of breast cancer cases and controls originally genotyped. However, exclusions of variants in the analyses presented in the paper were based on the allele frequencies computed, for each subgroup, on the selection of patients included in that specific subgroup. Please realise that the data online are not the most recent and estimates may have changed in analyses using updated follow-up data and/or another reference. In addition, for 234 variants we detected that the reference allele was reversed between iCOGS and OncoArray genotype data, leading to minor differences in the estimates compared to the results used in our publication (in Figures 1-2 and Supplementary Figures S1-S4). These variants are flagged in the results files. For all 234 estimates the p-value was far below genome-wide significant, with P-values>2.1E-06). These changes would hardly be visible in updated plots versus the published, therefore we did not revise the original manuscript.
Remark: There was one genome-wide significant association (P-value=2.2E-08) detected in subgroup 6 (patients diagnosed with TNM stage 1 tumors) with variant 15_92767653_G_A on chromosome 15. The estimated hazard ratio and 95% confidence interval for this variant were 0.005 (0.001-0.031). Given the low minor allele frequency of the variant (~0.02) the association p-value is likely inflated. In addition, the corresponding Bayesian False Discovery Probability (computed assuming the prior probability of true association equal to 10-4 and choosing the prior distribution of the log hazard ratio to be a Normal distribution with mean 0 and standard error equal to 0.2) was equal to 1.00, suggesting that this result is almost certainly a false positive.
Terms of Use
The sample size and precision of the data presented should preclude identification of any individual subject. However, in downloading these data, you undertake not to attempt to identify individual subjects and not to repost these data to a third-party website.