Couch, Fergus J.

Abstract Background: Polygenic risk scores (PRS) based on a large number of SNPs associated with breast cancer have recently been made available in combination with multigene panel testing for clinical management of breast cancer risk. Breast cancer risk assessment has historically been performed using various non-genetic risk models, which predict lifetime risk of breast cancer in unaffected women based on personal and family history information. While clinical use of PRS in combination with these models continues to increase, the predictive performance of a PRS combined with clinical information in real-world patient populations has not been thoroughly investigated. Methods: We assessed a 100-SNP breast cancer PRS in combination with the Tyrer-Cuzick model-estimated lifetime breast cancer risk in 5,374 Caucasian women from the case-control Mayo Clinic Breast Cancer Study (MCBCS), comprised of 3,373 breast cancer cases and 2,001 unaffected controls seen at Mayo Clinic from 2004 to 2016. Clinical, family history, and demographic information was collected on all MCBCS participants via questionnaires and medical record review. SNPs were selected for the PRS if they exceeded genome-wide significance in ≥2 large-scale breast cancer genome wide association studies (GWAS) in women of European descent. Selected SNPs were then used to construct a population standardized PRS, accounting for per-allele odds ratios reported in the largest GWAS to date and population-specific allele frequencies. PRS and Tyrer-Cuzick model associations with breast cancer and related clinical features were tested using multivariate logistic regression. Results: Among cases and controls, mean±SD age at diagnosis and study enrollment was 56.4±12.4 and 56.2±14.1, respectively. Approximately 36.9% of cases and 16.9% of controls had ≥1 first- or second-degree relative with breast or ovarian cancer, respectively. Among unaffected women, the median (IQR) estimated lifetime risk of breast cancer to age 85 based on Tyrer-Cuzick alone was 8.3% (6.9%), and 2.6% had a clinically actionable lifetime risk of ≥20%. The mean±SD sum of the risk alleles across 100 SNPs was significantly higher for cases vs. controls (94.8±6.3 vs. 92.7±6.2, p<0.001). Compared to women in the lowest quartile of PRS, those in the 2nd, 3rd and 4th quartiles were 1.47 (95% CI: 1.26-1.72), 1.87 (95% CI: 1.60-2.19), and 2.22 (95% CI: 1.89-2.61) times more likely to have breast cancer after adjustment for age and family history. The AUC was 0.59 (95% CI: 0.58-0.61) for PRS and 0.60 (95% CI: 0.58-0.61) for Tyrer-Cuzick model estimated risk alone; but when combined, the model achieved an AUC of 0.63 (95% CI: 0.62-0.65). Among unaffected women, 6.7% had ≥20% lifetime risk of breast cancer based on the combined PRS-clinical model. Conclusions: These findings suggest that the 100-SNP PRS significantly improves estimation of breast cancer risk based on non-genetic models, and can be used to further identify women at increased lifetime risk who would otherwise not be identified by clinical assessment alone. Citation Format: Mary Helen Black, Shuwei Li, Holly LaDuca, Sebastian Armasu, Eric C. Polley, Patrick Fitz-Gibbon, Chris G. Scott, Stacey J. Winham, Janet E. Olson, Kathryn J. Ruddy, Celine M. Vachon, Fergus J. Couch. Performance of a polygenic risk score combined with clinical assessment for breast cancer risk [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-07-06.

