Diagnostic Targeted Sequencing Panel for Hepatocellular Carcinoma Genomic Screening

Commercially available targeted panels miss genomic regions frequently altered in hepatocellular carcinoma (HCC). We sought to design and benchmark a sequencing assay for genomic screening of HCC. We designed an AmpliSeq custom panel targeting all exons of 33 protein-coding and two long noncoding RNA genes frequently mutated in HCC, TERT promoter, and nine genes with frequent copy number alterations. By using this panel, the profiling of DNA from fresh-frozen (n？=？10, 1495×) and/or formalin-fixed, paraffin-embedded (FFPE) tumors with low-input DNA (n？=？36, 530×) from 39 HCCs identified at least one somatic mutation in 90% of the cases.