TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline...

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Targeted therapies require molecular profiling to identify specific DNA mutations (germline and somatic).
• Classifying tumors by DNA alterations is increasingly important for off-label targeted therapy prescription.
• Distinguishing somatic from germline mutations is critical for appropriate treatment selection.

Purpose of the Study:

• To analytically validate TumorNext, a custom NGS panel for detecting various DNA alterations in 142 cancer-related genes.
• To validate the Affymetrix OncoScan platform for high-resolution copy number variant detection.
• To establish a combined NGS and array approach for precise tumor molecular profiling and identification of hereditary cancer "second hits".

Main Methods:

• Analytical validation of a custom probe-based NGS tumor panel (TumorNext) for single nucleotide variants, insertions/deletions, gene fusions, and structural variants.
• Utilized a matched control and custom bioinformatics pipeline for somatic-germline mutation differentiation.
• Validated Affymetrix OncoScan array technology for copy number variant detection (amplifications, hemizygous deletions).
• Tested 170 formalin-fixed paraffin-embedded (FFPE) tumor samples with the NGS panel and 80 FFPE samples with the OncoScan platform.

Main Results:

• TumorNext accurately detects single nucleotide variants, small insertions/deletions in 142 genes and structural variants in 15 oncogenes/tumor suppressors.
• The assay successfully differentiates between somatic and germline mutations.
• OncoScan effectively detects single copy amplifications and hemizygous deletions.
• Analysis of previously characterized samples demonstrated the utility of the combined approach, highlighting cases where germline status was critical for therapy decisions.

Conclusions:

• The validated TumorNext NGS panel combined with OncoScan array technology provides a comprehensive molecular profiling solution.
• This approach enables precise classification of DNA alterations, distinguishing somatic from germline mutations.
• The combined strategy is valuable for guiding targeted therapy selection and identifying the "second hit" in hereditary cancer patients.