Background: The ongoing, multi-center FLEX trial (NCT03053193) began in the United States in 2017, with the ultimate goal of 30,000 patients enrolled. The primary objective is to create a large-scale collaborative registry of early-stage breast cancer patients that links comprehensive clinical and full genome expression data to reveal new prognostic and/or predictive gene signatures. A key secondary objective of the trial is to enable investigator-initiated studies to explore early-stage breast cancer at a relatively low cost to the investigator. Methods: The prospective FLEX trial enrolls patients aged ≥ 18 years with histologically proven stage I-III breast cancer, with negative or 1-3 positive lymph nodes. Eligible patients have received MammaPrint, with or without BluePrint testing as standard of care, and consent to clinically annotated full transcriptome data collection. The FLEX base study protocol permits investigators to submit their own concept proposal, and upon review and approval by the Research and Scientific Review Committees, investigators interrogate clinical and genomic data from the FLEX database. The 10-year enrollment goal is a minimum of 30,000 patients. Since April 2017, 9,170 patients have been enrolled at over 109 sites in the United States. To date, 38 investigator-initiated substudies have been approved and are in progress, and 28 abstracts have been published in the US scientific congresses. To ensure inclusion of diverse populations, patients from local communities and 11 National Cancer Institute-designated Comprehensive Cancer Centers were included. Our diverse data set is helping meet the needs of historically under-represented patients with breast cancer. Of the self-reported ethnicities within the FLEX database, 65% are White or Caucasian, 8% Black or African American, 4% Latin American, and 2% Asian. There are 5 ongoing FLEX sub studies investigating racial disparities. The molecular profiling and differential gene expression analysis in early-stage breast cancer patients of African American, Asian, Hispanic ancestries helps to provide critical insights that correlate tumor biology with treatment outcomes. FLEX is expanding globally with sites anticipated in multiple European countries. The FLEX trial continues to expedite the discovery and development of novel genomic profiles, bringing precision oncology into the clinic to improve breast cancer management. Clinical trial information: NCT03053193.