Genomic Profiling of Breast Cancer in an Ecuadorian Cohort Reveals Clinically Relevant Variants and Ancestry-Related Interpretation Challenges

Background/Objectives: Breast cancer (BC) is the most frequently diagnosed malignancy among women worldwide, yet tumor genomic data from Latin American and admixed populations remain limited. This gap affects the interpretation of cancer-associated variants and may limit the representation of these populations in genomic research. This study aimed to characterize the genomic landscape of breast tumors from Ecuadorian women and contextualize variant interpretation through genetic ancestry analysis. Methods: Breast tissue samples from 23 Ecuadorian mestizo women with suspected malignancy were analyzed. After histopathological confirmation, 21 breast tumors were included in the final cohort. Targeted next-generation sequencing was performed using a 94-gene cancer panel. Variants were annotated and classified according to clinical significance. Because matched normal DNA was unavailable, variant allele frequency was used as an exploratory approach to infer putative somatic, putative germline, indeterminate, or putative homozygous germline profiles. Putative germline and indeterminate variants were interpreted using ACMG/AMP criteria, whereas putative somatic variants were evaluated using the AMP/ASCO/CAP framework. Genetic ancestry was inferred using ancestry-informative insertion/deletion markers. Results: Seventy-two unique variants across 40 genes were identified, including 14 pathogenic, 10 likely pathogenic, and 48 variants of uncertain significance. Pathogenic and likely pathogenic alterations were detected in clinically relevant genes, including TP53, BRCA2, PTEN, CDH1, RAD51C, MSH6, NF1, CYLD, and SDHB. Variants of uncertain significance represented 66.7% of all detected variants and affected several cancer-associated and DNA repair genes. The cohort showed a trihybrid ancestry profile, with predominant Native American ancestry, followed by European and African contributions. Conclusions: This study expands BC genomic data from an underrepresented Ecuadorian cohort and highlights the coexistence of clinically relevant alterations with a high burden of variants of uncertain significance. The findings underscore the limitations of tumor-only sequencing and current variant interpretation frameworks in admixed populations. Larger studies integrating matched normal DNA, ancestry-informed analyses, functional validation, and broader sequencing strategies could help improve variant interpretation in Latin American populations.