Breast Neoplasms study with RNA-Seq, SNV (.MAF) + 1 more data on dbGaP (107 participants)

phs001285 — Response and Resistance to ER-Directed Therapy in Metastatic Breast    Cancer

Despite the reduction in cancer recurrence and mortality provided by hormonal therapy, estrogen receptor positive (ER+) metastatic breast cancer (MBC) remains the most common cause of breast cancer death, resulting in more than 20,000 deaths in the U.S each year. Although several therapeutic options exist to target the estrogen receptor, resistance to these therapies invariably occurs. Genetic mechanisms of acquired resistance to targeted therapies in ER+ MBC are not well understood. To address this, we developed a prospective biopsy protocol where multiple research biopsies are collected from metastatic samples and used for pathology, ER/PR/HER2, OncoPanel (a CLIA 300 gene sequencing panel), whole exome sequencing (WES), transcriptome sequencing (RNA-Seq), and single-cell RNA-seq (scRNA-seq). In some cases, tissue is used for cell line and xenograft generation. Archival primary biopsies are also obtained when possible for parallel genomic studies. Patients are followed and serial metastatic biopsies are obtained. This data will be used to determine the landscape of genomic alterations in treatment-resistant ER+ MBC, and compared to data generated by TCGA for treatment-naive ER+ primary breast cancer. Comparison of genomic studies from resistant, metastatic specimens with corresponding pre-treatment primary samples will allow us to identify genomic association with resistance to specific therapies. Analysis of the serial metastatic biopsies collected over the course of multiple treatments will also shed light on tumor evolution under selective therapeutic pressure.Note<ol><li>A subset of the MBC blood biopsies that are included in our study can be accessed and downloaded from the <a href="https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bihttps://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001977.v1.p1">phs001977</a> accession.</li><li>Another subset of patients in this study participated in a clinical trial (<a href="https://clinicaltrials.gov/study/NCT02871791">NCT02871791</a>) and have their data deposited in the current study as well.</li></ol>