Utilizing cell-free DNA to predict risk of developing brain metastases in patients with metastatic breast cancer

We compared cell-free DNA (cfDNA) results at MBC diagnosis in patients who developed brain metastases (BM) vs those without (non-BM) to understand genomic predictors of BM. Patients with cfDNA testing at MBC diagnosis (Guardant360®, 73 gene next generation sequencing) were identified. Clinical and genomic features of BM and non-BM were compared (Pearson's/Wilcoxon rank sum tests). Eighteen of 86 patients (21%) with cfDNA at MBC diagnosis developed BM. Comparing BM vs non-BM, a higher prevalence of BRCA2 (22% vs 4.4%, p = 0.01), APC (11% vs 0%, p = 0.005), CDKN2A (11% vs 1.5%, p = 0.05), and SMAD4 (11% vs 1.5%, p = 0.05) was observed. Seven of 18 BM had ≥1 of the following 4 mutations in baseline cfDNA: APC, BRCA2, CDKN2A or SMAD4 vs 5/68 non-BM (p = 0.001). Absence of this genomic pattern had a high negative predictive value (85%) and specificity (93%) in excluding BM development. Baseline genomic profile varies in MBC that develops BM.

Abstract 4353: Utilizing scRNA sequencing to understand biomarkers of response and resistance to Sacitizumab Govetican in localized TNBC

Triple-Negative Breast Cancer (TNBC) is an aggressive breast cancer subset, which lacks expression of estrogen receptors, progesterone receptors, and human epidermal growth factor receptor-2. This subset of breast cancer disproportionately affects Black and African American women and improving TNBC treatment options is vital to reducing breast cancer mortality. The novel antibody-drug conjugate, Sacitizumab Govetican (SG), which targets TROP2 at the cell surface, has shown promising clinical results from the NeoSTAR trial (NCT04230109), a phase II study evaluating neoadjuvant SG therapy in a localized TNBC setting. As part of the NeoSTAR clinical trial, we have collected and processed pre- and post- SG treatment patient samples, with the aim of understanding response to this monotherapy. Herein, we identify biomarkers of response and resistance to SG monotherapy through the use of single cell RNA sequencing of matched pre- and post-treatment patient biopsies combined with exome sequencing these patient samples. Pre-treatment core needle biopsy samples, and if applicable, post-treatment residual disease biopsies were dissociated into single cell suspensions and subjected to single cell RNA sequencing. Additionally, fixed patient tissue samples were processed accordingly for exome sequencing analyses. Overall, we analyzed over 144,000 cells from 37 total scRNA seq libraries with an average of 3800 cells per biopsy sample, demonstrating the feasibility of this method. From these analyses, we observed several cell-type differences between patients who achieved a pathological complete response (pCR) and patients who had residual disease (RD). Specifically, our data shows that tumor infiltrating lymphocytes are a potential prognostic biomarker of response to SG. Furthermore, we detected alterations in among stromal and immune cell subsets, among non-responders, indicating that these cell types maybe indicative of SG resistance. Taken together, we outline biomarkers of response to SG treatment for an improved understanding of resistance mechanisms in the neoadjuvant setting to improve TNBC outcomes among patients.

Citation Format: Nicole Peiris, Simona Cristea, Mengran Zhang, Siang Koh, James Coates, Ilze Smidt, Veerle Bossuyt, Laura Spring, Aditya Bardia, Leif Ellisen. Utilizing scRNA sequencing to understand biomarkers of response and resistance to Sacitizumab Govetican in localized TNBC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4353.

Abstract PD1-10: Impact of Race on Clinical, Socioeconomic, and Genomic Characteristics, Clinical Trial Participation, and Receipt of Genotype-matched Therapy Among Patients with Metastatic Breast Cancer

Background: Clinical outcomes in breast cancer differ across racial and ethnic populations. We have previously demonstrated that receipt of genotype-matched therapy targeted to an actionable mutation may potentially improve patient outcomes (Vidula, CCR, 2021). We evaluated the impact of race on clinical, socioeconomic, and genomic characteristics, clinical trial participation, and receipt of genotype-matched therapy among patients with metastatic breast cancer (MBC). Methods: We conducted a retrospective study of patients with MBC at an academic institution who underwent cell-free DNA testing (cfDNA, Guardant360, 74 gene panel) as part of routine clinical care from 11/29/2016-11/2/2020. Patient demographics (including self-reported race and ethnicity) and clinical trial enrollment (at same institution) were determined by retrospective data collection. Mutations identified in cfDNA were characterized as actionable based on the variant interpretation performed by Guardant360 using vetted genomic databases, and receipt of genotype-matched therapy targeted to an actionable mutation was determined as previously described (Vidula, CCR, 2021). Pearson’s chi-squared and Wilcoxon rank-sum tests were used to compare categorical and continuous variables between groups, with p< 0.05 indicating statistical significance. Results: Four hundred and twenty-five patients with MBC and cfDNA results were identified, of which 369 were White (87%), 27 Black (6.4%), 15 Hispanic (3.5%), and 14 Asian (3.3%). There were no significant differences in median age at MBC diagnosis (p=0.064), disease subtype distribution (p=0.74), proportions of de-novo/recurrent MBC (p=0.95), presence of visceral metastases (p=0.84), Charleston comorbidity index (p=0.93), menopausal status (p=0.3), and level of education (p=0.44) across racial groups. Higher proportions of non-primary English speakers were seen in Hispanic (80%) and Asian (29%) races (p< 0.001). Median distance traveled to the institution also varied based on race, with White patients traveling further (White: 39.1 miles, Black: 21.8 miles, Hispanic 9.4 miles, Asian 9.1 miles, p< 0.001). In addition, type of insurance varied based on race, with White patients having the highest rates of commercial insurance and Medicare, Black patients having the highest rate of state-supported insurance, and Asian patients having the highest uninsured rates (p< 0.001). Clinical trial enrollment rates did not significantly differ by race (White: 44%, Black: 37%, Hispanic: 47%, and Asian 21%, p=0.34), but patients without insurance were significantly less likely to be enrolled on a trial than those with commercial insurance (p=0.03). The proportion of patients with ≥1 actionable mutation in cfDNA did not vary significantly by race (White: 78%, Black: 56%, Hispanic: 73%, Asian 86%, p=0.18) and the median number of actionable mutations found in cfDNA was similar across races (p=0.31). However, receipt of genotype-matched therapy targeted to an actionable mutation varied by race, with the highest rates of matched therapy in White patients (White: 28%, Black: 11%, Hispanic 13%, Asian 14%, p< 0.001). After multivariable logistic regression adjusting for subtype, commercial insurance versus other insurance types, and proximity to the center, White patients remained significantly more likely to receive matched therapy (p=0.029). Conclusions: We observed significant race-based differences in non-English speaking status, insurance type, and median distance traveled to the institution. Racial/ethnic minority patients were less likely to receive genotype-matched therapy than White patients. Further research is needed to identify barriers and reduce disparities in access to precision medicine.

Citation Format: Rupali Sood, Lianne Ryan, Andrzej Niemierko, Laura M. Spring, Dejan Juric, Steven J. Isakoff, Seth A. Wander, Jennifer Shin, Naomi Ko, Leif Ellisen, Beverly Moy, Aditya Bardia, Neelima Vidula. Impact of Race on Clinical, Socioeconomic, and Genomic Characteristics, Clinical Trial Participation, and Receipt of Genotype-matched Therapy Among Patients with Metastatic Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD1-10.

Abstract PD13-07: PD13-07 Combination therapy with the AKT inhibitor, ipatasertib, endocrine therapy, and a CDK4/6 inhibitor for hormone receptor positive (HR+)/HER2 negative metastatic breast cancer (MBC): results from the phase I TAKTIC trial

Background: Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in combination with endocrine therapy (ET) provide significant clinical benefit in patients with HR+/HER2- metastatic breast cancer (MBC) and have become a standard of care treatment. Prior insights from tumor profiling and preclinical analyses suggest that AKT1 activation can induce CDK4/6i resistance. We hypothesized that targeting AKT1 following CDK4/6i progression may be an effective therapeutic strategy and conducted a clinical trial to evaluate both doublet (ET+AKTi) and triplet (ET+AKTIi+CDK 4/6i) therapy in the ≥ 2nd line MBC setting. Methods: TAKTIC is an open-label phase Ib clinical trial (clinicaltrials.gov NCT03959891) evaluating the combination of the AKT inhibitor ipatasertib (ipat) with fulvestrant (Arm A), an aromatase inhibitor (Arm B), or the triplet combination (Arm C) with fulvestrant + palbociclib (palbo). The primary objective is to evaluate the safety (NCI CTCAE 5.0) and tolerability of ipat in combination with endocrine therapy +/- CDK4/6i. Secondary objectives include clinical efficacy, as determined by objective response rate (RECIST v1.1), clinical benefit rate (CBR), progression-free survival (PFS), and overall survival (OS). Key inclusion criteria include unresectable HR+/HER2- MBC; at least 1 prior therapy for MBC including any CDK4/6i; up to 2 prior lines of chemotherapy for MBC (no limit on prior endocrine therapy). Here, we present an updated interim analysis from all study arms. Results: The trial completed accrual with 77 pts enrolled from June 2019 – February 2022, including 19 on Arm A, 16 on Arm B, and 42 on Arm C. Median age was 62 (range 32-88) and 65/77 pts (84%) received prior CDK4/6i (median no. of prior lines = 3, range 1-13). 56/77 pts (73%) had measurable disease at baseline and 50/77 pts (65%) had visceral metastases in the liver/lung (68% Arm A, 44% Arm B, 71% Arm C). Pts enrolled on Arms A and B received ipat at 400mg in combination with fulvestrant or an aromatase inhibitor, respectively. In Arm C, 27/42 pts enrolled into the dose escalation phase and received ipat + palbo at varying doses in combination with fulvestrant. Two DLTs were observed in the 300mg ipat + 125mg palbo cohort (grade 4 neutropenia ≥ 7 days). ET+400mg ipat + 100mg palbo was determined to be the recommended phase 2 dose (R2PD), and the remaining 15/42 pts on Arm C were treated at this dose level in the expansion phase. Treatment was well tolerated in all arms. Grade 3 and 4 toxicities included neutropenia (39/77, 50.6%), leukopenia (15/77, 19.5%), diarrhea (11/77, 14/3%), transaminitis (7/77, 9.1%), lymphopenia (6/77, 7.8%), rash (6/77, 7.8%), and thrombocytopenia (3/77, 3.9%). As of 6/28/2022, 16/77 pts remain on treatment. The median treatment duration for all pts is estimated at 6 months (range 0.5-39). Among the 56 pts with measurable disease, 11 had partial response (PR) and 32 had stable disease (SD) as the best response. CBR, defined as percentage of pts who achieved PR or SD > 6 months, was 48% across the study (53% Arm A, 31% Arm B, 57% Arm C). The median PFS was 5.5 months (95% confidence interval [CI]: 3.8 – 7.4) and the median OS was 24.5 months (95% CI: 17.1 – 33.9). Conclusions: The combination of ipat with endocrine therapy +/- palbo is well tolerated in heavily pre-treated pts, with preliminary evidence of clinical activity. This trial demonstrates how molecular insights related to CDK4/6i resistance inform potential therapy combinations. Further studies are needed to evaluate AKTi-based combinations in pts with HR+ MBC.

