Supplementary Table 3. Results of the statistical analyses of SNPs from project 12 in BRCA-mutation carriers affected or non-affected with breast cancer and according to their estrogen receptor status.

Supplementary Table 2. Results of the statistical analyses in BRCA mutation carriers.

Supplementary Table 1. The 3,248 SNPs included in the study

Observational studies suggest that higher birth weight (BW) is associated with increased risk of breast cancer in adult life. We conducted a two-sample Mendelian randomisation (MR) study to assess whether this association is causal. Sixty independent single nucleotide polymorphisms (SNPs) known to be associated at P < 5 × 10−8 with BW were used to construct (1) a 41-SNP instrumental variable (IV) for univariable MR after removing SNPs with pleiotropic associations with other breast cancer risk factors and (2) a 49-SNP IV for multivariable MR after filtering SNPs for data availability. BW predicted by the 41-SNP IV was not associated with overall breast cancer risk in inverse-variance weighted (IVW) univariable MR analysis of genetic association data from 122,977 breast cancer cases and 105,974 controls (odds ratio = 0.86 per 500 g higher BW; 95% confidence interval 0.73–1.01). Sensitivity analyses using four alternative methods and three alternative IVs, including an IV with 59 of the 60 BW-associated SNPs, yielded similar results. Multivariable MR adjusting for the effects of the 49-SNP IV on birth length, adult height, adult body mass index, age at menarche, and age at menopause using IVW and MR-Egger methods provided estimates consistent with univariable analyses. Results were also similar when all analyses were repeated after restricting to estrogen receptor-positive or -negative breast cancer cases. Point estimates of the odds ratios from most analyses performed indicated an inverse relationship between genetically-predicted BW and breast cancer, but we are unable to rule out an association between the non-genetically-determined component of BW and breast cancer. Thus, genetically-predicted higher BW was not associated with an increased risk of breast cancer in adult life in our MR study.

Abstract There are increasing attempts to try to stratify cancer risks to enable more targeted early detection and prevention strategies and in particular to balance the risks and benefits of population screening for breast cancer. An increasing number of common genetic variants called Single Nucleotide Polymorphisms (SNPs) have been identified which alter breast cancer risk. Although individually their effect sizes are small they can be used multiplicatively to provide a polygenic risk score (PRS) that accurately predicts risk in both the familial and population setting. Although the first 18 SNPs produce a highly calibrated PRS that is ready for use there are now PRSs of 143 or even 313 SNPs that increase risk stratification although with some loss of calibration. Using data from 9362 women in the Predicting the Risk Of Cancer At Screening (PROCAS) study (500 prospective cancers) and 2000 women in the FH-Risk familial cohort (500 prospective cancers) we have validated the PRS alongside mammographic density (density residual-DR) and standard risk factors to assess future risk of different types of breast cancer. The combined score accurately predicts breast cancers rates with 18-21% of women being predicted in the moderate or high risk categories (≥5% 10 year risk) that developed 41.5-45% of the stage 2+ cancers. In contrast SNP143 is able to identify alongside density and standard risk factors 21% of the general population at <1.4% 10-year risk aged 46-73 years who develop only 9% of the breast cancers. These are also more likely to be potentially 'overdiagnosed' grade 1 and DCIS. The SNP143 is also predictive for oestrogen receptor negative cancers using a 20 SNP PRS. Conclusions: A combined approach using Tyrer-Cuzick, mammographic density and a PRS provides accurate risk stratification not only overall but also for worse prognosis cancers. This provides support for reducing screening intervals in the high and increasing them in the low risk groups. It is high time these highly informative tests were used in risk stratification Citation Format: Evans D. Polygenic risk scores for breast cancer: Ready or not? [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr CS1-1.

Previous research assessing the impact of pregnancy and age at first pregnancy on breast cancer risk in BRCA1 and BRCA2 mutation carriers has produced conflicting results, with some studies showing an increased risk following early first pregnancy in contrast to the reduced risk in the general population of women. The present study addresses these inconsistencies.

