1215P - Comparative analysis of cfDNA liquid biopsy and tumor-based next-generation sequencing (NGS) approaches

Background

NGS techniques can detect molecular alterations in cell-free DNA (cfDNA) isolated from plasma samples for biomarker discovery, diagnostics, and disease monitoring. We previously reported a 0.2% variant allele frequency (VAF) limit of detection (LOD) for single nucleotide variants (SNVs) and insertions and deletions (indels) with 98% and 99% accuracies and 91% and 83% sensitivities, respectively, for our cfDNA assay. To assess the clinical application of the cfDNA liquid biopsy, we compared findings with tumor-based NGS assays, including whole exome sequencing (WES) and RNA-seq.

Methods

A panel of 216 clinically actionable genes, including exonic and intronic regions, was used in the cfDNA assay. Commercial references and human cell lines were used for analytical validation. Our variant calling pipeline was used to analyze sequenced samples. WES, RNA-seq, and cfDNA analysis were performed on 65 matched patient samples. Gene fusions in cfDNA were validated with tumor RNA-seq data.

Results

Intersection was observed between traditional WES analysis and the developed liquid biopsy assay for 35.3% (23/65) patients. WES results were concordant with the cfDNA assay for a subset of mutations from the targeted gene panel for SNVs (sensitivity = 0.23) and indels (sensitivity = 0.29); for clinically actionable mutations, we observed a slightly stronger relationship (sensitivity = 0.35). The cfDNA assay identified an additional 66.2% and 31.4% SNVs and indels, respectively, within the clinically actionable gene panel compared to WES. With a LOD of 0.5% VAF, 95% sensitivity was observed for genomic fusion calling. The cfDNA assay detected clinically actionable fusion genes, such as EWSR1–ATF1.

Conclusions

While our WES and cfDNA analyses had low concordance, previous reports noted discordance in tumor DNA and cfDNA analyses due to tumor heterogeneity and other biological factors, such as cfDNA half-life and variations in shedding among clones. Our cfDNA panel also included genes from intronic regions and detected additional alterations not found by WES. These findings highlight the potential for this newly developed cfDNA assay to be used to guide clinical decision making.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

BostonGene, Corp.

Funding

BostonGene, Corp.

Disclosure

A. Yudina, S. Starikov, A. Efremov, D. Sookiasian, E. Nuzhdina, M. Chasse, T. Conroy, N. English, A. Love, D. Tabakov, A. Baisangurov, C. Tazearslan: Financial Interests, Personal, Full or part-time Employment: BostonGene, Corp.; Financial Interests, Personal, Stocks/Shares: BostonGene, Corp. S. Podsvirova: Financial Interests, Personal, Full or part-time Employment: BostonGene, Corp. N. Fowler: Financial Interests, Personal, Officer: BostonGene, Corp.; Financial Interests, Personal, Stocks/Shares: BostonGene, Corp.; Financial Interests, Personal, Leadership Role: BostonGene, Corp.; Financial Interests, Personal and Institutional, Research Funding: Celgene, Gilead, Roche; Financial Interests, Personal and Institutional, Speaker, Consultant, Advisor: Celgene, Gilead, Roche; Financial Interests, Personal, Full or part-time Employment: BostonGene, Corp. A. Bagaev: Financial Interests, Personal, Leadership Role: BostonGene, Corp.; Financial Interests, Personal, Full or part-time Employment: BostonGene, Corp.; Financial Interests, Personal, Stocks/Shares: BostonGene, Corp.