Abstract Background: BRCA1/2 carriers have higher scores in the 21-gene RS assay compared to non-carriers. Little is known about the 21-gene RS patterns in women harboring germline mutations in genes outside BRCA1/2. Methods: We utilized the Mayo Clinic Breast Cancer Study Registry to identify individuals with non-metastatic estrogen receptor positive breast cancer and clinical 21-gene RS results available. We cross-referenced this with an institutional registry of patients tested for hereditary cancer genes, either from the electronic health record or from a research study conducted using a custom QIAseq multiplex amplicon-based panel (Qiagen). The latter assay covered target regions of all coding regions for the following predisposition genes: ATM, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHEK2, ERCC2, FANCC, FANCM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, RECQL, PRSS1, STK11, TP53, and XRCC2. Student’s t-test was used to compare 21-gene RS between carriers, non-carriers, and specific carrier genes (JMP v 14.0). Results: 282 patients were identified with early stage breast cancer and 21-gene RS available, including 85 known mutation carriers and 197 non-carriers (or unknown carrier status). Germline mutations were identified in CHEK2 (n=25), BRCA2 (n=18), ATM (n=10), BRCA1 (n=5), PALB2 (n=5), TP53 (n=3), FANCM (n=2), MUTYH (n=2), PMS2 (n=2), PPM1D (n=2), RECQL (n=2), BARD1 (n=1), BLM (n=1), CDH1 (n=1), ERCC2 (n=1), FANCC (n=1), MSH6 (n=1), NBN (n=1), PRSS1 (n=1), and PTEN (n=1). In the entire cohort, the mean 21-gene RS was 20.4 in carriers and 18.0 in non-carriers (p=0.11). We performed individual analyses on specific genes identified in ≥ 5 patients (table 1). Compared to the mean RS in non-carriers (18.0), higher mean RS were observed in patients harboring BRCA1 (38.8, p=0.002), PALB2 (26.6, p=0.0724), and BRCA2 (23.2, p=0.0453). The RS in CHEK2 and ATM carriers were comparable to those of non-carriers. Conclusions: We observed differences in RS score distribution based on specific mutated breast cancer predisposition genes. Further validation of the distribution and performance of the 21-gene RS in germline carriers is needed. 21-gene RS scorenMedian RSMean≤1516-25≥26n%n%n%CHEK2251616.61248728624BRCA2182123.2211.11161.1527.8ATM101716.9330550220BRCA153635.8120120360PALB253326.6120120360None1971518.09950.367343115.7 Citation Format: Karthik V Giridhar, Grace M Choong, Siddartha Yadav, Eric C Polley, Roberto A Leon-Ferre, Minetta C Liu, Matthew P Goetz, Fergus J Couch. Distribution of the 21-gene recurrence score (RS) assay (Oncotype DX) in carriers of germline mutations associated with breast cancer predisposition syndromes [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-03-07.

Abstract Background The Circulating Cell-free Genome Atlas (CCGA; NCT02889978) study is a prospective, multi-center, observational, case-control study with longitudinal follow-up to support the development of a plasma cfDNA-based multi-cancer early detection assay. We previously reported that the fraction of tumor-derived cfDNA fragments in plasma (estimated tumor fraction [TF]) is associated with detection of multiple cancer types using a prototype whole-genome bisulfite sequencing (WGBS) assay in a pre-specified substudy. In addition, detectability of breast cancer varied by hormone-receptor (HR) status: HR negative (HR-) breast cancer had a higher detection rate than the overall breast cancer cohort. Here, we performed a planned in-depth analysis of the breast cancer cohort to understand the main clinical and biological determinants of detectability using our WGBS assay. Methods Blood samples were prospectively collected from participants (pts) with newly-diagnosed, untreated breast cancer. In a pre-specified CCGA substudy, 511 (31.4%) of 1,628 pts had a clinicopathologic diagnosis of breast cancer (any stage, excluding stage 0) and a WGBS result. Pre-specified biological and clinical factors were assessed for correlation with TF: clinical stage, pathologic N stage, lesion size (by imaging), T stage, histologic grade, hormone receptor (HR) status, and proliferative rate (Ki-67 by IHC [MIB-1 clone]) via univariate and multivariate analyses. Ki-67 was obtained from pathology reports provided by enrollment sites and also assessed centrally (Mayo Clinic [Rochester, MN]). Stage-specific differences in detection rates between HR positive (HR+) and HR- breast cancers due to biological differences such as