BACKGROUND Gene expression (expr) analyses are increasingly used for characterising the pharmacodynamic response of primary BC. This includes assessing ER+ BC9s dependence on estrogen (E) by measuring gene expr changes after AI-treatment. However, differences in tissue sampling and other preanalytic procedures between samples taken at diagnosis (D) and surgery (S), may lead to systematic artifactual changes that are falsely ascribed to the intervention. To identify genes whose expr is truly affected by AI, we measured global gene expr changes from paired core-cut biopsies at D and S from patients in the POETIC presurgical window trial. METHODS In POETIC, 4486 postmenopausal women with primary ER+ BC were randomised 2:1 to receive perioperative AI (2 weeks pre + 2 weeks post surgery, termed Tr) or no perioperative treatment (termed Con), allowing gene expr changes to be compared between Tr and Con. RNA was extracted from paired RNA-later stored core-cuts of 56 Con and 157 Tr patients and arrayed on Illumina whole genome expr BeadChips. Raw data was extracted, transformed, normalised and batch-corrected. Probes not detected (pu003e0.01) in u003e=25% of samples were discarded. Impact of AI on genes was evaluated based on difference of the expr mean changes (log 2 (S/D)) of the Tr and Con samples. RESULTS In the Con group, expr of 73 genes significantly changed (FDR MYC increase) but was unaffected in Tr. Such artifactual gene changes in Con tumors conceal true AI-induced changes that would not be detected in the absence of comparison with Con. 615 genes were down-regulated and 472 up-regulated in Tr but not Con. The majority of down-regulated genes were cell cycle or proliferation-associated or E-regulated, including ESR1, PDZK1, GREB1, HSPB1 . Functional mapping showed changes in the regulation of cyclins and cyclin dependent kinases impacting on G1/S and G2/M. Of note, up-regulated genes included CDK6 (target for CDK4/6 inhibitors) and CCND2, involved in G1/S checkpoint regulation ; SNAI2, TGFB3, TGFBR2, associated with tumour invasion and metastasis ; and other genes involved in aryl hydrocarbon receptor, Glioblastoma Multiforme, HIPPO and p53 signalling. CONCLUSION Expr of certain genes is altered by processes involved in presurgical window studies. In the absence of a Con group, these may be wrongly ascribed to an experimental intervention or wrongly considered as unaffected by the intervention (eg MYC in this study). Down-regulation of E-responsive and proliferation genes was an expected response to AI but increased expr of genes such as SNAI2 , CCND2 and CDK6 indicates immediate tumour re-wiring and provides mechanistic support for benefit from combination therapy with a CDK4/6 inhibitor. Citation Format: Gao Q, Lopez-Knowles E, Cheang MCU, Morden J, Martin L-A, Sidhu K, Evans D, Martins V, Dodson A, Skene A, Holcombe C, Mallon E, Abigail E, Bliss J, Robertson J, Smith I, Dowsett M. True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-09-02.

Abstract BACKGROUND Gene expression (expr) analyses are increasingly used for characterising the pharmacodynamic response of primary BC. This includes assessing ER+ BC's dependence on estrogen (E) by measuring gene expr changes after AI-treatment. However, differences in tissue sampling and other preanalytic procedures between samples taken at diagnosis (D) and surgery (S), may lead to systematic artifactual changes that are falsely ascribed to the intervention. To identify genes whose expr is truly affected by AI, we measured global gene expr changes from paired core-cut biopsies at D and S from patients in the POETIC presurgical window trial. METHODS In POETIC, 4486 postmenopausal women with primary ER+ BC were randomised 2:1 to receive perioperative AI (2 weeks pre + 2 weeks post surgery, termed Tr) or no perioperative treatment (termed Con), allowing gene expr changes to be compared between Tr and Con. RNA was extracted from paired RNA-later stored core-cuts of 56 Con and 157 Tr patients and arrayed on Illumina whole genome expr BeadChips. Raw data was extracted, transformed, normalised and batch-corrected. Probes not detected (p>0.01) in >=25% of samples were discarded. Impact of AI on genes was evaluated based on difference of the expr mean changes (log2(S/D)) of the Tr and Con samples. RESULTS In the Con group, expr of 73 genes significantly changed (FDR<5%); 70 of these changed by a similar magnitude in the Tr group, indicating their change was independent of AI therapy but would have been artifactually discovered as changed by AI in the absence on Con. The 8 genes most up-regulated in Tr were all among the 20 genes most up-regulated in Con: many were early-response or stress-associated genes. Three of the 8 most down-regulated in AI were the most down-regulated in Con: all were haemoglobin-related. Expr of some genes was changed in Con (eg MYC increase) but was unaffected in Tr. Such artifactual gene changes in Con tumors conceal true AI-induced changes that would not be detected in the absence of comparison with Con. 615 genes were down-regulated and 472 up-regulated in Tr but not Con. The majority of down-regulated genes were cell cycle or proliferation-associated or E-regulated, including ESR1, PDZK1, GREB1, HSPB1. Functional mapping showed changes in the regulation of cyclins and cyclin dependent kinases impacting on G1/S and G2/M. Of note, up-regulated genes included CDK6 (target for CDK4/6 inhibitors) and CCND2, involved in G1/S checkpoint regulation; SNAI2, TGFB3, TGFBR2, associated with tumour invasion and metastasis; and other genes involved in aryl hydrocarbon receptor, Glioblastoma Multiforme, HIPPO and p53 signalling. CONCLUSION Expr of certain genes is altered by processes involved in presurgical window studies. In the absence of a Con group, these may be wrongly ascribed to an experimental intervention or wrongly considered as unaffected by the intervention (eg MYC in this study). Down-regulation of E-responsive and proliferation genes was an expected response to AI but increased expr of genes such as SNAI2, CCND2 and CDK6 indicates immediate tumour re-wiring and provides mechanistic support for benefit from combination therapy with a CDK4/6 inhibitor. Citation Format: Gao Q, López-Knowles E, Cheang MCU, Morden J, Martin L-A, Sidhu K, Evans D, Martins V, Dodson A, Skene A, Holcombe C, Mallon E, Abigail E, Bliss J, Robertson J, Smith I, Dowsett M. True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-09-02.

