Cancer of Unknown Primary Genomic Profiling from Cell-Free DNA

A retrospective observational study applied a 92-gene targeted sequencing panel to liquid biopsy samples from 39 Cancer of Unknown Primary (CUP) patients. The dataset, authored by Roberta Roncarati and last updated in June 2026, analyzes circulating cell-free DNA alongside paired germline DNA to identify somatic, germline, and CHIP-related variants.

Use Cases

• Identify actionable mutations for therapy selection based on the 44 clinically relevant variants reported.
• Analyze pathway dysregulation in CUP based on mutated genes involved in cell-cycle regulation, receptor tyrosine kinase signaling, and NOTCH pathways.
• Distinguish somatic from germline and CHIP-associated variants based on the paired ccfDNA/gDNA analysis methodology described.
• Investigate recurrent genetic alterations based on the 15 genes with recurrent alterations, including canonical hotspot mutations.

Strengths

• Analyzes a clinically challenging cohort of 39 Cancer of Unknown Primary (CUP) patients.
• Profiles variants across a targeted panel of 92 CUP-specific genes.
• Includes paired germline DNA analysis for 17 patients with CHIP assessment to aid variant interpretation.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is very small at 55.3 KB, indicating limited scope.

Provenance

Source

figshare

Collection Method

Retrospective observational study applying targeted sequencing to liquid biopsy samples.

Freshness

Last updated 2026-06-03 04:52:48; freshness should be verified.