Abstract 5035: Use of Streck nucleic acid BCT with plasma nucleic acid next-generation sequencing workflows

Abstract

Abstract Introduction: Liquid biopsies, which interrogate body fluids in search of analytes released by cancer cells, are becoming increasingly common in clinical oncology. Foremost among the technologies used are those that employ nucleic acids, such as cell-free DNA (cfDNA) and cell-free RNA (cfRNA). Currently, many NGS-based tests perform near the limit of assay detection, making the identification of critical mutations, fusions, or expression patterns like finding a needle in a haystack. Further hindering successful assay development is the variability in analyte availability and detectability that can occur prior to analysis due to blood collection, transport, and storage. Here, we demonstrate that Nucleic Acid BCT stabilizes draw-time levels of plasma nucleic acids for downstream use with NGS-based assays. Methods: Blood from self-proclaimed healthy donors was drawn into EDTA and Nucleic Acid BCT and stored at ambient temperature for up to 7 days before plasma isolation with a general double-spin protocol and storage at -80 °C. Plasma nucleic acids were isolated using the MAGicBead cfDNA Kit (Zymo, cfDNA) or the QIAamp Circulating Nucleic Acid Kit (QIAGEN, cfRNA). Library prep for cfDNA was carried out with added synthetic mutant spike-in oligonucleotides using the Illumina TruSight Tumor 15 kit (Illumina). cfRNA library prep was done with the NEBNext Ultra II RNA Library Prep Kit for Illumina with upfront rRNA depletion (New England Biolabs). Sequencing was performed using an Illumina NextSeq 500 system, and all data were saved in and analyzed with Illumina BaseSpace applications. Results: When blood samples were stored in EDTA tubes for up to 7 days, spiked mutant alleles (EGFRL858R, EGFRdel19, KRASG12D, and PIK3CAE545K) were no longer detected, likely due to a dilution of the spiked DNA concentration following the release of genomic DNA containing wildtype alleles during white blood cell degradation. In contrast, equivalent blood samples stored in Nucleic Acid BCTs displayed mutant allele frequencies reflective of draw-time levels. Interrogation of plasma RNA expression patterns in samples stored in Nucleic Acid BCT versus EDTA revealed similar results, where differentially expressed plasma transcripts in blood samples stored in EDTA were found at high levels (>1,000 transcripts) versus donor-matched blood samples stored in Nucleic Acid BCT (<50 transcripts). Conclusions: Our data demonstrate that Nucleic Acid BCT maintains mutant allele frequencies and the plasma transcriptome profile of blood samples during ambient temperature storage. This provides precious sample integrity during whole blood storage and transport, offering laboratories and assay developers reduced preanalytical variability for NGS-based analysis of gene mutations, fusions, indels, and the plasma transcriptome. Nucleic Acid BCT is for Research Use Only. Not for use in diagnostic procedures. Citation Format: Nicholas M. George, Lisa Bartron. Use of Streck nucleic acid BCT with plasma nucleic acid next-generation sequencing workflows [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5035.