Citation Format: Seth A. Wander, Jennifer C. Keenan, Andrzej Niemierko, Dejan Juric, Laura M. Spring, Jeffrey Supko, Neelima Vidula, Steven J. Isakoff, Lianne Ryan, Sarah Padden, Elizabeth Fisher, Amber Newton, Beverly Moy, Leif Ellisen, Douglas S. Micalizzi, Aditya Bardia. PD13-07 Combination therapy with the AKT inhibitor, ipatasertib, endocrine therapy, and a CDK4/6 inhibitor for hormone receptor positive (HR+)/HER2 negative metastatic breast cancer (MBC): results from the phase I TAKTIC trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD13-07.

Abstract P5-02-13: TRK inhibitor in a patient with metastatic triple negative breast cancer and NTRK fusions identified via cell-free DNA analysis

Introduction: Tissue-agnostic indications for targeted therapies are expanding options for patients with advanced solid tumors. The FDA approvals of the PD-1 inhibitor pembrolizumab and the TRK inhibitors larotrectinib and entrectinib provide rationale for next generation sequencing (NGS) in effectively all advanced solid tumor patients, as findings may indicate targeted therapy even in disease that may seem otherwise refractory. Here, we present the case of a post-menopausal woman with metastatic triple negative breast cancer (TNBC) who had disease progression on multiple lines of therapy prior to the identification of two actionable NTRK mutations, identified via cell-free DNA (cfDNA) and tissue-based NGS. She was subsequently started on the TRK inhibitor larotrectinib and had a marked clinical response. Case Presentation: A 64-year-old woman presented with metastatic TNBC five years after being treated for a localized breast cancer. The cancer rapidly progressed through 4 lines of therapy in the metastatic setting, including immunotherapy [atezolizumab/nab-paclitaxel (progression after 5 months)], antibody-drug conjugate-based therapy [sacituzumab govitecan (progression after 2 months)], and chemotherapy [gemcitabine/carboplatin (progression after 3 months), eribulin (progression after 2 months)]. Her CA 15-3 had also been consistently increasing to a peak of 206 IU/mL. Germline genetic testing was negative. Ultimately, NGS evaluation of cfDNA via an 83-gene assay (Guardant Health, Inc.) identified two NTRK3 fusions: an ETV6-NTRK3 fusion [mutant allele fraction (MAF) = 10.9%] associated with the rare secretory breast carcinoma, and CRTC3-NTRK3 (MAF = 3.2%), a fusion partner previously undescribed in breast cancer. Liver biopsy was sent for whole exome sequencing and RNA-seq analysis (BostonGene, Inc), which provided orthogonal confirmation of both the ETV6-NTRK3 and CRTC3-NTRK3 fusions. Review of the tumor pathology showed invasive ductal carcinoma with secretory features; this pathology and the ETV6-NTRK3 fusion were consistent with a diagnosis of secretory breast carcinoma. She was started on the TRK inhibitor larotrectinib, and she had a significant clinical and radiographic response after only two months of therapy. Recheck of her CA 15-3 showed a decrease to 48 IU/mL, the lowest level in our records. Repeat cfDNA testing showed a decrease of the ETV6-NTRK3 fusion to MAF 0.40% and the CRTC3-NTRK3 fusion to MAF 0.07%. The patient took larotrectinib for 7 months with good disease control. Unfortunately, unrelated to her therapy, she had experienced multiple fractures secondary to her existing osseous metastases, and these led to significant morbidity. She and her family elected to transition to comfort measures, after which she passed away. Discussion: In the presented case, the identification of NTRK fusions by plasma-based genotyping resulted in matched selection of genotype-directed therapy, and this otherwise refractory TNBC exhibited marked response to targeted therapy. While TNBC had historically been considered a subtype of breast cancer without targetable options, the expanding roles of NGS testing and targeted therapies are changing the paradigm. The actionability of rare genomic events such as NTRK fusions makes identifying them critical for individual patients, particularly in heterogeneous diseases such as TNBC. Tissue-agnostic targeted therapies now give reason for NGS testing in most solid tumors, as reflected in updated consensus guidelines. This case demonstrates the significant potential benefits of NGS testing in advanced and refractory cancers.

Citation Format: Jennifer C. Keenan, Arielle J. Medford, Lauren J. Oshry, Baris Boyraz, Charles S. Dai, Lesli A. Kiedrowski, Sofia Menshikova, Anna Butusova, Tasos Gogakos, Rachel Occhiogrosso, Phoebe Ryan, Jochen Lennerz, Laura M. Spring, Beverly Moy, Leif Ellisen, Aditya Bardia. TRK inhibitor in a patient with metastatic triple negative breast cancer and NTRK fusions identified via cell-free DNA analysis. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-13.

Abstract PD17-03: Cell-free DNA monitoring in a phase II study of adjuvant endocrine therapy with CDK 4/6 inhibitor ribociclib for localized HR+/HER2- breast cancer (LEADER)

Background: While adjuvant endocrine therapy (ET) reduces recurrence risk in hormone receptor-positive (HR+) breast cancer, many patients still experience disease recurrence. Adjuvant therapeutic advances are needed to improve outcomes. Meanwhile, monitoring for circulating tumor DNA (ctDNA) in the adjuvant setting may detect molecular residual disease and/or emergences of molecular recurrence from tumor dormancy. Cyclin-dependent kinase 4 and 6 (CDK 4/6) inhibitors have shown efficacy in HR+/HER2- metastatic breast cancer, and abemaciclib is now approved for adjuvant use in high-risk HR+/HER2- breast cancer. Adjuvant clinical trials have evaluated upfront use of adjuvant CDK 4/6 inhibition; however, the optimal timing of adding a CDK 4/6 inhibitor for HR+/HER2- breast cancer remains unknown. We conducted a prospective phase II clinical trial to evaluate the addition of the CDK 4/6 inhibitor ribociclib in patients with at least one remaining year of adjuvant ET regardless of duration of ET prior to trial enrollment, and we prospectively collected plasma for ctDNA analysis. Methods: Eligible patients had Stage I-III HR+/HER2- breast cancer and had been on adjuvant ET (any number of years) with at least one year of treatment remaining. Patients were randomized to one of two ribociclib schedules: continuous (400 mg daily, 28-day cycle) or intermittent (600 mg daily days 1-21, 28-day cycle) for one year. Patients were concurrently treated with an aromatase inhibitor (plus GnRH agonist, if premenopausal). Time to recurrence was calculated using the Kaplan-Meier method. ctDNA monitoring was performed using the SignateraTM platform, a tumor-informed assay based on whole exome sequencing of the primary tumor for multiplex PCR-NGS ctDNA assay design with targeting of up to 16 single nucleotide variants. Plasma samples were collected at the start of ribociclib/ET and serially during follow-up visits. Results: Among 81 patients treated with adjuvant endocrine therapy and the CDK4/6 inhibitor ribociclib, 42 patients had samples suitable for ctDNA analysis: 3 (7%) had a single ctDNA test, 17 (40%) had 2 serial ctDNA tests, and 22 (52%) had 3 serial ctDNA tests. After a median follow-up of 20 months, 2 patients who received ribociclib (intermittent dosing) experienced disease recurrence with recurrence-free survival of 100% at 1 year from study entry and 97% (95% CI 88-99%) at 2 years. ctDNA was detected exclusively in the only 2 patients that experienced recurrence, with lead times of 7 months and 8 months prior to clinical recurrence. Both patients had no detectable ctDNA at the start of ribociclib/ET. One patient had detectable ctDNA [mean tumor molecules/mL (MTM/mL) = 0.1] while on ribociclib/ET for 5 months, after which she completed a full 12 months of treatment. One month after completing ribociclib/ET (8 months after ctDNA detection), she presented with metastases in the liver and bones. The second patient had 2 negative ctDNA tests at days 0 and 147 while receiving ribociclib/ET and became ctDNA positive (MTM/mL = 0.1) at day 350. She developed CNS-only metastatic disease 7 months after completing ribociclib/ET. Among the other 40 patients who did not have detectable ctDNA, none have experienced recurrence. Conclusions: Overall, only 2 patients had detectable ctDNA, and both patients developed recurrent metastatic disease after completion of ribociclib with ET. Notably, one of these patients developed CNS-only disease. While follow-up is early, the remaining patients did not have detectable ctDNA and have not developed recurrent disease. This study suggests monitoring for ctDNA may identify patients at increased risk for recurrence in the extended adjuvant period and potentially guide therapy escalation.

Citation Format: Arielle J. Medford, Lauren Scarpetti, Andrzej Niemierko, Steven J. Isakoff, Beverly Moy, Seth A. Wander, Elizabeth Deluca, Elizabeth Abraham, Jennifer Shin, Lowell Schnipper, Amy E. Comander, Therese Mulvey, Erik Spickard, Ekaterina Kalashnikova, Angel Rodriguez, Leif Ellisen, Aditya Bardia, Laura M. Spring. Cell-free DNA monitoring in a phase II study of adjuvant endocrine therapy with CDK 4/6 inhibitor ribociclib for localized HR+/HER2- breast cancer (LEADER) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD17-03.

