Diagnostic Targeted Sequencing Panel for Hepatocellular Carcinoma Genomic Screening

Area of Science:

• Oncology
• Genomics
• Molecular Biology

Background:

• Commercially available targeted sequencing panels often fail to detect critical genomic alterations in hepatocellular carcinoma (HCC).
• Accurate genomic profiling is essential for understanding HCC development and for identifying potential therapeutic targets.

Purpose of the Study:

• To design and validate a novel AmpliSeq custom sequencing panel for comprehensive genomic screening of HCC.
• To assess the panel's performance in detecting somatic mutations and copy number alterations in both fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) HCC tumor samples.

Main Methods:

• Designed a custom AmpliSeq panel targeting key genes, TERT promoter, and copy number alteration regions in HCC.
• Performed targeted sequencing on DNA from 39 HCC cases (10 fresh-frozen, 36 FFPE) with varying input amounts.
• Benchmarked the panel's performance against whole-exome sequencing (WES) for mutation and copy number alteration detection.

Main Results:

• The custom panel identified at least one somatic mutation in 90% of HCC cases.
• Achieved high concordance with WES, detecting 98-100% of WES-identified mutations.
• Discovered additional somatic mutations missed by WES and showed 86% concordance for copy number alterations.

Conclusions:

• Established a cost-effective and efficient targeted sequencing assay for detecting a wide range of genomic alterations in HCC.
• The developed panel offers improved sensitivity and comprehensive coverage for HCC genomic profiling compared to standard methods.