histologic grade and/or proliferative rate was also assessed. Results Of 511 pts, 94 (18.4%; 48.9% HR- and 12.3% in HR+) had WGBS-detected cancer. Higher TF was significantly associated with cancer detection (p<0.001). In univariate analyses, the variables significantly associated with TF were clinical stage, pathological N stage, and histologic grade (p<0.001 each). Primary lesion size was modestly correlated with TF (all stages combined: Spearman's correlation coefficient rs=0.4, p<0.001), and when grouped by early and late stages (stages I/II: rs=0.27, p<0.01; stages III/IV: rs=0.50, p<0.01); clinical T stage was significantly associated with TF only when all stages were combined (p<0.001). Proliferative rate (Ki-67) was positively correlated with TF at stages I/II (rs=0.29, p<0.05) but not III/IV (rs=-0.24, p=0.34); Ki-67 results obtained through Mayo were similar to that from enrollment sites (Pearson’s correlation coefficient rp=0.68, p<0.001). HR- breast cancers had significantly higher TF versus HR+ breast cancers only at stage II (p<0.001). In addition, compared to HR+ breast cancers, HR- breast cancers had a significantly higher proportion of high histologic grade (p<0.001 at stages I and II) and proliferative rate at earlier stages (p<0.05 at stages I, II, and III). In the multivariate analysis, clinical stage (stage III vs I and IV vs I) and HR status remained the most significantly associated with TF (p<0.001 each). Conclusions Using a prototype methylation-based plasma cfDNA cancer detection assay, TF was found to be associated with detection, and with clinical and biological features of breast cancer. Features routinely used to assess clinical aggressiveness (eg, HR- status and histologic grade) also demonstrated stage-specific associations with TF. Given the known relationship between TF and detection, these data suggest that clinical and biological cancer features may also provide insight into the variability of cancer detection using plasma-based cfDNA tests. Citation Format: Minetta C. Liu, Jodi M. Carter, Daniel W. Visscher, Karla Kopp, Rita Shaknovich, Xiaoji Chen, Kathryn N. Kurtzman, Shilpen Patel, Jacqueline D. Brooks, Carlo R. Cosenza, Jafi A. Lipson, Donald A. Richards, Fergus J. Couch, Zhao Dong, Hai Liu, Oliver Venn, Joerg Bredno, Eric T. Fung, Anne-Renee Hartman. Blood-based cancer detection in plasma cell-free DNA (cfDNA): Evaluating clinical and pathologic tumor characteristics in participants with breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-01.

Abstract Background: The clinical utility of routine annual mammogram after curative-intent treatment for male breast cancer is uncertain. There is potentially greater value after lumpectomy (as surveillance for ipsilateral recurrence) than mastectomy (as screening for a new contralateral cancer). The goal of this study was to assess real world use of mammography in men during the first year after lumpectomy or mastectomy to treat breast cancer. Methods: Administrative claims data from OptumLabs Data Warehouse (a large US database that includes privately insured patients and Medicare Advantage-insured enrollees from all 50 states and of all ages and ethnic and racial groups) were used to identify men treated with breast surgery for a new diagnosis of breast cancer between 2007 and 2017. We required continuous coverage starting at least 6 months prior to the non-metastatic breast cancer diagnosis and continuing until at least 13 months after the breast surgery. Our primary endpoint was the proportion of patients who had at least one mammogram during the year (13-month period, to allow for scheduling and other logistical delays) after lumpectomy or mastectomy. Univariate and multivariate testing were performed to identify predictors of mammography (with p<0.05 used as the threshold for statistical significance for both). Our secondary endpoint was the proportion with at least one mammogram within 24 months of surgery, performed in a subset who maintained their insurance coverage for at least that duration. Results: The 13-month analysis included 730 men with a median age at diagnosis of 62 years (Range: 25 to 87 years) and a median follow-up duration of 35 months (Range: 13 to 134 months). 