Abstract presented at AORTIC 2023, Dakar Senegal
OBJECTIVE
To characterise the somatic mutation landscape and identify potential novel breast cancer driver mutations in Ghanaian women.
METHODS
Whole exome sequencing was performed on 106 breast cancer FFPE tumour samples, with 94 samples having at least 30x coverage. Sequencing reads were aligned to the human reference genome (hg38) using Burrows Wheeler Aligner (BWA) after trimming adapters and low quality bases using Trimmomatic. Aligned reads in binary alignment and map (BAM) format were used for tumor-only somatic variant calling using Mutect2 from the Genome Analysis ToolKit (GATK) with 1000Genomes variants as panel of normals and Genome Aggregation Database (gnomAD) as germline resource. Variants were annotated with variant effect prediction scores, frequencies from publicly-available variant databases, variant significance from ClinVar database, among others, using Ensembl Variant Effect Predictor (VEP) and dbNSFP. We investigated mutations in known cancer genes based on the COSMIC Cancer Gene Census list.
RESULTS
Pathogenic/likely pathogenic variants in known cancer genes including TP53, PIK3CA, BRCA1, NF1, and BRCA2 were found in 86% (81/94) of samples with variant allele frequencies (VAFs) ranging from 5%-100%. Variants of uncertain significance (VUS) in BRCA1 and BRCA2 were found in 46% (6/13) of the remaining samples. Notably, a novel BRCA1 (p.E1046*) variant was found at a high VAF (75%), suggesting clonal origin in a sample without any known pathogenic variant/VUS.
CONCLUSIONS
The identification of somatic mutations, including novel driver mutations, in breast cancer within an African population provides valuable insights into the underlying carcinogenic processes specific to this population. These findings contribute to our understanding of the genetic factors involved in breast cancer development and progression in individuals of African descent. Further exploration of the functional and clinical implications of these mutations is crucial for the development of targeted therapies tailored to the unique genetic landscape of African breast cancer patients.