Analysis of tissue and circulating tumor DNA by next-generation sequencing of hepatocellular carcinoma.

Abstract

298 Background: Hepatocellular carcinoma (HCC) has limited treatment options. Molecular analysis of its mutational landscape may enable the discovery of new treatment option.However, biopsy is not routinely performed in HCC and involves risks. The utility of analyzing cell-free circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) is not established. Methods: We performed 32 ctDNA NGS and 10 tissue NGS analyses in 26 patients with advanced HCC (January 2015 – October 2015). ctDNA analysis (54 to 70 genes) was performed using Guardant 360, which detects single nucleotide variants, amplifications, fusions, and specific insertion/deletion mutations. The mutant allele fraction for detected alterations was calculated relative to wild type in ctDNA. Tissue NGS was performed using Foundation One or Molecular Health. The study ws conducted in accordance with UCSD Moores Cancer Center Institutional Review Board requirements. Results: Among 32 ctDNA NGS, at least one genomic alteration (excluding variants of uncertain significance (VUS)) was discerned in 27 samples (84.3%) (average = 2.1 alterations per patient [range, 0-5]) with a median mutant allele fraction of 0.92% (range, 0.06% - 40.57%). Ten patients had both ctDNA NGS and tissue NGS. The median time difference between the date of tissue and ctDNA NGS testing was 450 days (range, 29 – 876 days), possibly reflecting the challenge with doing a second tissue biopsy at the time of relapse. The most commonly mutated gene was TP53 (16 samples, 50.0%), followed by CTNNB1 (8 samples, 25.0%), ARID1A (6 samples, 18.6%), EGFR (4 samples, 12.5%) and MYC (4 samples, 12.5%). Amplification was observed in 11 genes, including CDK4, CDK6, CCNE1, EGFR, ERBB2, FGFR1, KRAS, and MYC. No fusions or indels were observed. At least one potentially actionable alteration was observed in 20 of the 26 patients (76.9%). In two patients treated on the basis of the ctDNA alterations alone, a response was seen. Conclusions: ctDNA profiling is feasible in advanced HCC, and may provide a tissue biopsy-free alternative in these difficult-to-biopsy patients. Further study of clinical validity and utility is ongoing.