Adrienne G. Waks

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-exome sequencing is concordant with metastatic tumour whole-exome sequencing.

Timeliness in Breast Cancer Treatment—The Sooner, the Better

Defining the impact of delays in breast cancer care is a difficult task. Although the question—“when should I undergo treatment?”—is simple, necessary, and asked by patients every day, our understanding of its therapeutic implications is incomplete. Prospective trials comparing longer vs shorter pretreatment intervals would not be ethically acceptable to patients or clinicians, and will not be performed. Therefore, we rely on retrospective and observational data. Numerous factors confound analysis of the correlation between treatment delay and survival outcomes, and many of these (including level of comorbidity, treatment compliance, social support, and access to health care) are impossible to capture fully even with highly granular data sets and sophisticated statistical models. However, despite the inherent pitfalls of retrospective analyses, the articles by Bleicher et al 1 and ChavezMacGregor et al 2 in this issue of JAMA Oncology are an important step toward defining the risks of delay.

Abstract S1-01: Whole exome and transcriptome sequencing of resistant ER+ metastatic breast cancer

Background: While great strides have been made in the treatment of estrogen receptor-positive (ER+) metastatic breast cancer (MBC), therapeutic resistance invariably occurs. A better understanding of the underlying resistance mechanisms is critical to enable durable control of this disease. Methods: We performed whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) on metastatic tumor biopsies from 88 patients with ER+ MBC who had developed resistance to one or more ER-directed therapies. For 27 of these patients, we sequenced the treatment-naive primary tumors for comparison to the resistant specimens. Tumors were analyzed for point mutations, insertions/deletions, copy number alterations, translocations, and gene expression. Detailed clinicopathologic data was collected for each patient and linked to the genomic information. Results: WES of all metastatic samples demonstrated several recurrently altered genes whose incidence differed significantly from primary, treatment-naive ER+ breast cancers sequenced in the TCGA study (TCGA). These include ESR1 mutations (n=17, 19.3%; 32.86 fold enrichment, q.value Comparing to matched primary samples from the same patient, many alterations were found to be acquired in several cases, including for ESR1, ERBB2, PIK3CA, PTEN, RB1, AKT1, and others. Initial analysis of RNA-seq data from metastatic samples (n=59) allowed classification of individual resistance mechanisms into broader resistance modes based on the observed transcriptional state. Conclusions: We present a genomic landscape of resistant ER+ MBC using WES and RNA-seq. Multiple genes were recurrently altered in these tumors at significantly higher rates than in ER+ primary breast cancer. When compared with matched primary tumors from the same patient, alterations in these and other genes were often found to be acquired after treatment, suggesting a role in resistance to ER-directed therapies and/or metastasis. Potential resistance mechanisms appear to fall into several categories; integrating RNA-seq data may enhance the ability to identify these categories even when genomic alterations are not identified. Multiple clinically relevant genomic and molecular alterations are identified in metastatic biopsies– with implications for choice of next therapy, clinical trial eligibility, and novel drug targets. Citation Format: Cohen O, Kim D, Oh C, Waks A, Oliver N, Helvie K, Marini L, Rotem A, Lloyd M, Stover D, Adalsteinsson V, Freeman S, Ha G, Cibulskis C, Anderka K, Tamayo P, Johannessen C, Krop I, Garraway L, Winer E, Lin N, Wagle N. Whole exome and transcriptome sequencing of resistant ER+ metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S1-01.

Chemotherapy and HER2-Directed Therapy for Metastatic Breast Cancer

Abstract Chemotherapy and HER2-directed therapy for metastatic breast cancer represent an important and quickly evolving area. Much of the significant progress since 2010 has focused on advances in HER2-directed therapy, including introduction (and US Food and Drug Administration approval) of the agents pertuzumab and trastuzumab-emtansine (T-DM1), which has led to large improvements in overall survival for patients with HER2-positive metastatic breast cancer. Another important advance has been the improving understanding of triple-negative breast cancer as a heterogenous and distinct disease subtype and the demonstration of clinical efficacy for platinum-type agents (cisplatin and carboplatin) in triple-negative disease specifically. Progress in systemic therapy for brain metastases, an evolving understanding of treatments specific to BRCA-deficient breast cancer, and the ongoing introduction of many novel therapies including immunotherapy are all exciting recent developments in this field.

The evolving understanding of small HER2-positive breast cancers: matching management to outcomes

Systemic therapy for small (stage I) HER2-positive breast cancers has long posed a dilemma for clinicians, as the majority of these patients were excluded from the large adjuvant trastuzumab trials. However in the decade since those trials were reported, data have accumulated to suggest that recurrence risk for these small but biologically aggressive tumors is nontrivial. In this review, we summarize data from numerous cohort studies describing the outcomes of small HER2-positive tumors, mostly in the absence of HER2-directed therapy. We then examine the potential impact of HER2-directed treatment in this population, culminating in the recently published prospective study of paclitaxel/trastuzumab therapy. The landscape of next generation anti-HER2 therapies is quickly evolving; a role for some of these agents in the small HER2-positive subpopulation may also be on the horizon.