Scientific publications
Laboratory Cross-Comparison and Ring Test Trial for Tumor BRCA Testing in a Multicenter Epithelial Ovarian Cancer Series: The BORNEO GEICO 60-0 Study
Zaida Garcia-Casado 1 , Ana Oaknin 2 , Marta Mendiola 3 4 , Gorka Alkorta-Aranburu 5 , Jose Ramon Antunez-Lopez 6 , Gema Moreno-Bueno 4 7 8 , Jose Palacios 4 9 10 11 , Alfonso Yubero 12 , Raul Marquez 7 , Alejandro Gallego 13 , Ana Beatriz Sanchez-Heras 14 , Jose Antonio Lopez-Guerrero 1 15 16 , Cristina Perez-Segura 17 , Pilar Barretina-Ginesta 18 , Jesus Alarcon 19 , Lydia Gaba 20 , Antonia Marquez 21 , Judit Matito 22 , Juan Cueva 23 , Isabel Palacio 24 , Maria Iglesias 25 , Angels Arcusa 26 , Luisa Sanchez-Lorenzo 27 , Eva Guerra-Alia 28 , Ignacio Romero 29 , Ana Vivancos 22
Abstract
Germline and tumor BRCA testing constitutes a valuable tool for clinical decision-making in the management of epithelial ovarian cancer (EOC) patients. Tissue testing is able to identify both germline (g) and somatic (s) BRCA variants, but tissue preservation methods and the widespread implementation of NGS represent pre-analytical and analytical challenges that need to be managed.
This study was carried out on a multicenter prospective GEICO cohort of EOC patients with known gBRCA status in order to determine the inter-laboratory reproducibility of tissue sBRCA testing.
The study consisted of two independent experimental approaches, a bilateral comparison between two reference laboratories (RLs) testing 82 formalin-paraffin-embedded (FFPE) EOC samples each, and a Ring Test Trial (RTT) with five participating clinical laboratories (CLs) evaluating the performance of tissue BRCA testing in a total of nine samples. Importantly, labs employed their own locally adopted next-generation sequencing (NGS) analytical approach. BRCA mutation frequency in the RL sub-study cohort was 23.17%: 12 (63.1%) germline and 6 (31.6%) somatic.
Concordance between the two RLs with respect to BRCA status was 84.2% (gBRCA 100%). The RTT study distributed a total of nine samples (three commercial synthetic human FFPE references, three FFPE, and three OC DNA) among five CLs. The median concordance detection rate among them was 64.7% (range: 35.3-70.6%). Analytical discrepancies were mainly due to the minimum variant allele frequency thresholds, bioinformatic pipeline filters, and downstream variant interpretation, some of them with consequences of clinical relevance.
Our study demonstrates a wide range of concordance in the identification and interpretation of BRCA sequencing data, highlighting the relevance of establishing standard criteria for detecting, interpreting, and reporting BRCA variants.
CITATION J Pers Med. 2022 Nov 4;12(11):1842. doi: 10.3390/jpm12111842.
