Abstract 528: Automated liquid biopsy pan-cancer genomic profiling panel demonstrates utility for screening of targeted biomarkers
Authors: Frady Lauren , Unselt Desiree , Pufky John , Torres Fernando , Sims Jennifer , Mason Jennifer 
Published: June 2022

Background: Liquid biopsy testing has demonstrated the utility of capturing the heterogeneity of solid tumors and relevant actionable mutations using a less invasive sample collection method. The Genexus™ Integrated Sequencer provides a viable pathway to deploy an automated platform for a sensitive pan-cancer liquid biopsy assay to meet the needs of quick turn-around and cost effectiveness for multi-site implementation. The Oncomine™ Precision Assay GX (OPAGX) is an amplicon-based next-generation sequencing (NGS) assay that enables detection of biomarkers across 50 genes from both solid tissue and liquid biopsy samples. OPAGX uses AmpliSeq™ HD technology which includes unique molecular tags for sequencing error correction and increased sensitivity. The assay’s detection of hotspot mutations was evaluated for liquid biopsy samples.

Methods: Automated library preparation was completed on the Genexus™ Integrated Sequencer using 20 ng of cfTNA derived from plasma or from well characterized control samples (Acrometrix, Agilent, Horizon, and SeraSeq). After reverse transcription was completed, gene targets of interest were amplified from DNA and cDNA. Amplicons were labeled with dual molecular barcodes during library preparation. Subsequently, libraries were bead normalized, pooled, and sequenced on a GX5™ chip to a targeted depth of 12,000,000 reads per sample. Sensitivity and positive predictive value were examined by evaluating the correctness of calling true positive variants compared to false negative and false positive variant calls, respectively. Precision and limit of detection (LoD) were examined by evaluating the concordance of variants across replicate samples with the range of AF between 0.1% - 35% for SNVs and 0.2% - 15% for insertions and deletions. Specificity and accuracy were examined by evaluating the correctness of calling true negative variants compared to false positive and all other variant calls, respectively.

Results: Accuracy was 98% for SNVs and 100% for insertions and deletions above 0.25% allele frequency (AF). Sensitivity was 95% for SNVs and 81% for insertions and deletions above 0.5% AF. Specificity and PPV were 100% for SNVs and insertions and deletions above 0.1% AF. Intra-run precision was 95% for SNVs and 92% for insertions and deletions above 0.5% and 0.25% AF, respectively. Inter-run precision was 93% for SNVs and 76% for insertions and deletions above 0.5% and 0.25% AF, respectively. The estimated AF LoD was 0.6% for SNVs, which is slightly above the advertised 0.5% provided by the vendor. Additionally, CNV gain calls were 100% for ERBB2 above 0.25% AF, MET above 0.5% AF, and FGFR3 at all AFs.

Conclusions: The demonstrated performance of OPAGX presents a viable liquid biopsy platform which lays the foundation for global standardization of genomic profiling liquid biopsy samples with minimal nucleic acid input.

Citation Format: Lauren Frady, Desiree Unselt, John Pufky, Fernando Torres, Jennifer Sims, Jennifer Mason. Automated liquid biopsy pan-cancer genomic profiling panel demonstrates utility for screening of targeted biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 528.