Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel...

Area of Science:

• Oncology
• Genetics
• Molecular Diagnostics

Background:

• Synthetic lethal-based cancer therapies rely on targeting specific genetic vulnerabilities.
• Accurate assessment of gene-specific loss of heterozygosity (LOH) and biallelic loss of function (LOF) is crucial for patient selection.
• Existing methods may require further optimization for clinical application in formalin-fixed, paraffin-embedded (FFPE) samples.

Purpose of the Study:

• To introduce and validate SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel.
• To assess the capability of SNiPDx in detecting LOH and biallelic LOF alterations in DNA damage response genes.
• To evaluate the clinical feasibility and diagnostic accuracy of SNiPDx using FFPE tumor samples.

Main Methods:

• Development of a targeted NGS panel (SNiPDx) covering 26 DNA damage response genes and 7632 genome-wide single-nucleotide polymorphisms.
• Optimization of the Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing (FACETS) algorithm for tumor purity and copy number assessment.
• Validation of SNiPDx performance against whole genome sequencing and existing NGS-based clinical tests using 80 FFPE solid tumor samples.

Main Results:

• SNiPDx demonstrated high sensitivity (95%) and specificity (91%) for LOH detection compared to whole genome sequencing.
• Positive agreement with local NGS testing for genetic alterations reached 95%.
• SNiPDx accurately identified biallelic ATM loss of function mutations (93%) and all ATM LOH events (100%).

Conclusions:

• SNiPDx is a novel, clinically feasible NGS test for analyzing allelic status in FFPE tumor samples.
• The panel exhibits high accuracy comparable to existing NGS-based approaches.
• SNiPDx has the potential to improve patient stratification for synthetic lethal-based cancer therapies.