Abstract P1-08-01: Virtual molecular and precision medicine (vMAP) clinic to improve access to clinical trials for patients with metastatic breast cancer: an academic-community collaboration

Background: Despite improved outcomes for patients with metastatic breast cancer (MBC), attributed in part to advancements in precision therapeutics, clinical trial enrollment and genomic testing are relatively underutilized in the community oncology setting. To address this need, we launched a virtual molecular and precision medicine (vMAP) clinic to improve access for patients in our community network. Here we describe the initial results from the virtual clinic initiative. Methods: In 2020, the vMAP clinic was launched to provide real-time access to precision medicine expertise through virtual, email-based consultation directed to a multidisciplinary team. As part of the service, providers contacted vMAP regarding patients with MBC at the time of initial presentation or disease progression. Upon receipt, the vMAP team (including breast medical oncologists, a breast oncology research nurse, a research assistant, and ad hoc consultation from cancer genetics and molecular pathology representatives) engaged in discussion to identify potential clinical trials with slot availability or standard of care (SOC) options and provided recommendations to the referring provider within 72 hours. Relevant patient data and vMAP referral outcomes were recorded. Providers across the community network were surveyed at project onset and after seventeen months. Results: In its first 14-month period (June 2020-July 2021), 47 cases from 16 providers across seven community oncology sites and one academic site were referred to vMAP. A majority (88.6%) of patients had undergone somatic genomic testing (tissue-based, plasma-based, or both) to inform treatment guidance. All cases were screened for available clinical trials as well as SOC options at the time of referral. The average response time to the referring provider with a finalized recommendation was 1.77 days (range 0-5). Forty cases (85.1%) had clinical trial options identified on vMAP pre-screen. Subsequently, 22 patients (46.8%) screened for vMAP recommended clinical trials with 18 (38.3%) initiating enrollment. Of the remaining patients that did not pursue clinical trial screening, 17 (36.2%) started vMAP-recommended SOC treatment, five (10.6%) pursued a different treatment, one (2.1%) was not a candidate for further treatment, and two (4.3%) opted to receive care at a non-affiliated institution, and subsequent treatment information was not available. Reasons that patients did not enroll on trials included trial ineligibility, formal clinical trial screening failure, and patient/provider preference. At project onset, network provider survey results confirmed a previously suggested demand for improvements in processes surrounding genomic testing interpretation and clinical trial enrollment. Post-referral survey results indicated vMAP recommendations and pre-screenings improved the processes surrounding interpretation of genomic testing and clinical trial screening and enrollment, with high rates of referring provider satisfaction. Conclusion: A precision medicine virtual clinic demonstrated an efficient and flexible means to offer real-time interpretation of genomic and molecular test results and identification of appropriate treatment options, including clinical trials when applicable, for patients with MBC. The service highlights an example of an academic-community collaboration model to expand precision medicine and clinical trial access for patients with metastatic breast cancer.

Citation Format: Lindsey Mortensen, Jennifer C. Keenan, Elizabeth Abraham, Sarah Padden, Annie Ma, Elyssa Denault, Lianne Ryan, Arielle J. Medford, Leif Ellisen, Joel H. Schwartz, Aditya Bardia, Laura M. Spring. Virtual molecular and precision medicine (vMAP) clinic to improve access to clinical trials for patients with metastatic breast cancer: an academic-community collaboration [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-08-01.

Abstract OT1-11-01: Phase II study of talazoparib, a PARP inhibitor, in somatic BRCA1/2 mutant metastatic breast cancer identified by cell-free DNA or tumor tissue genotyping

Background: PARP inhibitors are currently approved for the treatment of germline BRCA1/2 mutant metastatic breast cancer (MBC), which accounts for 5-10% of breast cancer. We hypothesize that a PARP inhibitor may also have efficacy in somatic BRCA1/2 mutant MBC, expanding the potential clinical applicability of PARP inhibitors. We previously demonstrated that somatic BRCA1/2 mutations can be identified by both cell-free DNA and tumor tissue genotyping in a subset of patients with MBC who are not germline BRCA1/2 carriers. Furthermore, a PARP inhibitor was demonstrated to induce cell growth inhibition in a circulating tumor cell culture model generated from a patient with pathogenic somatic BRCA1 mutant MBC (Vidula, Dubash, CCR, 2020). In this trial, we are evaluating the efficacy of a PARP inhibitor in somatic BRCA1/2 mutant MBC. Trial Design: This phase II investigator-initiated clinical trial is enrolling 30 patients with somatic BRCA1/2 mutant MBC identified via cell-free DNA or tumor tissue genotyping. Patients are treated with talazoparib, a PARP inhibitor, until disease progression. At baseline and every 3 months, patients undergo CT chest, abdomen, and pelvis, and a bone scan for disease assessment. Patients undergo blood collection at baseline for the Cancer Risk B (CR-B) assay, a novel flow variant assay to assess double-strand break repair mutations in circulating blood cells (Syeda, 2017) and monthly blood collection for cell-free DNA analysis to evaluate changes in the genomic environment. Eligibility Criteria: Patients with MBC with a pathogenic somatic BRCA1/2 mutation identified by cell-free DNA or tumor tissue genotyping are eligible. Both patients with triple-negative breast cancer (≥ 1 prior chemotherapy) or hormone receptor positive/HER2- MBC (≥ 1 prior hormone therapy) are eligible. Patients should not be known germline BRCA1/2 carriers. There is no limit on prior therapies including receipt of a prior platinum (in the absence of disease progression on prior platinum). A prior PARP inhibitor is not allowed. Adequate performance status and organ function are needed. Specific Aims: Primary aim is progression-free survival (PFS) assessed by RECIST 1.1. Secondary aims include objective response rate and toxicity assessed by NCI CTCAE v 5.0. Exploratory aims include assessing impact of BRCA1/2 reversion mutations in cell-free DNA, studying serial changes in BRCA1/2 mutant allelic frequency in cell-free DNA, comparing pre- and post-treatment cell-free DNA results to identify changes in the genomic environment, assessing the CR-B assay positivity rate, and correlating these biomarker analyses with patient response. Statistical Methods: This study uses a two-stage design with 80% power to demonstrate that talazoparib is associated with “success” (PFS > 12 weeks) in 53% patients (4% alpha). Accrual: This study (NCT03990896) is open at Massachusetts General Hospital, MD Anderson, University of California San Francisco, and Emory, with pending activation at Northwestern, Cornell, and Vanderbilt. Five patients are enrolled as of 7/2022. Funding: This study is supported by a Pfizer ASPIRE award and Conquer Cancer Foundation of ASCO–Breast Cancer Research Foundation- Career Development Award. Contact information: Neelima Vidula, MD, Massachusetts General Hospital, nvidula@mgh.harvard.edu

Citation Format: Neelima Vidula, Senthil Damodaran, Erica L. Blouch, Nora Horick, Nathan Royce Ruffle-Deignan, Manali Bhave, Ami N. Shah, Leticia Varella, Vandana Abramson, Joseph Sparano, Leif Ellisen, Ishraq Alim, Harry Ostrer, Hope Rugo, Aditya Bardia. Phase II study of talazoparib, a PARP inhibitor, in somatic BRCA1/2 mutant metastatic breast cancer identified by cell-free DNA or tumor tissue genotyping [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT1-11-01.

Abstract ED3-3A: Mechanisms of resistance

Antibody Drug Conjugates (ADCs) are emerging as promising therapeutics for all subtypes of breast cancer. ADCs are composed of a monoclonal antibody directed against a tumor-expressed antibody, conjugated via a variety of linker chemistries to a cytotoxic or other tumor-active payload. Tumor-selective drug delivery via ADCs has the potential to substantially improve the therapeutic window and efficacy for a variety of therapeutic agents. Indeed, recent clinical data have demonstrated significant improvements in overall survival with the use of single-agent ADCs across the spectrum of advanced breast cancer. However, both de novo and acquired resistance to ADCs is common, and may involve a diverse array of potential mechanisms that reflect the complexity of ADC action. These include alteration or downregulation of the ADC target, deregulation of intracellular trafficking or endolysosomal processing of the internalized ADC, and a variety of payload-specific mechanisms of resistance such as induction of drug efflux or activation of cell survival pathways. Which mechanism(s) dominates in a given setting may depend on both ADC-specific and tumor-specific factors. For example, linker design is likely to have a major influence on potential ADC resistance: ADCs with a non-cleavable linker (e.g. trastuzumab emtansine) are dependent upon fusion with acidified lysosomes for degradation and payload release, and attenuated acidification has been demonstrated pre-clinically as a resistance mechanism. In contrast, ADCs with a cleavable peptide linker (e.g. trastuzumab deruxtecan) may not require lysosomal processing for payload release. Furthermore, highly genetically unstable tumors may simultaneously generate multiple types of resistance mechanisms. We recently demonstrated the emergence of distinct acquired resistance mutations to sacituzumab govitecan, involving the ADC antibody target (TROP2) and the payload target (topoisomerase 1), within different metastatic lesions of an individual patient. General strategies to overcome ADC resistance include the sequential use of multiple ADCs, and/or the up-front use of select combination therapies incorporating ADCs. Clearly, the success of these approaches will require a more thorough evaluation and understanding of resistance mechanisms as they occur in patients. Fortunately, the relative success of ADCs for breast cancer treatment to date is spurring the identification of new targets, approaches for linker design, and a wide diversity of payloads that will be instrumental for efforts to overcome resistance.

Citation Format: Leif Ellisen. Mechanisms of resistance [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr ED3-3A.

Abstract P1-13-07: Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis

Background: CDK4/6 inhibitors (CDK4/6i) are standard of care for the management of HR+/HER2- metastatic breast cancer (MBC). Genomic alterations that drive resistance to CDK4/6i are diverse, and while the molecular landscape is heterogeneous, several mechanisms of CDK4/6i resistance converge on the RAS/MAPK and PI3K/AKT/mTOR signaling pathways. NF1 downregulates RAS and dampens cellular proliferation. Laboratory-based models demonstrate that loss of NF1 is associated with resistance to endocrine therapy (ET), and emergence of NF1 mutations (NF1m) are correlated with progressive disease (PD) in circulating tumor DNA (ctDNA). While NF1m may diminish CDK4/6i susceptibility, a clear relationship has not been elucidated. The primary objective of this study was to characterize patient (pt) response to CDK4/6i in NF1m HR+/HER2- MBC. Methods: We identified 47 pts with NF1m via a database with one or more ctDNA samples sequenced at variable time-points as part of routine care for MBC. NF1m were categorized as pathogenic (p)NF1m or variants of uncertain significance (VUS) based on their associated Guardant report. We identified 27 pts with HR+/HER2- MBC and NF1m that received at least 1 line of CDK4/6i in the metastatic setting. Intrinsic resistance was defined as PD < 6 months on a CDK4/6i regimen, and acquired resistance was defined as PD >6 months. Pts with intrinsic resistance or acquired resistance and NF1m detected post-PD were categorized as having a resistance phenotype potentially driven by NF1m. Pts with NF1m detected prior to therapy and >6 months clinical response on a CDK4/6i were categorized as having NF1m tumors sensitive to CDK4/6i. Results: The NF1m cohort (n = 27) had 9 pts with pNF1m, while 18 pts expressed VUS. The median age at MBC diagnosis was 54 years, and 67% had visceral metastasis at ctDNA collection. Pts received a median of 1 prior line (range: 0 - 6) of ET or chemotherapy in the metastatic setting before CDK4/6i. Amongst pts with pathogenic variants (n = 9), we found 3 pts with pNF1m were intrinsically resistant to CDK4/6i. Acquired resistance was seen in 1 pt with pNF1m detected post-PD, and 2 pts had evidence of both acquired and subsequent intrinsic resistance to a later line of CDK4/6i. Overall, 67% (6/9) of pNF1m pts demonstrated a CDK4/6i resistance phenotype; mutant allele fraction (AF) ranged from 0.2% - 29.9%, and the mean maximum allele fraction (MAF) was 6.0%. Pre- and post-treatment samples were available on 3 pts with pNF1m, and 1 of these pts had an AF rise from 2.7% to 12.3% when comparing ctDNA pre- and post-CDK4/6i. ctDNA from 4 of 6 resistant tumors harbored other putative drivers including alterations in FGFR, KRAS, PTEN, and RB. We identified 2 counter-examples of pNF1m tumors sensitive to CDK4/6i. These pts expressed relatively low NF1m AF, ranging 0.1% - 0.5% with a mean MAF 0.3%. Another pNF1m pt had intrinsic resistance to initial CDK4/6i but was sensitive to later-line CDK4/6i. In the subgroup of pts with VUS-NF1m (n = 18), a more mixed picture of resistance and sensitivity was seen. 8 pts had intrinsic or acquired resistance, 8 pts had NF1m tumors sensitive to CDK4/6i, and 1 pt had evidence of both; 61% (n = 11) of pts expressed alterations in other resistance mediating genes. 1 pt stopped therapy due to toxicity rather than PD. Conclusions: Our work demonstrates that tumor expression of pNF1m may be associated with CDK4/6i resistance in pts with HR+/HER2- MBC, and allele fraction could be predictive of drug susceptibility. Tumors harboring VUS had varied sensitivity, suggesting that some of these mutations may not be pathogenic, and counter-examples of pNF1m MBC benefiting from CDK4/6i plus ET highlight the complexities in predicting drug response based on single gene alteration. Future effort is warranted to explore the potential impact of NF1 on CDK4/6i resistance, as well as the potential role for therapies targeting the MAPK pathway in this patient population.