209 (29%) of these men underwent mammography within 13 months after surgery. The characteristics of patients who underwent mammography and those who did not are shown in Table 1. Mammography was more likely after lumpectomy than mastectomy (41% vs. 27%) and after radiation therapy (41% vs. 32% in those who did not receive radiation). In a multivariate logistic regression model, more recent diagnosis (2015+) was associated with lower odds of undergoing mammography, while receipt of radiation was associated with higher odds of undergoing mammography. In the subset of patients with two or more years of post-surgery coverage (n=527), the proportion who had at least one mammogram during that 24-month period was 49% after lumpectomy and 40% after mastectomy. Conclusions: In this insured cohort, 73% of men did not undergo mammography within a year after mastectomy, and 59% did not within a year after lumpectomy. Mammography was less likely in patients diagnosed more recently (perhaps due to acknowledgment of the unique aspects of male breast cancer including a relatively low risk of contralateral second primary tumors), and more likely in those who received radiation. These variations in practice likely result from the paucity of evidence-based guidelines for male breast cancer survivorship care. More research is needed pertaining to whether or not mammograms improve clinical outcomes after curative intent treatment for male breast cancer. Table 1: Patient characteristics associated with receipt of mammogram within first 13 months after male breast cancer surgeryUnivariate AnalysisMultivariate AnalysisNo Mammogram (N=521)Mammogram (N=209)P-value, chi-square testOdds Ratio (OR) and 95% CIP-value for ORAge Group:0.1225-4966 (12.7%)32 (15.3%)Reference50-64216 (41.5%)98 (46.9%)0.99 (0.60, 1.63)0.9665-74112 (21.5%)44 (21.1%)0.87 (0.48, 1.57)0.6575+127 (24.4%)35 (16.7%)0.57 (0.30, 1.07)0.08Census Region:0.52Midwest138 (26.5%)59 (28.2%)ReferenceNortheast97 (18.6%)47 (22.5%)1.10 (0.68, 1.78)0.69South223 (42.8%)79 (37.8%)0.74 (0.49, 1.11)0.15West63 (12.1%)24 (11.5%)0.83 (0.47, 1.47)0.51Year of diagnosis:0.072007-2010126 (24.2%)65 (31.1%)Reference2011-2014199 (38.2%)82 (39.2%)0.80 (0.54, 1.20)0.292015+196 (37.6%)62 (29.7%)0.63 (0.41, 0.96)0.03Elixhauser Category:0.250148 (28.4%)69 (33.0%)Reference1-2218 (41.8%)74 (35.4%)0.85 (0.56, 1.28)0.433+155 (29.8%)66 (31.6%)1.18 (0.75, 1.87)0.47Surgery Type:0.005Lumpectomy55 (10.6%)38 (18.2%)ReferenceMastectomy466 (89.4%)171 (81.8%)1.57 (0.97, 2.55)0.07Chemotherapy:0.79No301 (57.8%)123 (58.9%)ReferenceYes220 (42.2%)86 (41.1%)0.79 (0.54, 1.16)0.23Radiation:0.02No355 (68.1%)124 (59.3%)ReferenceYes166 (31.9%)85 (40.7%)1.51 (1.03, 2.20)0.03 Citation Format: Siddhartha Yadav, Lindsey Sangaralingham, Stephanie R. Payne, Karthik V. Giridhar, Tina J. Hieken, Judy C. Boughey, Robert W. Mutter, John R. Hawse, Rafael E. Jimenez, Rachel A. Freedman, Sadia Choudhery, Fergus J. Couch, Celine M. Vachon, Nilay Shah, Roberto A. Leon-Ferre, Kathryn J. Ruddy. Surveillance mammography after treatment for male breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-17-08.

Abstract Background: It has become increasingly clear that effective treatment of metastatic breast cancer (MBC) requires an in-depth understanding of the molecular differences between primary tumors and metastases. The AURORA US Network was established to collect primary breast cancer-metastasis pairs for multi-platform genomic profiling in order to identify the molecular drivers of metastatic disease. AURORA US has both a retrospective and prospective phase. This is the first report of the retrospective phase. Methods: Archived tissue samples from the primary tumor and at least one distant metastasis were retrospectively collected from 83 MBC patients. Following internal quality assessment, samples from 55 pts, including 105 distinct metastatic lesions, were subject to DNA low pass whole genome and exome sequencing, DNA methylation arrays, and RNA sequencing. Early analyses of these multi-platform data include: DNA methylation, tumor gene expression and microenvironmental signatures, somatic and germline variants, DNA copy number changes, and structural variants between breast primaries and matched metastases. Results: Median age at diagnosis was 49 years (25-76); 32 (58%) were Stage I or II at presentation, 27 (49%) had a family history of breast cancer, and 20 (36%) had a second breast primary. Median disease-free interval before developing MBC was 2 years (range 0-36, 5 patients presented with Stage IV). Median overall survival from initial presentation was 4 years (range 0-37). Median survival after developing MBC was 1 year (range 0-13), with a median of three treatments. Primary