Testing for germline BRCA1/2 mutations has an established predictive role in breast and ovarian cancer risk assessment and EQA on germline mutation testing have been performed for a long time. With the European extension of indication for the PARP inhibitors, the screening of tumors first is increasingly important. However, tumoral BRCA1/2 testing is a different analytical process on formalin-fixed, paraffin-embedded (FFPE) material and with some challenging variants as large rearrangements. Validation of the test method and participation in external quality assessment programs are therefore required.
In the French national quality control programs (Gen&tiss) of 2017 and 2018, laboratories received 5 samples from ovarian cancer patients and 1 educational artificial sample with mutations present at different variant allelic frequencies in BRCA1/2 and a large rearrangement in BRCA1.
The number of participants was 21 in 2017 and 26 in 2018. The number of labs with severe error was 3 in 2017 (14%) and 4 in 2018 (15%). For BRCA1, the average score remained stable between 2017 [9.6/10 (N = 21)] and 2018 [9.6/10 (N = 26)]. In both years, 2 laboratories made severe errors (false positive/false negative). In 2017 only 11 laboratories (N = 20) identified the educational variant present at 7% VAF. For BRCA2 the score slightly decreased from 9.8/10 (N = 22) to 9.4/10 (N = 26) and the number of laboratories with severe errors increased from 1 to 3. Half of the laboratories (N = 20) detected all three mutations present in the educational sample (VAF 10% to 30%) in the 2017 scheme. In 2018 a large deletion in BRCA1 present in the educational sample was only detected by 4 out of 20 laboratories. Three out of 26 laboratories detected the additional RAD51C variant and none the RAD51D variant. The main methods applied in France focus on BRCA1 and BRCA2 genes and amplification-based enrichment.
The genotype results were very similar between 2017 and 2018: acceptable but there are still more than 14% with severe errors. The limit of detection is a critical point. Few labs are ready to extend testing beyond BRCA1/2 genes. The question of large rearrangements is not yet solved for tumoral screening. EQA on tumoral BRCA1/2 testing is therefore essential to improve laboratory performance.
Clinical trial identification
Legal entity responsible for the study
Gen&tiss - GFCO and AFAQAP.
All authors have declared no conflicts of interest.