Citation Format: Maxwell R. Lloyd, Lianne Ryan, Arielle J. Medford, Jennifer C. Keenan, Laura M. Spring, Neelima Vidula, Beverly Moy, Dejan Juric, Leif Ellisen, Aditya Bardia, Seth A. Wander. Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-13-07.

Abstract P5-02-07: Cell-free DNA detection of GATA3 mutations in metastatic hormone receptor positive breast cancer: a retrospective, observational multi-institutional analysis

Background GATA3 mutations (GATA3mut) have been reported in 10-20% of hormone receptor positive (HR+) breast cancers. It has been shown that targeting GATA3mut HR+ breast cancer with MDM2 inhibitors invokes synthetic lethality. MDM2 is an E3 ubiquitin ligase that targets p53 for degradation, and research suggests that restoring p53 by blocking MDM2 may be effective in treating GATA3mut HR+ breast cancer. One potential mechanism of this efficacy has been shown to be through the PI3K-AKT pathway. We thus sought to characterize the GATA3mut landscape in a multi-institutional cell-free DNA (cfDNA) analysis and to determine the association between GATA3mut and TP53 mutations, as well as alterations in the PI3K-AKT pathway and the impact of GATA3 on survival. Methods We analyzed cfDNA data collected at the Massachusetts General Hospital and at Washington University in St Louis via Guardant360, a next generation sequencing assay that analyzed up to 74 genes during the study period. The association of GATA3mut and co-mutations as well as number of prior therapies was estimated using Pearson’s chi-squared test for categorical variables, two-sample Wilcoxon rank-sum test for continues variables, and multivariable logistic regression. The impact of GATA3mut and GATA3 wildtype (WT) on progression-free survival (PFS) and overall survival (OS) was analyzed using multivariable Cox regression analysis, adjusting for age, number of prior therapies, visceral metastases, and de novo metastases. PFS and OS were evaluated in the overall study population, as well as in subgroups of patients that received endocrine monotherapy and chemotherapy. Results Out of 647 patients with HR+ MBC, 10% (n = 68) had non-synonymous GATA3 mutations. Among these 68 GATA3mut patients, 37% (n = 25) were mutations in exon 5, all but two of which were in the second zinc finger, and 62% (n = 42) were in exon 6. 62% (n = 42) were frameshift mutations, 20% (n = 14) were indels, and 18% (n = 12) were point mutations. Median mutant allele fraction (MAF) of GATAmut was 0.95% (range 0.03 – 30.5%). There was no statistically significant association of GATA3mut with the number of prior therapies, PR status, or the presence of ESR1, TP53, or PI3K-AKT pathway mutations. In the GATA3mut population, TP53 co-mutations (n = 21) were found with a median MAF of 0.6%. PI3K-AKT pathway alterations occurred in 47% (n=32) of GATA3mut patients (PIK3CA n = 27; AKT n = 2; PTEN n = 3). In the combined cohort, there was no significant difference in PFS or OS after adjusting for visceral metastases, de novo disease, number of prior therapies, and age. In a cohort of 80 patients that received endocrine monotherapy (GATA3 WT n = 74, GATA3mut n = 6), GATA3mut were associated with borderline worse PFS (HR 2.6; p = 0.061) and worse OS (HR 4.5; p = 0.009). There was no statistically significant difference in PFS or OS in a subgroup that received chemotherapy. Conclusions GATA3 mutations can be identified via cfDNA in patients with HR+ MBC. Co-mutations in TP53 occurred at overall low MAF. Further research is needed to characterize the functional impact of these low level TP53 co-mutations and develop therapeutic strategies to target GATA3 mutant MBC.

Citation Format: Arielle J. Medford, Marko Velimirovic, Andrzej Niemierko, Whitney L. Hensing, Andrew A. Davis, Katherine K. Clifton, Jennifer C. Keenan, Charles S. Dai, Lesli A. Kiedrowski, Ami N. Shah, Lorenzo Gerratana, Laura M. Spring, Leif Ellisen, Robert C. Doebele, Massimo Cristofanilli, Aditya Bardia. Cell-free DNA detection of GATA3 mutations in metastatic hormone receptor positive breast cancer: a retrospective, observational multi-institutional analysis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-07.

Abstract 2638: Sacituzumab Govitecan, combination with PARP inhibitor, Talazoparib, in metastatic triple-negative breast cancer (TNBC): Translational investigation

Background: Sacituzumab Govitecan (SG), the first antibody-drug conjugate approved for metastatic TNBC (mTNBC), is comprised of SN-38 (active metabolite of irinotecan), a topoisomerase I (TOP1) inhibitor, coupled via a hydrolyzable linker to monoclonal antibody targeting trophoblast cell surface antigen 2 (Trop-2), an antigen overexpressed in mTNBC. Poly (ADP-ribose) polymerase inhibitors (PARPi) block resolution of TOP1 cleavage complexes (TOP1CCs) induced by TOP1 inhibitors, thus unmasking the inability of remaining pathways to repair DNA damage. However, previous clinical trials combining PARPi with standard TOP1 inhibitors (irinotecan, topotecan) were terminated early due to dose-limiting myelosuppression. We evaluated the combination of SG with PARP inhibitor in both pre-clinical models and phase 1b clinical trial.

Methods and Results: In pre-clinical models we demonstrated that the targeted antibody-based delivery of SN-38 increased the ratio of tumor-to-normal cell SN-38, resulting in stabilized TOP1CCs, enhanced DNA damage and increased cytotoxicity with the combination, selectively in tumor cells but not normal cells, despite temporal separation of SG and PARPi exposure. To validate the hypothesis, we conducted a phase 1b investigator-initiated clinical trial combining SG with PARPi (talazoparib) in patients with mTNBC (NCT04039230). Inclusion criteria included female patients ≥ 18 years of age with mTNBC (per ASCO/CAP guidelines) and previous treatment with at least one prior therapeutic regimen for mTNBC. Clinical outcomes were assessed by Objective Response Rate per RECIST v1.1. In the phase 1b clinical trial (SG day 18, every 21 days with talazoparib), the staggered schedule with supportive therapy was relatively well-tolerated without DLTs, as predicted by the pre-clinical models. Furthermore, the staggered schedule demonstrated promising clinical activity. Molecular analysis of paired pre-treatment and on-treatment specimens demonstrated γ-H2AX accumulation, confirming pharmacodynamic inhibition with combination therapy. The dose-escalation portion of clinical trial successfully completed enrollment with a recommended phase-2 dose (R2PD) of sequential SG (10 mg/kg on days 1,8) with talazoparib (1 mg on days 15-21), every 21 days.

Conclusion: Staggered dosing of SG and PARPi, leveraging the selective drug delivery mechanism of SG to minimize toxicity while maintaining efficacy, was feasible and demonstrated encouraging evidence of clinical activity with objective responses among patients with mTNBC. The translational study highlights how mechanistic insights and innovative scheduling could be utilized to develop promising drug combinations, including previously rejected combinations, for patients with mTNBC.

Citation Format: Aditya Bardia, James T. Coates, Laura Spring, Sheng Sun, Dejan Juric, Nayana Thimmiah, Andrzej Niemierko, Phoebe Ryan, Ann Partridge, Jeffrey Peppercorn, Heather Parsons, Seth Wander, Kelsey Pierce, Victoria Attaya, Donna Fitzgerald, Brenda Lormil, Maria Shellock, Aiko Nagayama, Veerle Bossuyt, Bev Moy, Sara Tolaney, Leif Ellisen. Sacituzumab Govitecan, combination with PARP inhibitor, Talazoparib, in metastatic triple-negative breast cancer (TNBC): Translational investigation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2638.