tissue samples were banked from 1977-2017 and metastases were banked from 1999-2017. Clinical phenotypes of the primaries included 27 HR+ (49%), 15 triple negative (TNBC, 27%), and 11 HER2+ (20%, 12 missing HER2 status). Intrinsic subtype distribution of the primaries included 17 Basal-like (31%), 17 Luminal A (31%), 7 Normal-like (13%), 5 HER2-enriched (9%), and 1 Luminal B, with 8 pending. All metastases from the Basal-like cases remained Basal-like, while metastases from luminal primaries tended to gain HER2-Enriched subtype features (5/18, p = 0.01). Overall, we identified significant metastasis-enriched alterations in metabolism pathways, an increase in proliferation, and the loss of differentiation signatures and immune infiltrates with progression; the latter being the most pronounced in brain metastases. The most frequent somatic mutations in this cohort were in TP53, NCOR1, and RUNX1. Interestingly, ERBB2, EGFR, and ATM were also mutated in ≥10% of the tumors sequenced. In almost all cases, CpG island hypermethylation was clonally present in the primary tumor and persisted stably in the majority of metastatic lesions. Promoter CpG island hypermethylation was also identified in some metastatic lesions at JAM3, an important cellular adhesion molecule,and this was accompanied by reduced mRNA expression. CONCLUSIONS: Collection of banked primary and metastatic tissue pairs identified a young MBC cohort with a high frequency of breast cancer family history and second breast primaries. Molecular characterization of luminal tumor pairs highlighted acquisition of aggressive traits including increased proliferation and loss of differentiation in the metastases. In contrast, basal-like pairs remained relatively unchanged, except for the loss of immune activation. Ongoing analyses to be presented include clonal heterogeneity and phylogeny, novel metastasis signature discovery, gene fusion, and endogenous retrovirus detection. Citation Format: Tari A King, Minetta C Liu, Marni B McClure, Toshinori Hinoue, Benjamin J Kelly, Chad J Creighton, Jay Bowen, Kristen Leraas, Robyn T Burns, Sara Coppens, Salma Rezk, Amy L Garrett, Justin M Balko, Joel S Parker, Ben H Park, Ian Krop, Carey Anders, Katherine A Hoadley, Julie Gastier-Foster, Mothaffar F Rimawi, Rita Nanda, Nancy U Lin, Claudine Isaacs, P. Kelly Marcom, Anna Maria Storniolo, Fergus J Couch, Elaine R Mardis, Adrian V Lee, Uma Chandran, Peter W Laird, Susan G Hilsenbeck, Larry Norton, Andrea L Richardson, W. Fraser Symmans, Lisa A Carey, Antonio C Wolff, Nancy E Davidson, Charles M Perou, the AURORA US Network. Multiplatform analysis of matched primary and metastatic breast tumors from the AURORA US Network [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr GS3-08.

Abstract Background The risks of breast cancer in African American (AA) women associated with inherited mutations in breast cancer predisposition genes are not well defined. Thus, whether multigene germline hereditary cancer testing panels are applicable to this population is unknown. We assessed associations between mutations in panel-based genes and breast cancer risk in 5054 AA women with breast cancer and 4993 unaffected AA women drawn from 10 epidemiologic studies. Methods Germline DNA samples were sequenced for mutations in 23 cancer predisposition genes using a QIAseq multiplex amplicon panel. Prevalence of mutations and odds ratios (ORs) for associations with breast cancer risk were estimated with adjustment for study design, age, and family history of breast cancer. Results Pathogenic mutations were identified in 10.3% of women with estrogen receptor (ER)-negative breast cancer, 5.2% of women with ER-positive breast cancer, and 2.3% of unaffected women. Mutations in BRCA1, BRCA2, and PALB2 were associated with high risks of breast cancer (OR = 47.55, 95% confidence interval [CI] = 10.43 to >100; OR = 7.25, 95% CI = 4.07 to 14.12; OR = 8.54, 95% CI = 3.67 to 24.95, respectively). RAD51D mutations were associated with high risk of ER-negative disease (OR = 7.82, 95% CI = 1.61 to 57.42). Moderate risks were observed for CHEK2, ATM, ERCC3, and FANCC mutations with ER-positive cancer, and RECQL mutations with all breast cancer. Conclusions The study identifies genes that predispose to breast cancer in the AA population, demonstrates the validity of current breast cancer testing panels for use in AA women, and provides a basis for increased referral of AA patients for cancer genetic testing.

