Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection

Area of Science:

• Molecular Oncology
• Genomics
• Biotechnology

Background:

• Solid tumors cause significant cancer-related mortality globally.
• Circulating tumor DNA (ctDNA) analysis offers non-invasive cancer detection and personalized treatment strategies.
• Evaluating commercially available ctDNA sequencing panels is crucial for clinical application.

Purpose of the Study:

• To compare the performance of two major ctDNA sequencing panels: Roche's Avenio ctDNA Expanded panel and QIAgen's QIAseq Human Comprehensive Cancer panel.
• To assess panel coverage, specificity, sensitivity, concordance, and sequencing uniformity for detecting clinically relevant variants.
• To inform researchers and clinicians in selecting appropriate ctDNA analysis technologies.

Main Methods:

• Comparative analysis of two ctDNA platforms using identical human blood samples.
• Ultra-deep next-generation sequencing was employed for comprehensive variant detection.
• Key performance metrics evaluated included variant coverage, specificity, sensitivity, concordance, and sequencing depth.

Main Results:

• QIAseq panel covered a higher percentage of patients (nearly 90%) with more variants per patient (8) compared to Avenio (over 70% patients, 3 variants).
• Both panels showed comparable on-target rates and read mapping percentages.
• Avenio demonstrated more uniform sequencing coverage across varying GC content regions and exhibited higher sensitivity and concordance at equivalent sequencing depths.

Conclusions:

• Both Avenio and QIAseq panels have distinct strengths for ctDNA analysis in solid tumors.
• Avenio offers superior sensitivity and coverage uniformity, suitable for applications requiring high precision.
• QIAseq provides broader patient coverage and higher variant detection rates, beneficial for screening diverse populations.