Phase II multicenter study of talazoparib for somatic BRCA1/2 mutant metastatic breast cancer

TPS1110

Background: PARP inhibitors are approved for the treatment of HER2 negative metastatic breast cancer (MBC) with germline BRCA1/2 mutations, based on phase III studies demonstrating an improvement in progression-free survival (PFS) compared to chemotherapy in this population and better patient reported outcomes (Robson, NEJM, 2017; Litton, NEJM, 2018). However, germline BRCA1/2 mutations account for only 5-10% of breast cancer, limiting the current clinical applicability of PARP inhibitors. Somatic BRCA1/2 mutations are detectable in circulating cell-free DNA (cfDNA) in ̃13.5% of patients with MBC; in pre-clinical models, pathogenic somatic BRCA1/2 mutations have been shown to respond to PARP inhibition (Vidula, CCR, 2020). The purpose of this study is to evaluate the efficacy of talazoparib, a PARP inhibitor, in patients with MBC who have somatic BRCA1/2 mutations detectable in cfDNA, in the absence of a germline BRCA1/2 mutation, which we hypothesize will be effective in this setting. This study may help expand the population of patients with MBC who benefit from PARP inhibitors. Methods: This is an investigator initiated multicenter, single arm, phase II clinical trial studying the efficacy of talazoparib in 30 patients with MBC who have pathogenic somatic BRCA1/2 mutations detected in cfDNA. Patients with MBC who are found to have pathogenic somatic BRCA1/2 mutations detected in cfDNA in the absence of a germline BRCA1/2 mutation are eligible. Patients may have triple negative (with ≥ 1 prior chemotherapy), or hormone receptor positive/HER2 negative breast cancer (with ≥ 1 prior hormone therapy). Patients may have received any number of prior lines of chemotherapy, including a prior platinum (in the absence of progression). They must have adequate organ function and ECOG performance status ≤2, and should not have previously received a PARP inhibitor. Patients are treated with talazoparib 1 mg daily until disease progression or intolerability, with serial imaging using CT chest/abdomen/pelvis and bone scan performed at baseline and every 12 weeks, and cfDNA collection every 4 weeks. Primary endpoint is PFS by RECIST 1.1. Patients are being enrolled in a two-stage design with 80% power to demonstrate that the treatment is associated with “success” (PFS > 12 weeks) in ≥53% patients (4% alpha). Secondary endpoints include objective response rate and safety (NCI CTCAE v 5.0). Exploratory analyses include studying serial changes in cfDNA BRCA1/2 mutant allelic frequency and comparing pre-and post-treatment cfDNA for the emergence of BRCA1/2 reversion and resistance mutations. This study is activated and open at Massachusetts General Hospital, where 2 patients are completing screening. It is also opening soon at 6 other academic centers (NCT03990896). Grant support includes a Pfizer ASPIRE award and 2020 Conquer Cancer Foundation of ASCO – Breast Cancer Research Foundation – Career Development Award. Clinical trial information: NCT03990896 .

Abstract PD9-07: Genomic landscape of metastatic breast cancer (MBC): Comprehensive cell-free DNA analysis from over 10,000 patients and comparison with primary breast cancer

Background: Current tissue-based genomic sequencing datasets typically reflect early stage, mostly treatment-naïve cohorts, and fail to capture the genomic landscape of advanced disease, including mutations conferring acquired resistance to therapy. Plasma cell-free DNA (cfDNA) can provide information on somatic alterations non-invasively and can capture spatial tumor heterogeneity. Here, we studied cfDNA from 15,564 blood samples from 12, 827 patients (11.5% of patients had serial samples) with MBC, and analyzed the differences in mutational landscape between cohorts of heavily pre-treated and primary untreated breast cancers. Materials and methods: Deidentified aggregate genomic data from stage III/IV breast cancer clinical samples submitted for cfDNA next-generation sequencing (NGS) analysis with Guardant360 (Guardant Health, Inc; Redwood City, CA, USA) assay between 11/25/16 and 5/26/20. This clinical assay detects somatic single nucleotide variants (SNVs), indels, copy number gains, and fusions in either all or a subset of exons in up to 74 genes. We compare the observed alterations to events detected from whole-exome sequencing data representing ~1,000 untreated primary breast cancers from The Cancer Genome Atlas (TCGA) project. Results: In the overall cohort (N = 12, 827), the average patient age was 61 (range 18-100); 99% were female. Of the 11,290 pts with at least one samples with a non-synonymous alteration, the most frequently mutated genes were TP53 (53%), PIK3CA (38%), ESR1 (28%), ATM (13%), GATA3 (10%), and ARID1A (10%) at varying allelic frequencies with dynamic changes over time (in pts with serial specimens) highlighting clonal heterogeneity and temporal evolution. Copy-number gains were most frequent in FGFR1 (13%), CCND1 (11%), EGFR (9%) and PIK3CA (9%), but fusions were infrequent (below 1%), with fusions involving FGFR3 (n=22), FGFR2 (n=12), ALK (n=7), NTRK1 (n=6), RET (n=4), and ROS1 (n=1). Overall, patients had significantly higher frequency of actionable alterations based on ctDNA analysis, as compared to that observed in TCGA. Similarly, non-synonymous mutations were identified in genes associated with acquired resistance, including ESR1 (28%), ERBB2 (9%), PTEN (8.1%), RB1 (7.7%), NF1 (6.2%), and AKT1 (4%), mutated at frequencies significantly exceeding those observed in TCGA. Finally, we developed a novel classifier to identify the breast cancer receptor subtypes based on differential genomic profile, which was further validated in an independent genomic dataset. Conclusions: In the largest dataset to date, we provide the comparative genomic landscape of the various SNVs, indels, copy-number gains, and fusions identified by next generation sequencing of cfDNA in patients with MBC, compared to primary breast cancer. Interestingly, both targetable genomic alterations and resistance mutations occur at frequencies much higher than observed in primary breast cancer, highlighting the genomic complexity of MBC and potential need for combinatorial therapy. Finally, we describe a novel classifier for detection of HR+ and HER2+ tumors, which could be particularly valuable clinically given the receptor switch with tumor evolution and practical difficulty with serial tissue biopsies in MBC. Comparison of genomic signature profiles between MBC and primary breast cancer will be presented at the meeting.

Citation Format: Aditya Bardia, Massimo Cristofanilli, Justin Cha, Lesli Kiedrowski, Dejan Juric, Ben H Park, Adam Brufsky, Joyce O’Shaughnessy, Becky Nagy, Leif Ellisen, Ignaty Leshchiner, Gaddy Getz. Genomic landscape of metastatic breast cancer (MBC): Comprehensive cell-free DNA analysis from over 10,000 patients and comparison with primary breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-07.

Abstract B42: YAP1/Hippo pathway and SWI/SNF as critical players in squamous cancers and normal development

Cancer development is a multistep process involving deregulation of transcription/epigenetic factors and signaling pathways. Accordingly, gene expression lies at the nexus of oncogenic cellular processes. The recent advent of The Cancer Genome Atlas (TCGA) has shed light on multiple genes involved in signaling, transcription, and other cellular processes that are subjected to genomic alterations in multiple cancers. These oncogenic drivers are involved in regenerative proliferation, metastasis, and other cellular processes that contribute to tumorigenesis. Epithelial-stromal interactions and the infiltrating immune response contribute significantly to tumor progression. Our recent studies revealed Hippo pathway activation as a critical component in ACTL6A (subunit of SWI/SNF chromatin remodeling complex) amplified squamous cancers. Our published genetic studies indicate that YAP is a key mediator of the oncogenic function of ACTL6A/p63 in head and neck squamous cancers. P63 is a master transcription factor in epithelial development. We have shown that YAP and p63 biochemically interact to maintain airway architecture and regeneration. YAP and p63 deletion are phenocopies and are required to maintain normal respiratory epithelial stem cells. P63/ACTL6A act as upstream regulators of YAP in squamous cancers. ACTL6A and p63 physically interact and cooperatively control a transcriptional program that promotes proliferation and suppresses differentiation, through activation of the Hippo-YAP pathway via regulators including WWC1 and GPRC5A. Consequently, loss of ACTL6A or p63 in tumor cells induces YAP phosphorylation and inactivation, associated with growth arrest and terminal differentiation, all phenocopied by WWC1 overexpression. YAP activation predicts poor patient survival in squamous cancers. These findings are also in keeping with the emerging role of the YAP pathway as a tumor driver in multiple contexts. Given interest in YAP as a therapeutic target, our studies reveal contribution of p63 and TEAD to YAP function as evident from global transcription profiling. Our most recent studies also indicate contribution of YAP in tumor progression by evading host immune response. All these indicate an important intrinsic role of YAP in development and disease, making it one of the ideal therapeutic targets to control cancer.

Citation Format: Leif Ellisen, Purushothama Rao Tata, Rui Zhao, Jayaraj Rajagopal, Srinivas Vinod Saladi. YAP1/Hippo pathway and SWI/SNF as critical players in squamous cancers and normal development [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr B42.

Novel antibody-drug conjugates for triple negative breast cancer

Triple negative breast cancer (TNBC) is a heterogenous subtype of breast cancer often associated with an aggressive phenotype and poor prognosis. Antibody–drug conjugate (ADC), comprising of a monoclonal antibody linked to a cytotoxic payload by a linker, is gaining increasing traction as an anti-cancer therapeutic. Emerging ADC drugs such as sacituzumab govitecan (IMMU-132) and trastuzumab deruxtecan (DS-8201a) are in late stages of clinical development for patients with metastatic breast cancer, including TNBC. In this article, we review and discuss the development and clinical application of ADCs in patients with advanced TNBC.

Abstract OT2-03-03: Evaluation of talazoparib, a PARP inhibitor, in patients with somatic BRCA mutant metastatic breast cancer: Genotyping based clinical trial

Background: Metastatic breast cancer (MBC) accounts for most breast cancer deaths. In 2018, two Poly(ADP-ribose) polymerase (PARP) inhibitors, olaparib and talazoparib, were approved for the treatment of MBC patients with germline BRCA1 or 2 mutations based on the OlympiAD and EMBRACA trials (Robson, NEJM, 2017 and Litton, NEJM, 2018), which demonstrated improvement in progression-free survival (PFS) with PARP inhibitors compared to chemotherapy. These landmark findings have triggered much interest in studying PARP inhibitors in MBC, but germline BRCA mutations only account for 5-10% of breast cancer patients. A critical question is whether PARP inhibitors may also be beneficial in MBC with somatic BRCA1 or 2 mutations, similar to somatic BRCA mutant ovarian cancer where they are effective(George, Oncotarget, 2017). Liquid biopsies via circulating cell-free DNA (cfDNA) may unveil somatic mutations. We previously demonstrated (Vidula, SABCS, PD1-13, 2017) that a subset of MBC patients have detectable somatic cfDNA BRCA1 or 2 mutations, in the absence of germline BRCA mutations, highlighting the role of liquid biopsies for detection of somatic BRCA mutations in MBC. Based on our preliminary data, we hypothesize that we can utilize liquid biopsies to detect somatic BRCA1 or 2 mutations and guide therapy selection with a PARP inhibitor in patients with MBC.

Methods: In this single arm phase II clinical trial we will evaluate the efficacy and safety of a PARP inhibitor, talazoparib, in patients with somatic BRCA mutant MBC (N=30). Patients will undergo cfDNA screening to identify cfDNA somatic BRCA1 or 2 deleterious mutations. Patients without known BRCA germline mutations who have cfDNA BRCA1 or 2 mutations will be enrolled at the Massachusetts General Hospital and University of California San Francisco. The study will enroll both patients with hormone receptor positive/HER2 negative breast cancer and triple-negative breast cancer whose disease has progressed on at least 1 prior line of endocrine therapy and at least 1 prior line of chemotherapy for MBC, respectively. Patients may have received any number of prior lines of therapy.

