Abstract A011: Whole genome sequencing of the Alabama Hereditary Cancer Cohort to identify African American breast cancer genetic risk variants

Abstract

Abstract Regardless of having higher rates of triple-negative breast cancer (TNBC) and breast cancer-related deaths, African Americans are drastically understudied in hereditary breast cancer research. Our group has established the Alabama Hereditary Cancer Cohort to carry out next-generation sequencing (NGS) to address this gap. These efforts aim to identify inherited breast cancer risk variants in African Americans. Interestingly, African American TNBC tumors have been investigated through NGS, identifying somatic mutations unique to African American breast cancer. Now, African American-specific variants associated with inherited risk need to be identified, including those in genes harboring somatic mutations in African American TNBC. This study carried out whole genome sequencing (WGS) to investigate inherited African American breast cancer risk. All coding and non-coding regions of the nuclear genome and the entirety of the mitochondrial genome were explored, all of which can play a role in hereditary breast cancer risk. Individuals provided a blood or saliva sample for DNA extraction upon study consent. Subsequently, paired-end Illumina sequencing was carried out. Fastq files were trimmed using Trimmomatic and further processed according to the Genome Analysis ToolKit Best Practices, resulting in variant call format (VCF) files. Coding, non-coding, and mitochondrial regions were individually extracted using VCFtools and UCSC Table Browser tracks. Coding and mitochondrial variants were annotated using Annovar and MSeqDR, respectively. Coding variants were further filtered for minor allele frequency (MAF) classes (i.e., rare and low-frequency) and mutation type (i.e., protein-truncating variants; PTVs) using R (v. 4.2). Preliminary WGS data of 60 African American hereditary breast cancer cases have identified statistically significant rare and low-frequency PTVs in genes reported to harbor somatic mutations exclusively in African American TNBC tumors. Furthermore, we have identified variants in prostate cancer susceptibility genes that are statistically associated with African American breast cancer risk. We have also identified multiple variants in the mitochondrial genome that are statistically linked to breast cancer risk, some African American-specific. Our data shows that WGS is an invaluable tool for identifying breast cancer susceptibility variants. Further sequencing and functional analyses will validate our preliminary findings. Citation Format: Troy LoBue, Isaac Mcneely, Nancy Merner. Whole genome sequencing of the Alabama Hereditary Cancer Cohort to identify African American breast cancer genetic risk variants [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A011.