Assessing the utility of liquid biopsy for detecting actionable genetic mutations among indigenous Ghanaian women with metastatic breast cancer.
Authors: Amoako Emmanuella Faith , Ofori Emmanuel Owusu , Akakpo Patrick Kafui , Aniakwo Luke Adagrah , Jimah Bashiru Babatunde , Ulzen-Appiah Kofi , Akligoh Harry , Ibrahim Barikisu Anna , Tackie Randy , Manu Aida , Paemka Lily , Yong Elena , Lim Nicole , Xia-Zhu David , Soo James , Delgado Lauren , Challis Jack , Tan Min-Han , Rahman Ganiyu A. , Bediako Yaw 
Published: June 2023

e13017

Background: Breast cancer is the leading cancer diagnosis in women worldwide, and the leading cause of cancer-related mortality in Ghanaian women. Up to 70% of breast cancer diagnoses in Ghanaian women are advanced-stage, leading to fewer opportunities for early intervention. Late presentation of breast cancer may be attributed to lack of comprehensive screening programs, among other factors. Next-Generation Sequencing (NGS)-based liquid biopsy of circulating free DNA (cfDNA) is non-invasive and been demonstrated to support diagnosis, monitoring and treatment selection in cancer. Unfortunately, people of African ancestry are under-represented in evaluations of this technology and little is known about the feasibility of such approaches in low-resource settings. Methods: The AMBER-01 study recruited 20 newly diagnosed, histologically confirmed, treatment-naive women with metastatic breast cancer at the Cape Coast Teaching Hospital. Testing was conducted at CAP and CLIA accredited laboratories (Lucence, Palo Alto; Singapore). Tissue NGS and cfDNA liquid biopsy analysis was ordered on a total of 20 patients following tissue quality analysis outcomes. All 20/20 (100%) liquid biopsy samples were acceptable for analysis, whereas only 6/20 (30%) passed QC for tissue NGS testing. cfDNA liquid biopsy and tissue NGS analyses were performed using Lucence LiquidHALLMARK and Tissue500 technology, respectively. Results: Liquid biopsy detected 42 cfDNA mutations in 17/20 patients. Of the 17 patients found to have mutations on liquid biopsy, 3 (17.6%) patients had mutations associated with African ancestry, including BRCA K719E, ARAF S262I and GATA3 G125dup. Eight actionable mutations specific to breast cancer were found in 7/17 (41.2%) patients while actionable mutations non-specific to breast cancer were detected in 12/17 (70.6%) patients. Tissue biopsy analysis detected mutations in all 6 patients tested, with 3/6 (50%) patients presenting actionable mutations specific to breast cancer. Of the 20 patients recruited, liquid biopsy was able to identify actionable treatments for 7 patients, while tissue was only able to identify actionable treatment for 3 patients. Of the 6 patients with matched liquid and tissue results, liquid biopsy detected additional mutations in 3 (50%) patients that were not detected by tissue analysis including: BRCA2 Q1379E, GNAQ Q176*, and a low Microsatellite Instability (MSI) reported as stable in tissue. Conclusions: Liquid biopsy detected multiple actionable variants in Ghanaian women with breast cancer that a tissue-only workflow missed. cfDNA analysis featured less variations in sample preparation which is a key consideration in resource-limited settings. Further work will optimize NGS panels to account for novel ancestry specific variants. Liquid biopsy presents a great opportunity to improve cancer care in Africa.