Upgrade Rates and Breast Cancer Development Among Germline Pathogenic Variant Carriers with High-Risk Breast Lesions

BACKGROUND

High-risk lesions (HRL) of the breast are risk factors for future breast cancer development and may be associated with a concurrent underlying malignancy when identified on needle biopsy; however, there are few data evaluating HRLs in carriers of germline pathogenic variants (PVs) in breast cancer predisposition genes.

METHODS

We identified patients from two institutions with germline PVs in high- and moderate-penetrance breast cancer predisposition genes and an HRL in an intact breast, including atypical ductal hyperplasia (ADH), flat epithelial atypia (FEA), and lobular neoplasia (LN). We calculated upgrade rates at surgical excision and used Kaplan-Meier methods to characterize 3-year breast cancer risk in patients without upgrade.

RESULTS

Of 117 lesions in 105 patients, 65 (55.6%) were ADH, 48 (41.0%) were LN, and 4 (3.4%) were FEA. Most PVs (83.8%) were in the BRCA1/2, CHEK2 and ATM genes. ADH and FEA were excised in most cases (87.1%), with upgrade rates of 11.8% (95% confidence interval [CI] 5.5-23.4%) and 0%, respectively. LN was selectively excised (53.8%); upgrade rate in the excision group was 4.8% (95% CI 0.8-22.7%), and with 20 months of median follow-up, no same-site cancers developed in the observation group. Among those not upgraded, the 3-year risk of breast cancer development was 13.1% (95% CI 6.3-26.3%), mostly estrogen receptor-positive (ER +) disease (89.5%).

CONCLUSIONS

Upgrade rates for HRLs in patients with PVs in breast cancer predisposition genes appear similar to non-carriers. HRLs may be associated with increased short-term ER+ breast cancer risk in PV carriers, warranting strong consideration of surgical or chemoprevention therapies in this population.

Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.

Abstract P6-08-08: Concurrent DNA and RNA genetic testing identifies more patients with hereditary breast cancer than DNA testing alone

BACKGROUND: Germline genetic testing is routinely incorporated into clinical care for breast cancer patients to inform management decisions and reduce risk for developing subsequent cancers. While the diagnostic yield of cancer genetic testing has increased over the years due to adoption of multigene panels, a substantial portion of breast cancer patients remain without a molecular diagnosis yet are suspected to have a genetic mutation that could not be detected and/or classified with standard DNA testing techniques. We assessed the ability of a novel genetic testing approach involving simultaneous DNA and RNA analysis to increase the diagnostic yield and decrease the number of variants of unknown significance (VUS). METHODS: Women with a personal history of breast cancer were ascertained from a larger cohort of patients referred for concurrent RNA sequencing alongside DNA hereditary cancer panel testing by ordering clinicians from 18 collaborating medical centers across the United States. Test result classifications were evaluated for women whose testing included sixteen clinically-actionable hereditary breast and/or ovarian cancer (HBOC) genes (ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53). RESULTS: In this cohort of 746 breast cancer patients, the addition of RNA sequencing increased the pathogenic variant detection rate from 8% to 9% across sixteen HBOC genes. These RNA-related positive results included two pathogenic variants in BRCA1 occurring outside the standard analytical range of DNA testing and three VUS (one each in ATM, BRCA2, and PMS2) that were reclassified as likely pathogenic as a result of additional information provided by RNA sequencing. In addition, two VUS were reclassified to benign/likely benign (one each in MSH2 and BRCA2). Together, these five variant reclassifications contributed to a 3% relative decrease in the number of unique VUS classifications (reduced from 182 to 177 unique VUS). In addition, 31 previously-tested patients received reclassification reports. CONCLUSIONS: Concurrent DNA and RNA genetic testing has shown immediate promise in this pilot study, leading to the identification of five breast cancer patients with mutations in clinically actionable genes that would otherwise have received inconclusive or negative results with DNA testing alone. By increasing the detection of germline pathogenic variants and reducing VUS classifications, concurrent DNA and RNA genetic testing increases the diagnostic yield and clinical impact of hereditary cancer testing for breast cancer patients.

Citation Format: Holly LaDuca, Lily Hoang, Jill Dolinsky, Jessica Profato, Amal Yussuf, Carolyn Horton, Cara Dresbold, Cassie Garcia, Catherine Koptiuch, Danielle Dondanville, Danielle McKenna, Danielle Menashe, Deborah Wham, Deepika Nathan, Diane Samad, Elizabeth Hoodfar, Gayle Patel, Jen Moore, Jennifer Geurts, John Lee, Kara Milliron, Khateriaa Pyrtel, Meagan Farmer, Meredith Seidel, Morgan Depas, Nichole Morman, Olivia Tan, Rebekah Krukenberg, Rob Pilarski, Samantha Stachowiak, Sandra Jenkinson, Sara Pirzadeh-Miller, Shraddha Gaonkar, Tiffani Demarco, Brigette Tippin Davis, Elizabeth C Chao, Rachid Karam. Concurrent DNA and RNA genetic testing identifies more patients with hereditary breast cancer than DNA testing alone [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 P6-08-08.

Evaluating and improving the implementation of a community-based hereditary cancer screening program

Healthcare disparities exist in the provision of cancer genetic services including genetic counseling and testing related to BRCA1/2 mutations. To address this in a community health setting a screening tool was created to identify high-risk women. This study evaluates the implementation of the tool and identifies opportunities for improved cancer genetic screening, including regular clinician education. A mixed-method approach was used to evaluate clinician utilization of the screening tool at Planned Parenthood affiliates. Novel surveys that evaluated acceptance and implementation were administered to clinicians (n = 14) and semi-structured interviews (n = 6) were used to explore clinicians' perspectives and identify gaps in its utilization. Educational modules that addressed gaps were developed, implemented, and evaluated using a post-education survey (n = 8). Clinicians reported confidence in administering and interpreting the screening tool, but reported less confidence in their knowledge of cancer genetics and ability to connect clients with genetic counseling and testing (p = .003). Educational modules resulted in significant gains in clinician knowledge on genetic topics (p < .05) and increased self-reported confidence in connecting clients with genetic services. The modules reinforced the belief that genetic testing is beneficial for patients at increased risk (p = .001) and is important to inform subsequent medical management (p = .027). While building community clinicians' capacity to connect clients with genetic services is crucial, it is challenged by knowledge and confidence gaps in discussions of genetic services with clients. Consistent genetic-focused education with non-genetic clinicians can improve confidence and knowledge, enabling a more effective screening program in community health settings.

Breast Cancer Risk Assessment: A Guide for Clinicians Using the NCCN Breast Cancer Risk Reduction Guidelines

Breast cancer, a complex and heterogeneous disease, is the most common malignancy diagnosed in women in the United States, with over 180,000 new cases and approximately 44,000 deaths per year. Breast cancer risk is influenced by a large number of factors, including age, family history, reproductive and hormonal history, proliferative breast conditions, physical activity, diet, and environmental exposures. These factors all interact in a complex manner to contribute to the risk of developing breast cancer. Because the interactions between risk factors are poorly understood at the molecular level, it is difficult to accurately evaluate the breast cancer risk of a given person presenting with an individual constellation of factors. To better define the population at increased risk that may warrant specific intervention, several models exist to estimate a woman's risk for developing breast cancer and for harboring a germline mutation in a cancer susceptibility gene. This article summarizes these models and gives brief guidelines about which model may be preferable given a specific family history.