Introduction: The Predicting Risk of Cancer at Screening study in Manchester, UK, is a prospective study of breast cancer risk estimation. It was designed to assess whether mammographic density may help in refinement of breast cancer risk estimation using either the Gail model (Breast Cancer Risk Assessment Tool) or the Tyrer-Cuzick model (International Breast Intervention Study model). Methods: Mammographic density was measured at entry as a percentage visual assessment, adjusted for age and body mass index. Tyrer-Cuzick and Gail 10-year risks were based on a questionnaire completed contemporaneously. Breast cancers were identified at the entry screen or shortly thereafter. The contribution of density to risk models was assessed using odds ratios (ORs) with profile likelihood confidence intervals (CIs) and area under the receiver operating characteristic curve (AUC). The calibration of predicted ORs …

Introduction: Rates of contralateral risk-reducing mastectomy (CRRM) are rising, despite a decreasing global incidence of contralateral breast cancer. Reasons for requesting this procedure are complex and we have previously shown a variable practice amongst breast and plastic surgeons in England. We propose a protocol, based on a previous national survey and the Manchester experience of CRRM.

Circumscribed masses are a common cause of recall for assessment but most are benign. The aim of this study is to compare the accuracy of digital breast tomosynthesis (DBT) with digital mammography (DM) in assessing the margin of circumscribed lesions as a predictor of benign or malignant disease.

Introduction: This multicentre randomised controlled trial investigated whether a computed tomography (CT) scan of the axilla could more accurately assess whether the axillary lymph nodes were involved with malignancy in patients with newly diagnosed breast cancer and therefore influence surgical decision-making with regard to axillary surgery. Methods: Patients with newly diagnosed breast cancer (via screening and symptomatic routes) at two NHS Trusts in the North East of England were recruited and randomised in equal numbers. Both groups received routine diagnostic and surgical care (usual care). In addition, one group received a CT scan of their axilla on the same side as the breast cancer. Results: The study recruited 297 patients, of whom 291 contributed to findings. CT scan-guided care did not result in a change in the need for a second operation, with about 20% of both groups needing further surgery. Patients within the two groups were similar before treatment, had similar types and grade of cancer, experienced similar pattern complications and reported similar experiences of care. Conclusion: New diagnostic imaging technologies regularly enter NHS centres of excellence as research tools. It is important these are evaluated rigorously before becoming routine care. In patients newly diagnosed with breast cancer, CT-augmented diagnosis of cancer in the axilla was not found to improve surgical outcomes or patient experience. O2 Preoperative assessment of breast volume to aid surgical planning: comparison of software-based mammographic measurements with subsequent mastectomy volumes. Introduction: The proportion of breast volume excised during conservation surgery for breast cancer is crucial to cosmetic outcomes. Validated, expedient methods for accurate preoperative quantification of breast volume are lacking. This study evaluated breast volume measurements calculated by Volpara® breast density software, by comparing them with actual mastectomy volumes. Methods: From a prospective clinical database, 31 patients were identified for whom Volpara® (Matakina Technology Limited, New Zealand) volume measurements and mastectomy volumes were available. All patients had undergone skin-sparing mastectomy (SSM), bilateral in one case. Specimen volumes had been measured using a water-displacement technique. Volpara® volumes for the corresponding CC and MLO view of each of the 32 breasts were averaged and compared with the mastectomy volumes. Correlation was assessed using the Pearson correlation coefficient. Results: Volpara® breast volumes were, as expected, consistently higher than SSM volumes but with a very strong correlation (Pearson correlation coefficient for average Volpara® volumes and mastectomy volumes = 0.82 (P < 0.01)). Conclusion: The excellent correlation between Volpara® and …