Targeted Molecular Profiling of Circulating Cell-Free DNA in Patients With Advanced Hepatocellular Carcinoma

Abstract

Purpose: Next-generation sequencing (NGS) of tumor-derived, circulating cell-free DNA (cfDNA) may aid in diagnosis, prognostication, and treatment of patients with hepatocellular carcinoma (HCC). The operating characteristics of cfDNA mutational profiling must be determined before routine clinical implementation.

Methods: This was a single-center, retrospective study with the primary objective of defining genomic alterations in circulating cfDNA along with plasma-tissue genotype agreement between NGS of matched tumor samples in patients with advanced HCC. cfDNA was analyzed using a clinically validated 129-gene NGS assay; matched tissue-based NGS was analyzed with a US Food and Drug Administration-authorized NGS tumor assay.

Results: Fifty-three plasma samples from 51 patients with histologically confirmed HCC underwent NGS-based cfDNA analysis. Genomic alterations were detected in 92.2% of patients, with the most commonly mutated genes including TERT promoter (57%), TP53 (47%), CTNNB1 (37%), ARID1A (18%), and TSC2 (14%). In total, 37 (73%) patients underwent paired tumor NGS, and concordance was high for mutations observed in patient-matched plasma samples: TERT (83%), TP53 (94%), CTNNB1 (92%), ARID1A (100%), and TSC2 (71%). In 10 (27%) of 37 tumor-plasma samples, alterations were detected by cfDNA analysis that were not detected in the patient-matched tumors. Potentially actionable mutations were identified in 37% of all cases including oncogenic/likely oncogenic alterations in TSC1/2 (18%), BRCA1/2 (8%), and PIK3CA (8%). Higher average variant allele fraction was associated with elevated alpha-fetoprotein, increased tumor volume, and no previous systemic therapy, but did not correlate with overall survival in treatment-naïve patients.

Conclusion: Tumor mutation profiling of cfDNA in HCC represents an alternative to tissue-based genomic profiling, given the high degree of tumor-plasma NGS concordance; however, genotyping of both blood and tumor may be required to detect all clinically actionable genomic alterations.

FIG 1.

OncoPrint of the most frequently altered genes in 51 cfDNA samples from patients with histologically confirmed HCC. The average variant allele frequency detected per sample is highlighted in the top bars. Select clinicopathologic parameters are shown below. AFP, alpha-fetoprotein; cfDNA, cell-free DNA; HCC, hepatocellular carcinoma; VAF, variant allele fraction.

FIG 2.

Prevalence of genomic alterations identified in the MSK cfDNA cohort compared with a previously published cohort of HCC tumors analyzed using tissue-based tumor genomic profiling. AXIN1 and BAP1 were not covered by MSK-ACCESS platform. ^aOnly one exon of JAK1 and ARID2 were covered by MSK-ACCESS. cfDNA, cell-free DNA; MSK-ACCESS, MSK-Analysis of Circulating cfDNA to Examine Somatic Status; N/A, not available.

FIG 3.

(A) Fraction of genomic alterations detected (green) versus not detected (gray) in cfDNA that were previously called in tumor tissue-based genomic profiling for each individual patients who had both cfDNA (MSK-ACCESS) and tumor (MSK-IMPACT) genomic profiling. (B) Total number of alterations called in cfDNA (green) or not called (gray) that were previously identified in tissue. Orange bars indicate alterations detected in plasma but not previously identified by MSK-IMPACT analysis of tumor tissue. Of note, samples 2 and 22 were from the same patient. cfDNA, cell-free DNA; MSK-ACCESS, MSK-Analysis of Circulating cfDNA to Examine Somatic Status; MSK-IMPACT, MSK-Integrated Mutation Profiling of Actionable Cancer Targets.