TPS11120 Background: Currently there is no biomarker to predict specific benefit from DNA-damaging anthracycline and cyclophosphamide-based chemotherapy in the clinic. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA-damage response pathway occurs in approximately 25% of breast cancer and results in sensitivity to DNA-damaging agents. We therefore developed an assay to detect loss of the FA/BRCA pathway, for the purpose of predicting benefit from chemotherapy. Methods: 21 FA patient samples were analyzed to identify genetic processes associated with loss of the FA/BRCA pathway. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples and a molecular subgroup was identified that was defined by the molecular processes representing loss of the FA/BRCA pathway. A 44-gene DNA Damage response deficient (DDRD) assay was developed that could identify this subgroup from formalin fixed, paraffin embedded (FFPE) samples in the clinic. Results: In a publicly available independent cohort of 204 patients, the assay predicted response to neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline and cyclophosphamide) with an odds ratio of 4.01, (95% Cl:1.69-9.54). We also analysed samples from an independent cohort of 114 node-negative breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin and cyclophosphamide treatment at the Northern Ireland Cancer Centre. The DDRD assay significantly predicted 5-year relapse free survival with a hazard ratio of 0.27 (95% Cl:0.10-0.83). The assay was not predictive of survival in patients who did not receive chemotherapy. Conclusions: An FFPE tissue-based assay that detects loss of the FA/BRCA pathway has been developed and independently validated as a predictor of response and prognosis following DNA damaging anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings.

PURPOSE To determine the sensitivity and specificity of genetic testing criteria for the detection of germline pathogenic variants in women with breast cancer. MATERIALS AND METHODS Women with breast cancer enrolled in a breast cancer registry at a tertiary cancer center between 2000 and 2016 were evaluated for germline pathogenic variants in 9 breast cancer predisposition genes ( ATM , BRCA1, BRCA2, CDH1, CHEK2, NF1, PALB2, PTEN, and TP53). The performance of the National Comprehensive Cancer Network (NCCN) hereditary cancer testing criteria was evaluated relative to testing of all women as recommended by the American Society of Breast Surgeons. RESULTS Of 3,907 women, 1,872 (47.9%) meeting NCCN criteria were more likely to carry a pathogenic variant in 9 predisposition genes compared with women not meeting criteria (9.0% v 3.5%; P < .001). Of those not meeting criteria (n = 2,035), 14 (0.7%) had pathogenic variants in BRCA1 or BRCA2. The sensitivity of NCCN criteria was 70% for 9 predisposition genes and 87% for BRCA1 and BRCA2, with a specificity of 53%. Expansion of the NCCN criteria to include all women diagnosed with breast cancer at ≤ 65 years of age achieved > 90% sensitivity for the 9 predisposition genes and > 98% sensitivity for BRCA1 and BRCA2. CONCLUSION A substantial proportion of women with breast cancer carrying germline pathogenic variants in predisposition genes do not qualify for testing by NCCN criteria. Expansion of NCCN criteria to include all women diagnosed at ≤ 65 years of age improves the sensitivity of the selection criteria without requiring testing of all women with breast cancer.

AbstractPrevious transcriptome‐wide association studies (TWAS) have identified breast cancer risk genes by integrating data from expression quantitative loci and genome‐wide association studies (GWAS), but analyses of breast cancer subtype‐specific associations have been limited. In this study, we conducted a TWAS using gene expression data from GTEx and summary statistics from the hitherto largest GWAS meta‐analysis conducted for breast cancer overall, and by estrogen receptor subtypes (ER+ and ER−). We further compared associations with ER+ and ER− subtypes, using a case‐only TWAS approach. We also conducted multigene conditional analyses in regions with multiple TWAS associations. Two genes, STXBP4 and HIST2H2BA, were specifically associated with ER+ but not with ER– breast cancer. We further identified 30 TWAS‐significant genes associated with overall breast cancer risk, including four that were not identified in previous studies. Conditional analyses identified single independent breast‐cancer gene in three of six regions harboring multiple TWAS‐significant genes. Our study provides new information on breast cancer genetics and biology, particularly about genomic differences between ER+ and ER− breast cancer.