Eligible patients will be treated with talazoparib 1 mg daily until progression (evaluated with serial CT chest/abdomen/pelvis and bone scan) or unacceptable toxicity. The primary endpoint is to determine PFS by RECIST 1.1. Patients will be enrolled in a two-stage design, providing 80% power to demonstrate that the treatment is associated with “success” (PFS > 12 weeks) in ≥53% patients (4% alpha). Secondary endpoints include objective response rate and safety/tolerability (NCI CTCAE v5.0). Serial cfDNA will be collected at baseline and during treatment to evaluate for changes in the BRCA cfDNA mutant allelic fraction in response to therapy. The impact of pre-existing resistance mutations in baseline cfDNA, particularly BRCA reversion mutations that can occur with prior platinum exposure (Weigelt, CCR, 2017), on outcomes will be studied. Paired liquid biopsies (pre- and post-treatment) will be compared to generate hypotheses about potential novel targets for future combination studies with talazoparib to improve response(exploratory objective). This study may help expand the applicability of talazoparib in MBC. This study was activated in July 2019. Funding support for the clinical trial is provided by a Pfizer ASPIRE award. (NCT03990896).

Citation Format: Neelima Vidula, Nora Horick, Erin Basile, Sara Sutherland, Ruth Fax, Daniel Haber, Leif Ellisen, Hope S. Rugo, Aditya Bardia. Evaluation of talazoparib, a PARP inhibitor, in patients with somatic BRCA mutant metastatic breast cancer: Genotyping based clinical trial [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 OT2-03-03.

Abstract P4-09-06: Brain metastases (BM) in patients with metastatic breast cancer (MBC) and circulating cell-free DNA (cfDNA) somatic BRCA mutations

Background: BM in MBC patients cause significant morbidity and mortality. BRCA1 germline mutations have previously been shown to be associated with an increased risk of developing BM (Lee et al, 2011), with an incidence as high as 15% (Zavitsanos et al, 2016). We previously reported that a subset of MBC patients may have somatic BRCA mutations in the absence of germline BRCA mutations (Vidula N, SABCS, 2017). In this study, we evaluated the incidence and clinical characteristics of BM in MBC patients with somatic BRCA mutations detected by cfDNA.

Methods: MBC patients with somatic BRCA1 or 2 mutations detected by cfDNA (Guardant360TM, next generation sequencing, 73 gene panel; mutations classified as somatic by Guardant360TM) with at least 4 months of follow-up post-testing at an academic institution were identified. From this cohort, we identified patients who developed BM post cfDNA testing. A retrospective review of medical records and Guardant360TM reports was conducted to identify demographics, tumor subtype, type of cfDNA BRCA mutation, whether the BRCA mutation was known to be pathogenic, germline BRCA mutation status, mutant allele fraction (MAF), clonality (MAF ratio of BRCA mutation/gene mutation with highest MAF ≥ 0.25 for clonal, and <0.25 for subclonal) and the coexisting genomic environment. Clinical and genomic features of BM and non-BM patients (patients without BM) were compared using a chi-squared test for categorical variables and Wilcoxon rank-sum test for continuous variables. Brain tumor tissue from available cases of BM patients was used to evaluate somatic BRCA mutation status on the tumor tissue and correlated with cfDNA results.

Results: Of 36 MBC patients with somatic BRCA mutations, 9 (25%) developed BM and 27 (75%) did not have BM (non-BM). The median time to development of BM was 6.7 months after cfDNA testing. Of the BM patients, 5 (56%) had triple-negative (TN) and 4 (44%) had hormone receptor positive (HR+)/HER2- MBC in comparison with the non-BM cases where 5 (19%) had TN, 19 (70%) had HR+/HER2-, and 3 (11%) had HER2+ MBC. Very few patients (1 BM and 2 non-BM) had known co-existing separate germline BRCA mutations (rest not known BRCA carriers confirmed by negative germline testing and/or absence of family history suggestive of a germline BRCA phenotype). The median age at MBC diagnosis was similar for BM and non-BM patients (57 years). PIK3CA and TP53 mutations were commonly seen in both BM and non-BM cases. Additionally, MYC, EGFR, and CCNE1 mutations were commonly seen in BM cases. As outlined in Table 1, among patients with BM, the somatic BRCA mutations were commonly BRCA1, clonal, known to be pathogenic (56%), and present at a higher MAF, but these findings did not reach statistical significance possibly due to the small sample size. Brain tumor tissue mutation status in BM patients and correlation with cfDNA results will be presented at the meeting.

Conclusions: We observed a relatively high incidence (25%) of BM in MBC patients with somatic BRCA mutations detectable by cfDNA, which were often known to be pathogenic mutations (56%), and often associated with co-existing MYC, EGFR, and CCNE1 mutations. Further research using a larger cohort with adequate statistical power is needed to validate these findings, and may help identify MBC patients at risk for BM using a liquid biopsy.

Table 1.Characteristic BMNon-BMPrior anthracycline and/or platinum6 (67%)16 (59%)Type of somatic BRCA mutationBRCA16 (67%)11 (41%)BRCA22 (22%)15 (56%)BRCA1 and 21 (11%)1 (4%)Median BRCA MAF0.40.17ClonalityClonal6 (67%)13 (48%)Subclonal3 (33%)14 (52%)Mutation known to be pathogenic5 (56%)7 (26%)Common co-existing mutationsPIK3CA5 (56%)12 (44%)TP535 (56%)15 (56%)MYC5 (56%)8 (30%)EGFR5 (56%)8 (30%)CCNE15 (56%)6 (22%)KIT3 (33%)5 (19%)

Citation Format: Neelima Vidula, Andrzej Niemierko, Giuliana Malvarosa, Priscilla Brastianos, Erica Blouch, Kristen Shannon, Steven Isakoff, Seth Wander, Laura Spring, Jerry Younger, Kristin Price, Beverly Moy, Dejan Juric, Leif Ellisen, Aditya Bardia. Brain metastases (BM) in patients with metastatic breast cancer (MBC) and circulating cell-free DNA (cfDNA) somatic BRCA mutations [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 P4-09-06.

Blood-based monitoring identifies acquired and targetable driver HER2 mutations in endocrine-resistant metastatic breast cancer

Plasma genotyping identifies potentially actionable mutations at variable mutant allele frequencies, often admixed with multiple subclonal variants, highlighting the need for their clinical and functional validation. We prospectively monitored plasma genotypes in 143 women with endocrine-resistant metastatic breast cancer (MBC), identifying multiple novel mutations including HER2 mutations (8.4%), albeit at different frequencies highlighting clinical heterogeneity. To evaluate functional significance, we established ex vivo culture from circulating tumor cells (CTCs) from a patient with HER2-mutant MBC, which revealed resistance to multiple targeted therapies including endocrine and CDK 4/6 inhibitors, but high sensitivity to neratinib (IC50: 0.018 μM). Immunoblotting analysis of the HER2-mutant CTC culture line revealed high levels of HER2 expression at baseline were suppressed by neratinib, which also abrogated downstream signaling, highlighting oncogenic dependency with HER2 mutation. Furthermore, treatment of an index patient with HER2-mutant MBC with the irreversible HER2 inhibitor neratinib resulted in significant clinical response, with complete molecular resolution of two distinct clonal HER2 mutations, with persistence of other passenger subclones, confirming HER2 alteration as a driver mutation. Thus, driver HER2 mutant alleles that emerge during blood-based monitoring of endocrine-resistant MBC confer novel therapeutic vulnerability, and ex vivo expansion of viable CTCs from the blood circulation may broadly complement plasma-based mutational analysis in MBC.

Abstract LB-103: Defining oncogenic SWI/SNF complex mediated immune reprogramming in squamous cell carcinoma

Squamous cell carcinoma (SCC) remains among the most treatment-refractory of human cancers, reflecting in part a limited understanding of the key pathways and mechanisms that drive this disease. The p53-related transcription factor p63 is a central tumor maintenance factor subject to overexpression and/or genomic amplification in a high fraction of SCCs. Loss-of-function mutations in SWI/SNF chromatin remodeling subunit genes are observed in many cancers, but an oncogenic role for SWI/SNF is not well established. We reveal that ACTL6A, encoding a SWI/SNF subunit linked to stem and progenitor cell function, is frequently co-amplified and highly expressed together with p63 in head and neck, and lung squamous cell carcinoma (HNSCC & LUSC). ACTL6A and p63 physically interact and cooperatively control a transcriptional program that promotes proliferation and suppresses differentiation, in part through activation of the Hippo-YAP pathway via regulators including WWC1. Consequently, loss of ACTL6A or p63 in tumor cells induces YAP phosphorylation and inactivation, associated with growth arrest and terminal differentiation, all phenocopied by WWC1 overexpression. In vivo, ectopic ACTLC6A/p63 expression promotes tumorigenesis, while ACTL6A expression and YAP activation are highly correlated in primary HNSCC and predict poor patient survival. More recently, we show the major cell-autonomous pathway repressed by ACTL6A is the interferon response in vitro, while we find ACTL6A amplification in HNSCC is associated with immunologically “cold” tumors despite a high mutation burden in vivo. Collectively, these findings reveal that ACTL6A orchestrates a tumor cell-intrinsic mechanism of immune evasion and define ACTL6A as a potent driver of human SCC.These findings establish a fundamental mechanism for ACTL6A and p63 to alter epigenetic states, and uncover a critical oncogenic function for SWI/SNF, which has been largely viewed as a tumor suppressor in human cancer. Furthermore, by revealing the Hippo-YAP pathway as a major target of ACTL6A/p63 linked to tumor behavior, this work suggests potential therapeutic approaches for refractory HNSCC cases.

Citation Format: SrinivasVinod Saladi, Robert Morris, Kenneth Ross, mihriban Karaayvaz, Purushothama Rao Tata, hongmei mou, Jayaraj Rajagopal, Michael Lawrence, Leif Ellisen. Defining oncogenic SWI/SNF complex mediated immune reprogramming in squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-103.

Abstract P4-01-06: Comparison of tumor genotyping and cell-free circulating tumor DNA sequencing in metastatic breast cancer patients and their utility in the selection of matched therapy

Background: Oncogenic mutations are potential targets for therapeutic intervention in metastatic breast cancer (MBC). While tumor genotyping (TG) has been viewed as the gold standard for identifying oncogenic mutations, cell-free circulating tumor DNA (cfDNA) is emerging as an alternate technique. We previously reported the selection of matched therapy targeted to an actionable mutation based on either TG or cfDNA testing (Vidula N, ASCO, 2018). Therefore, we are now comparing TG and cfDNA results in MBC patients undergoing both tests to examine their relative utility in the selection of matched therapy.

