Genetic landscape of Pakistani familial breast cancer patients using multigene panel testing

Pathogenic/likely pathogenic (P/LP) variants in high-, moderate-, and low-penetrance genes account for approximately half of all familial breast cancer (BC) cases. In Pakistan, data on P/LP variants beyond BRCA1/2 remain limited. This study investigated the frequency and distribution of P/LP variants in Pakistani familial BC patients using a 14-gene hereditary breast and ovarian cancer (HBOC) core panel. A total of 160 familial BC patients previously tested negative for protein-truncating variants in BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53 using conventional methods were included. Next-generation sequencing (NGS) was performed using the Illumina MiSeq platform, and all identified P/LP variants were validated by Sanger sequencing. Twenty-four unique P/LP variants were identified across seven genes: BRCA1 (n = 10), BRCA2 (n = 6), TP53 (n = 3), CHEK2 (n = 2), PALB2, ATM, and RAD51C (n = 1 each). Two recurrent BRCA1 variants, p.Gln169Ter and p.Val757Phefs*8, were identified in three patients each. NGS-detected P/LP variants were identified in 18.1% (29/160) of patients. When combined with previous germline testing in the same cohort, the overall detection rate increased to 50.2% (132/263): BRCA1 (101/263; 38.4%), BRCA2 (22/263; 8.4%), TP53 (3/263; 1.1%), CHEK2 (2/263; 0.8%), PALB2 (2/263; 0.8%), ATM (1/263; 0.4%) and RAD51C (1/263; 0.4%). Among these, BRCA1/2 variants accounted for 93.2% (123/132) of all P/LP variants. Our findings demonstrate that P/LP variants are concentrated in a limited number of genes, with BRCA1/2 as the predominant contributors. We propose a cost-effective, first-tier genetic testing panel comprising seven genes (ATM, BRCA1, BRCA2, CHEK2, RAD51C, PALB2, and TP53) for familial BC risk assessment in Pakistan.