Abstract SP021: Understanding current platforms

Abstract

Abstract Next-generation sequencing (NGS) of breast cancer is becoming increasingly integrated into clinical practice. The fast pace of advances coupled with the dizzying array of technologies and platforms challenges the oncologist to select the right test for each patient. The choice could depend on a host of factors including the accessibility of clinical trials, clinical scenario and sample type, and the interest in turning up improbable but profoundly useful findings. Here, I will review the various types of clinical NGS platforms—including tumor and circulating-tumor DNA—particularly highlighting the unique features of commercial platforms that are widely available. Performance characteristics differ by technology: amplification technologies can detect mutations with smaller specimens, whereas capture-based NGS platforms may perform better for detecting novel genomic alterations. Assays integrating RNA-based analysis may enhance detection of rare but impactful gene fusions, such as of FGFR1-3 and NTRK1-3. Some potentially actionable genomic alterations only emerge after therapy, and are detected only with repeat tumor biopsy or cell-free DNA. Some assays include parallel germline testing which can clearly distinguish inherited from somatic (tumor-specific) findings, but may offer logistical challenges. An ever expanding set of ‘genomic phenotypes’ may be captured in these updated assays, with their limitations, including tumor mutational burden, microsatellite instability and homologous recombination. Newer platforms are now including exome and whole-genome sequencing, which may require more tissue and offer research insights, but currently add little to directing clinical care. New technologies, such as long-read and single-cell platforms of the future, may elucidate genomic features that are undetectable with current bulk short-read platforms, and will enable new genomic biomarkers. Despite the differences in genomics platforms, practical matters such as reimbursement, ease of use, and turn-around-time will likely govern platform selection for most oncologists in the near future. Citation Format: M Burkard. Understanding current platforms [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 SP021.