GWAS summary statistics of PhD Thesis "Identifying Genetic Factors Associated with Breast or Ovarian Cancer Risk in BRCA1 Pathogenic Variant Carriers"

In this study, we conducted a genome-wide association study (GWAS) involving 406 female carriers of BRCA1 pathogenic variants (PV) (c.4035del or c.5266dup) in Latvian population. The cohort included individuals affected by breast cancer (BC) or ovarian cancer (OC) and unaffected individuals. We compared three groups: (1) carriers affected with cancer (BC or OC) vs. unaffected individuals, (2) carriers affected with BC vs. unaffected individuals, and (3) carriers affected with OC vs. unaffected individuals. Genotyping of all study samples was performed using the Infinium OncoArray-500K BeadChip (Illumina, San Diego, CA, USA) at the Institute of Oncology and Molecular Genetics, Rīga Stradiņš University. The dataset underwent standard genotype quality control (QC), followed by imputation of missing genotypes using the Estonian population-based high-coverage whole-genome sequencing (WGS) dataset (n = 2244) as a reference panel. Association analysis was performed using the R v4.0.2 package SAIGE v0.38 to implement a mixed logistic regression model, adjusted for relatedness, the first four principal components (PCs), age at recruitment/disease onset, and BRCA1 PV type.