Gene Panel Testing for Breast Cancer Reveals Differential Effect of Prior BRCA1/2 Probability

SIMPLE SUMMARY: Previous studies reporting large gene panels in breast cancer have mainly reported on the contribution of additional genes compared to BRCA1/2. We have shown a very large differential additional effect from non-BRCA genes dependent on a priori likelihood of BRCA1 and BRCA2 combined. We have undertaken panel testing beyond BRCA1/2 in 1398 patients with breast cancer and identified 95 (6.3%) with actionable breast cancer genes. The highest rate was found for grade 3 ER+ Her2− breast cancers. Those with the lowest likelihood of BRCA1/2 by Manchester score had a 3-fold higher rate of non-BRCA genes whereas those with predicted rates of ~80% had 5-fold higher rate of BRCA1/2. Unless those referring patients with breast cancer for extended panel testing are certain there is no loss of sensitivity for BRCA1/2 they should opt of a bespoke BRCA1/2 test first in those with high prior likelihoods of BRCA1/2 pathogenic variants. ABSTRACT: Whilst panel testing of an extended group of genes including BRCA1/2 is commonplace, these studies have not been subdivided by histiotype or by a priori BRCA1/2 probability. Patients with a breast cancer diagnosis undergoing extended panel testing were assessed for frequency of actionable variants in breast cancer genes other than BRCA1/2 by histiotype and Manchester score (MS) to reflect a priori BRCA1/2 likelihood. Rates were adjusted by prior testing for BRCA1/2 in an extended series. 95/1398 (6.3%) who underwent panel testing were found to be positive for actionable non-BRCA1/2 breast/ovarian cancer genes (ATM, BARD1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, TP53). As expected, PALB2, CHEK2 and ATM were predominant with 80-(5.3%). The highest rate occurred in Grade-3 ER+/HER2− breast cancers-(9.6%). Rates of non-BRCA actionable genes was fairly constant over all likelihoods of BRCA1/2 but adjusted rates were three times higher with MS < 9 (BRCA1/2 = 1.5%, other = 4.7%), but was only 1.6% compared to 79.3% with MS ≥ 40. Although rates of detection of non-BRCA actionable genes are relatively constant across BRCA1/2 likelihoods this disguises an overall adjusted low frequency in high-likelihood families which have been heavily pre-tested for BRCA1/2. Any loss of detection sensitivity for BRCA1/2 actionable variants in breast cancer panels should lead to bespoke BRCA1/2 testing being conducted first.