NANOTECHNOLOGY-ENABLED GENE CHIP PLATFORMS FOR PRECISION BREAST CANCER GENOMICS: FIRST ALBANIAN EXPERIENCE

Abstract

Background: Recent advances in nanotechnology have transformed cancer genomics through the development of high-density DNA microarray (gene chip) platforms capable of genome-wide analysis with high analytical resolution. Technologies such as CytoScan™ 750K and OncoScan® CNV Assay integrate thousands of miniaturized oligonucleotide and molecular inversion probes on biochips, enabling comprehensive detection of copy number alterations (CNAs), copy-neutral loss of heterozygosity (LOH), and chromosomal imbalances from clinical specimens, including FFPE tissues. This study presents the first application of these nanotechnology based genomic platforms for breast cancer characterization in Albania. Methods: A retrospective cohort of 252 breast cancer patients diagnosed between 2021 and 2024 was evaluated for clinicopathological characteristics. Based on hereditary risk criteria, 17 FFPE tumor samples underwent genome-wide analysis using the OncoScan® Array Chip, while the study highlights the complementary role of CytoScan™ 750K as a high-resolution genome wide platform for constitutional and somatic genomic profiling. Genomic findings were correlated with molecular subtypes and immunohistochemical biomarkers. Results: The cohort was dominated by patients older than 45 years (92.5%), with invasive ductal carcinoma accounting for 81.6% of cases and stage II representing 69.8%. Genome-wide analysis revealed BRCA1 deletions in 29.4% and LOH in 47.1% of tumors, whereas BRCA2 deletions and LOH were detected in 17.6% and 35.3% of samples, respectively. BRCA1 alterations were predominantly associated with triple-negative breast cancer, while BRCA2 abnormalities were mainly observed in Luminal A, Luminal B, and HER2-enriched tumors. The high-resolution gene chip technology enabled precise identification of clinically relevant genomic alterations that are not detectable by conventional diagnostic approaches. High-density gene chip platforms based on nanotechnology represent a powerful tool for precision oncology by enabling genome-wide detection of clinically actionable genomic alterations from routine clinical samples. Conclusions: The complementary application demonstrates how advanced biochip technologies can support molecular diagnosis, patient stratification, targeted therapy selection, hereditary cancer risk assessment, and implementation of personalized medicine. This work establishes the first experience in Albania using nanotechnology-driven genomic microarrays for breast cancer profiling and provides a foundation for integrating advanced genomic diagnostics into routine oncological practice.