Clinical actionability enhanced through deep targeted sequencing of solid tumors

Area of Science:

• Oncology
• Genomics
• Cancer Research

Background:

• Accurate cancer therapy relies on comprehensive profiling of somatic mutations within tumor subpopulations.
• Intratumor heterogeneity's extent and clinical impact remain incompletely understood.
• A deep targeted sequencing platform was developed to address these knowledge gaps.

Purpose of the Study:

• To establish and validate a deep targeted sequencing platform for identifying actionable DNA alterations.
• To assess the prevalence and clinical significance of intratumor heterogeneity in cancer samples.
• To evaluate the utility of high-depth sequencing for routine cancer care.

Main Methods:

• Analyzed 515 formalin-fixed paraffin-embedded (FFPE) tumor samples and matched germline DNA from 475 patients across 11 disease sites.
• Employed targeted sequencing of all exons in 201 cancer-related genes with a mean depth of 1000-fold.
• Collected data on mutations, insertions/deletions (indels), and copy number variations.

Main Results:

• Identified 4794 nonsynonymous mutations, with 15.2% at <10% allele frequency, often at oncogenic hotspots.
• Detection of low-frequency mutations identified actionable gene alterations in 24.84% of patients, with 9.8% becoming actionable.
• Ultrahigh sequencing depth ensured a low false discovery rate (<2.2%) in FFPE samples.

Conclusions:

• The developed platform matches the accuracy of commercial hotspot panels but detects more actionable gene mutations.
• High sequencing depth is critical for comprehensive profiling of clinical tumor samples.
• This platform is valuable for implementing routine sequencing in cancer care settings.