Methods: Patients with MBC at an academic institution who underwent both TG (Next Generation Sequencing/NGS, institutional platform, 104 gene assay) and cfDNA testing (NGS/Guardant360, 73 gene assay) between 1/2016-10/2017 were identified. A chart review was conducted to identify tumor subtype, demographics, treatment, TG and cfDNA results, and clinical outcomes. The relative utility of these tests in the selection of matched therapy was determined, and linked with clinical outcomes (progression-free survival and overall survival).

Results: Thirty patients who underwent both TG and cfDNA testing were identified. The median age was 60 years, the majority (97%) had hormone receptor (HR) positive/HER2 negative disease, and most patients had recurrent disease (83.3%) at MBC diagnosis. The median number of therapies prior to obtaining either test was 1 (cfDNA range 0-9, TG range 0-8). The majority had simultaneous cfDNA and tumor genotyping testing (83.3%) versus sequential testing (16.7%). Twenty-four (80%) patients had actionable mutations detected by cfDNA compared to 19 (63.3%) patients with actionable mutations detected by TG. The median number of actionable mutations detected by cfDNA was 2 (range 0-11) compared with a median of 1 (range 0-4) detected by TG. Failure of TG occurred in 2 of 30 patients (6.7%) but no test failures were seen with cfDNA. Eleven of 30 patients (36.7%) had ≥ 1 concordant mutation via cfDNA and TG. Altogether, 12 out of 30 (40%) patients received matched therapy, 5 of which were based on cfDNA actionable mutations alone (ESR1, ERBB2, CCND1, and PIK3CA), and 7 based on cfDNA and TG results (ESR1, PIK3CA, STK11, and BRCA). Twelve of 24 (50%) patients with actionable cfDNA mutations went on to receive matched therapy compared with 7 of 19 (36.8%) patients with actionable TG results. Matched therapies included SERDs, inhibitors of CDK 4/6, PI3K, mTOR, HER2 directed therapy, and DNA damaging chemotherapy. The impact of matched therapy on survival outcomes will be presented at the meeting.

Conclusions: In patients undergoing both TG and cfDNA testing, both tests identify a significant cohort of HR+ MBC patients with actionable mutations, with greater detection of actionable mutations by cfDNA. Greater application of matched therapy occurred via cfDNA, which independently informed the selection of matched therapies. Further research is needed to prospectively evaluate the clinical utility of blood based genotyping assays versus TG for patients with MBC.

Citation Format: Vidula N, Juric D, Niemierko A, Spring L, Moy B, Malvarosa G, Yuen M, Habin K, Shin J, Peppercorn J, Isakoff S, Ellisen L, Iafrate AJ, Bardia A. Comparison of tumor genotyping and cell-free circulating tumor DNA sequencing in metastatic breast cancer patients and their utility in the selection of matched therapy [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 P4-01-06.

Complete Remission Following Pembrolizumab in a Woman with Mismatch Repair-Deficient Endometrial Cancer and a Germline BRCA1 Mutation

Endometrial cancer is the most common gynecologic malignancy in the U.S. and, although the majority of cases present at an early stage and can be treated with curative intent, those who present with advanced disease, or develop metastatic or recurrent disease, have a poorer prognosis. A subset of endometrial cancers exhibit mismatch repair (MMR) deficiency. It is now recognized that MMR-deficient cancers are particularly susceptible to programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) inhibitors, and in a landmark judgement in 2017, the U.S. Food and Drug Administration granted accelerated approval to pembrolizumab for these tumors, the first tumor-agnostic approval of a drug. However, less is known about the sensitivity to PD-1 blockade among patients with known mutations in double-strand break DNA repair pathways involving homologous recombination, such as those in BRCA1 or BRCA2. Here we report a case of a patient with an aggressive somatic MMR-deficient endometrial cancer and a germline BRCA1 who experienced a rapid complete remission to pembrolizumab.

KEY POINTS

Endometrial cancers, and in particular endometrioid carcinomas, should undergo immunohistochemical testing for mismatch repair proteins.Uterine cancers with documented mismatch repair deficiency are candidates for treatment with programmed cell death protein 1 inhibition.Genomic testing of recurrent, advanced, or metastatic tumors may be useful to determine whether patients are candidates for precision therapies.

Abstract P2-02-18: Higher mutation burden and mutant allele fraction of circulating tumor DNA corresponds to worse progression free survival in metastatic breast cancer patients

Introduction: Genomic profiling of circulating tumor DNA (ctDNA) allows non-invasive monitoring of tumor genetic changes and molecular heterogeneity. In addition to actionable mutations, mutational landscape derived from ctDNA could provide a better representation of overall tumor burden and tumor heterogeneity, as well as potentially impact clinical outcomes. To evaluate this hypothesis, this study assessed the association of mutation burden and average mutant allele fraction (MAF) with tumor subtype, therapeutic response, and survival in patients with metastatic breast cancer.

Methods: Whole blood samples from patients with metastatic breast cancer were collected during clinic visits before start of a new therapy. Plasma-derived cell-free DNA underwent complete next-generation sequencing of 73 cancer-related genes with the Guardant360 test. Mutation burden was defined as the number of genes with mutations, and average MAF was calculated as the sum of the highest MAF for each mutated gene divided by the number of genes with mutations. Time to progression was measured from the date of new treatment initiation after circulating tumor DNA collection to the date of progression. Multivariate cox proportional hazard models assessed the association of mutation burden and average MAF with progression free survival (PFS), adjusted for age, receptor subtype (hormone receptor positive, HR+; human epidermal growth factor 2 positive, HER2+; triple negative breast cancer, TNBC), treatment subtype (chemotherapy vs. targeted therapy), and number of prior metastatic breast cancer therapies. A p value of 0.05 was considered statistically significant.

Results: The study population consisted of 158 women with metastatic breast cancer (108 HR+, 14 HER2+, 19 TNBC) with a median age of 59 years and a median of 2 prior metastatic breast cancer therapies. Median follow up time was 4.0 months, and median PFS was 15.7 months. Mutation burden was greater in triple negative compared to hormone receptor positive breast cancer (7.5 vs. 4.8, p = 0.02) but no different in patients with > 2 prior metastatic therapies vs. not (5.1 vs. 4.7, p = 0.60) and age >45 vs. not (5.0 vs. 3.9; p = 0.26). In univariate models, high mutation burden (> median of 2) and high MAF (> median of 1.4) were significantly associated with worse PFS (Table). These results were similar in effect size and significance when adjusted for age, receptor subtype, treatment subtype, and number of prior metastatic breast cancer therapies. Impact of mutation burden on response to specific therapies will be presented at the meeting.

VariableHazard Ratio95% Confidence Intervalp valueHigh mutation burden1.991.12-3.540.02High mutant allele fraction1.881.06-3.330.03

Conclusions: Higher ctDNA mutation burden and average MAF is associated with worse progression free survival and possibly reflects a more treatment refractory phenotype. Whether immunotherapy, alone or in combination, could influence the clinical outcomes in metastatic breast cancer patients with high ctDNA mutation burden is unclear and warrants additional research.

Citation Format: Keenan T, Juric D, Niemierko A, Spring L, Park H, Malvarosa G, Beeler M, Moy B, Ellisen L, Isakoff S, Bardia A. Higher mutation burden and mutant allele fraction of circulating tumor DNA corresponds to worse progression free survival in metastatic breast cancer patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-18.

Abstract P5-20-02: HER2 mutations detected by ctDNA in ER+/HER2- metastatic breast cancer patients: Incidence and impact on clinical outcomes

Background: While the human epidermal growth factor receptor 2 (HER2) gene has long been linked with the pathogenesis and prognosis of breast cancer, its significance has been recognized only when the receptor has been amplified. However, rare, but actionable, somatic mutations in HER2, without HER2 gene amplification, have been described in breast cancer based on molecular analysis of metastatic specimens (frequency ˜ 1%). Little is known about the incidence based on blood-based genotyping assays, as well as impact of HER2 mutations on clinical outcomes in patients with ER+/HER2- metastatic breast cancer (MBC).

Methods: We evaluated the presence of HER2 mutations based on routine tissue and blood-based genotyping assays, ordered by treating oncologists at our institution, for patients with estrogen receptor positive (ER+)/HER2 negative MBC. The tissue analysis was based on SNAPSHOT-NGS, an anchored multiplex polymerase chain reaction assay that detects single nucleotide variants (SNV) and insertions/deletions (indel), and the blood-based genotyping analysis was based on circulating tumor DNA (ctDNA) detection using the Guardant 360 panel, a next-generation sequencing (NGS) assay capable of detecting mutations with comparable sensitivity to SNAPSHOT. Patients with acquired HER2 mutations were identified, and multivariate analysis was performed to evaluate the hazard ratio (HR) for the association between HER2 mutations and progression free survival (PFS), adjusting for age and number of prior therapies.

Results: Among the ER+/HER2- MBC patients (N=118), 11% (N= 13) were found to have acquired HER2 mutation by ctDNA analysis, but no HER2 mutations were identified in any of patients based on tissue-based molecular analysis of archival specimens. Among patients with HER2 mutant, ER+/HER2- MBC, the median age at metastatic diagnosis was 57.34 (range 51.5-67.1) years, 7.7% had de-novo metastatic disease, and 30.8% had prior CDK 4/6 inhibitor therapy. In terms of outcomes, in the multivariate model, patients with HER2 mutant breast cancer had similar PFS when treated with endocrine and targeted therapy combination (HR = 0.24; p = 0.21), and trended towards worse PFS with chemotherapy (HR = 2.69; p = 0.06), as compared to non-HER2 mutant group, albeit duration of follow up was limited (median duration = 6.7 months). Of note, most of the detected HER2 mutations were activating or deleterious, but not all were clonal. Updated outcome data, including overall survival, will be presented at the meeting.

Conclusions: A much larger subset of patients with ER+/HER2- MBC have HER2 mutations detectable by ctDNA, but not by tissue, which highlights the need for blood-based biomarker monitoring for identification of actionable mutations, as well as the potential clinical utility in development of genotype driven trials for patients with HER2 mutant, ER+/HER2- MBC.

Citation Format: Medford A, Juric D, Niemierko A, Malvarosa G, Park H, Shellock M, Spring L, Moy B, Isakoff S, Ellisen L, Bardia A. HER2 mutations detected by ctDNA in ER+/HER2- metastatic breast cancer patients: Incidence and impact on clinical outcomes [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-20-02.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Abstract P4-12-07: Technical evaluation of multigene testing for hereditary breast and ovarian cancer

Introduction: Next Generation Sequencing, or NGS technology is gaining acceptance in diagnostic laboratories for multigene panel testing. However questions remain about the sensitivity, specificity and clinical implications of this new technology and the expanded testing it enables. Moreover, questions are raised as to whether new laboratories using these methods, typically without the benefit of large historical proprietary databases, can provide similar assessments of pathogenicity as do the previously established providers. Expanding on our recently published work (Kurian et al., JCO 2014) we considered whether NGS testing in an independent laboratory can replace traditional BRCA1/2 tests in patients indicated for hereditary breast/ovarian cancer testing.

