Detecting gene copy number alterations by Oncomine Comprehensive genomic profiling in a comparative study on FFPE...

Area of Science:

• Oncology
• Genomics
• Molecular Diagnostics

Background:

• Copy number alterations (CNAs) are critical in cancer development and precision medicine.
• Formalin-fixed paraffin-embedded (FFPE) tissues are standard for diagnostics, but CNA detection can be challenging.
• Next-Generation Sequencing (NGS) offers genome-wide CNA discovery, yet requires validation in FFPE samples.

Purpose of the Study:

• To evaluate the performance of the Oncomine Comprehensive Assay plus (OCA+) for detecting CNAs in FFPE samples.
• To compare OCA+ CNA detection with a whole-genome assay and orthogonal fluorescence in situ hybridization (FISH) tests.
• To assess the sensitivity and specificity of NGS-based CNA detection in routine diagnostic FFPE material.

Main Methods:

• Analysis of 14 FFPE samples using the OCA+ targeted NGS assay.
• Comparison of OCA+ results against a whole-genome assay.
• Validation of detected CNAs using orthogonal FISH assays.

Main Results:

• The OCA+ targeted NGS assay demonstrated lower sensitivity but equal specificity for detecting copy number gains and losses compared to whole-genome analysis.
• OCA+ accurately identified copy number gains ≥5.2 based on its proprietary software pipeline.
• No optimal threshold was identified to differentiate true and false positive losses.
• FISH validation confirmed seven CNAs with copy number gain ≥6 or complete loss.

Conclusions:

• Targeted NGS assays like OCA+ require further validation for reliable CNA detection in FFPE tissues.
• While promising, the sensitivity limitations of current NGS panels necessitate careful interpretation of results for clinical application.
• Robust validation studies are essential to fully leverage the potential of NGS for CNA-based precision oncology in FFPE samples.