Spectrum of germline variants in moderate to high penetrance non-BRCA breast cancer susceptibility genes in a Pakistani early-onset cohort.

Background

Hereditary factors account for a significant lifetime risk of breast cancer. Approximately 20% is attributable to pathogenic variants in the highly penetrant BRCA1/2 of the homologous recombination repair (HRR) pathway. Other HRR pathway genes (ATM, CHEK2, BARD1, TP53) are also linked to breast cancer susceptibility; however, the contribution of these genes remains underexplored in Pakistani populations.

Methods

A cohort of 66 early-onset breast cancer patients underwent next-generation sequencing (NGS) of BRCA1/2 followed by four non-BRCA breast cancer susceptibility genes (ATM, CHEK2, BARD1, and TP53) using a multigene panel. The present analysis focused primarily on variants identified in the four non-BRCA genes, which were annotated using ANNOVAR and in silico prediction algorithms. Variant classification was assessed using ClinVar and ACMG/AMP guidelines.

Results

A total of 478 variants were identified. Two pathogenic stop-gain variants in CHEK2 were detected in three patients (4.5%), while two missense and one 5'UTR variant of uncertain significance (VUS) in ATM were identified in three patients (4.5%). Further, based on MAF < 1%, n= 123 (47.85%) variants were recurrent, and 15 (5.8%) novel alleles were detected; of these, two novel missense variants were identified in exonic region in BARD1 and CHEK2.

Conclusion

This study highlights the contribution of pathogenic variants in CHEK2, supports the clinical relevance in breast cancer, and identifies recurrent variants alongside potentially novel, population-specific alleles in BARD1 and CHEK2. The identification of VUS in ATM underscores the need for functional and population-based studies to elucidate their clinical significance and to advance precision oncology in Pakistan.