Methods: We recruited over 800 patients who were indicated for BRCA1/BRCA2 testing under clinical management guidelines, and collected over 200 additional samples to increase the power of this ongoing study. All were tested using an NGS-based multigene panel which reported both DNA sequence and copy-number alterations for BRCA1/2 and 27 other known cancer risk genes. Traditional genetic testing results using established technologies were also available for comparison. In this report we focus on the results for BRCA1/2 and 27 other known cancer risk genes.

Results: Sensitivity was high: 261 alterations (196 pathogenic and 65 others) were reported in the traditional genetic data, and all were detected by NGS when the corresponding test was available. In this set are 141 alterations considered technically challenging for NGS: insertions, deletions, and complex sequence changes, as well as very large (chromosome) and small (single exon) copy number changes. Specificity was also high: all NGS variants for which we sought confirmation using independent methods (n>2000) were confirmed, including 51 alterations not previously reported. Determination of pathogenicity was also highly concordant: in all but 2 cases positive reports agreed, and in these 2 cases data were available in the literature to support pathogenicity, although not at a level which meets recent guidelines from the American College of Medical Genetics (ACMG). It is not clear from the diagnostic reports exactly what evidence supported pathogenicity in the traditional data for these 2 cases. Rates of Variants of Unknown Significance (VUS) in BRCA1/2 were somewhat different: about 7% of cases in the NGS data vs. about 4% of fully tested cases in the traditional data had an uncertain report. The root of this difference is also unclear as details are not provided in the traditional reports.

Conclusions: NGS can be a viable replacement for traditional genetic testing for hereditary breast and ovarian cancer. Interpretation concordance is high but fully evaluating the details of this is hampered by the limited reporting of proprietary data by some established laboratories. Recent efforts to establish large public databases of genetic information (particularly ClinVar) will promote greater transparency and accountability and thus can help improve access to high quality care for hereditary conditions.

Note: All of the variants in this study and their interpretations will be released to public databases by the time of the meeting.

Citation Format: Stephen Lincoln, Allison Kurian, Andrea Desmond, Geoffrey Nilsen, Kevin Jacobs, Shan Yang, Reece Hart, Federico Monzon, Leif Ellisen, James Ford. Technical evaluation of multigene testing for hereditary breast and ovarian cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-12-07.

Abstract P4-12-04: Clinical evaluation of multigene testing for hereditary breast and ovarian cancer

Background: Advances in DNA sequencing technology have fueled the development of multigene panels for hereditary cancer testing. While such assays are potentially both practical and affordable for routine clinical genetic testing, there remains uncertainty regarding their proper application and interpretation. Among the unanswered questions are which patients are appropriate candidates for such expanded testing; what is the likelihood that finding deleterious variants will alter risk assessment and management, and what is the prevalence of variants of unknown significance (VUS) that may create uncertainty for providers and anxiety for patients.

Methods: 821 patients who met NCCN guidelines for BRCA1/2 testing for hereditary breast/ovarian cancer (HBOC) were prospectively recruited at two major academic medical centers. These patients received traditional BRCA1/2 tests as part of their clinical care and also were later tested for a panel of 29 known cancer risk genes. This panel also re-tested BRCA1/2. Both sequence changes and deletions/duplications were reported, and the panel-testing laboratory was blind to the earlier results. Panel testing results were validated by comparison with the earlier data or by independent testing using established technologies. Family history information was collected directly by genetic counselors.

Results: 13.8% of the patients carried BRCA1 or BRCA2 mutations, with >99% concordance between the traditional and panel results for these two genes. 53 (7.6%) of the BRCA1/2-negative patients carried mutations in other cancer risk genes. Some of these findings confer a high risk for breast/ovarian cancer (e.g. TP53), while others (i.e. CHEK2, BRIP1, PALB2, RAD51C, CDKN2A, ATM, and NBN) confer a moderate increase in risk. 10 of these 55 patients were positive for genes involved in Lynch syndrome (MLH1, MSH2, MSH6, and PMS2), although breast and ovarian cancer are not uniformly accepted as part of this syndrome. 40% of these patients were heterozygous carriers of pathogenic variants in MUTYH, which have a less clear impact on breast/ovarian cancer, although this rate (3%) is higher than the expected carrier frequency in this population.

About 60% of patients had one or more VUS in the 29 genes. The rate of VUS was highly gene dependent, with ATM, APC, and PTCH1 providing the largest number. A small but significant subset of patients did not have personal or family histories consistent with the classical presentation of their identified mutation. Nevertheless, a majority of the non-BRCA1/2 findings would have prompted consideration of a management change for the tested patient even considering the personal and family cancer history.

Conclusions: Multigene panel testing for hereditary cancer risk assessment increased the yield of findings with potential clinical impact for almost 8% of patients. This is consistent with prior data from our laboratory and others. This study, carried out in a uniform clinical practice setting and with data collected directly by health care providers, provides a representative view of the benefit from such testing in an unselected patient population.

Citation Format: Leif Ellisen, Allison Kurian, Stephen Lincoln, Andrea Desmond, Meredith Mills, Kristen Shannon, Michelle Gabree, Michael Anderson, Yuya Kobayashi, Federico Monzon, James Ford. Clinical evaluation of multigene testing for hereditary breast and ovarian cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-12-04.

Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel

BACKGROUND

Next-generation sequencing (NGS) allows for simultaneous sequencing of multiple cancer susceptibility genes and, for an individual, may be more efficient and less expensive than sequential testing. The authors assessed the frequency of deleterious germline mutations among individuals with breast cancer who were referred for BRCA1 and BRCA2 (BRCA1/2) gene testing using a panel of 25 genes associated with inherited cancer predisposition.

METHODS

This was a cross-sectional study using NGS in 2158 individuals, including 1781 who were referred for commercial BRCA1/2 gene testing (cohort 1) and 377 who had detailed personal and family history and had previously tested negative for BRCA1/2 mutations (cohort 2).

RESULTS

Mutations were identified in 16 genes, most frequently in BRCA1, BRCA2, CHEK2, ATM, and PALB2. Among the participants in cohort 1, 9.3% carried a BRCA1/2 mutation, 3.9% carried a mutation in another breast/ovarian cancer susceptibility gene, and 0.3% carried an incidental mutation in another cancer susceptibility gene unrelated to breast or ovarian cancer. In cohort 2, the frequency of mutations in breast/ovarian-associated genes other than BRCA1/2 was 2.9%, and an additional 0.8% had an incidental mutation. In cohort 1, Lynch syndrome-related mutations were identified in 7 individuals. In contrast to BRCA1/2 mutations, neither age at breast cancer diagnosis nor family history of ovarian or young breast cancer predicted for other mutations. The frequency of mutations in genes other than BRCA1/2 was lower in Ashkenazi Jews compared with non-Ashkenazi individuals (P=.026).

CONCLUSIONS

Using an NGS 25-gene panel, the frequency of mutations in genes other than BRCA1/2 was 4.3%, and most mutations (3.9%) were identified in genes associated with breast/ovarian cancer.

Abstract C102: Identify novel pathways conferring PARP inhibitor resistance in BRCA-associated breast and ovarian cancer

Inhibitors of poly(ADP-ribose) polymerase (PARP) enzymes hold great promise in treating BRCA1/2 associated breast and ovarian cancers, which have profound homologous recombination (HR) defect. However, not all BRCA1/2 patients respond to PARP inhibitor treatment, and the majority of the responders eventually relapsed. Little is known about the resistance mechanisms that are clinical relevant.

We recently developed a highly versatile insertional mutagenesis system, using transposons to insert a CMV promoter randomly into the genome and thereby activate nearby genes. We constructed genome-wide insertional libraries using both human and mouse BRCA1-deficient cancer cell lines. When these mutated cells were treated with the PARP inhibitor, resistant colonies formed at extremely low frequency. Resistant colonies were re-grown and maintained in drug-free medium for extended period of time and robust resistance was retained. Insertion sites for these colonies were then determined, many of which are near genes whose alteration in expression can up-regulate activities of MEK/ERK pathway or PI3K/AKT pathway. Next we hope to investigate the resistance mechanism. We hypothesize that resistance is mediated via decreased DNA damage, improved DNA repair, or increase in general survival pathway after PARP inhibitor treatment. We have access to tumor specimens from a recently-completed clinical trial using ABT-888 in combination with temozolomide in a BRCA1/2 carrier-enriched population. The expression level and mutational status of these genes will be surveyed and correlated with clinical response. Finally based on the insight gained from aforementioned mechanism study, we hope to find inhibitors that specifically target the resistance mechanism; by combining this inhibitor with PARP inhibitor, we could develop effective therapy to treat the subset of patients resistant to PARP inhibitor.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C102.

Citation Format: Lei He, Li Chen, Saranya Ramakrishnan, Kristine Torres-Lockhart, Leif Ellisen. Identify novel pathways conferring PARP inhibitor resistance in BRCA-associated breast and ovarian cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C102.

Abstract LB-212: Mcl-1 and FBW7 control a dominant survival pathway underlying HDAC and Bcl-2 inhibitor synergy in squamous cell carcinoma

Effective targeted therapeutics for squamous cell carcinoma (SCC) are lacking. Here we uncover Mcl-1 as a dominant and tissue-specific survival factor in SCC, providing a roadmap for a new therapeutic approach. Treatment with the HDAC inhibitor vorinostat regulates Bcl-2 family member expression to disable the Mcl-1 axis and thereby induce apoptosis in SCC cells. Although Mcl-1 dominance renders SCC cells resistant to the BH3 mimetic ABT-737, vorinostat primes them for sensitivity to ABT-737 by shuttling Bim from Mcl-1 to Bcl-2/Bcl-xl, resulting in dramatic synergy for this combination and sustained tumor regression in vivo. Moreover, somatic FBW7 mutation in SCC is associated with stabilized Mcl-1 and high Bim levels, resulting in a poor response to standard chemotherapy but a robust response to HDAC inhibitors and enhanced synergy with combination vorinostat/ABT-737. Collectively, our findings provide a biochemical rationale and predictive markers for the application of this therapeutic combination in SCC.

Citation Format: Lei He, Kristine Torres-Lockhart, Nicole Forster, Saranya Ramakrishnan, Patricia Greninger, Mathew J. Garnett, Ultan McDermott, S. Michael Rothenberg, Cyril Benes, Leif Ellisen. Mcl-1 and FBW7 control a dominant survival pathway underlying HDAC and Bcl-2 inhibitor synergy in squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-212. doi:10.1158/1538-7445.AM2013-LB-212