Single‐tube two‐pronged approach using both cell‐free DNA and RNA for multimodal biomarker tests at the time of biopsy

Abstract

Abstract The emergence of noninvasive liquid biopsy procedures as an alternative to surgical biopsies has fueled an intensive research effort and investment into the detection of cell‐free disease biomarkers. By pairing next‐generation sequencing (NGS) and RT‐qPCR technologies on cell‐free DNA (cfDNA) and RNA (cfRNA), respectively, we have established and validated a high‐throughput and quick‐turnaround workflow for highly sensitive detection of genomic alterations using a single tube of blood. This emphasizes the importance of our cfDNA/cfRNA recovery and enrichment knowhow to maximize the chance to capture relevant rare biomarkers. On the cfDNA‐NGS axis, sensitivity and specificity of 95% and 98% were recorded for somatic variants of ≥1% VAF, with high concordance observed between the in‐house and orthogonal assays. Overall accuracy for the cfRNA and RT‐qPCR portion of the workflow was >95%. Real‐world data of patients underwent the two‐pronged testing scheme revealed dramatic beneficial outcomes guided by genomic‐matched treatments. When implemented at the time of biopsy to expedite treatment decision‐making in the earliest possible way, the single‐tube two‐pronged approach can effectively reduce time to treatment initiation by about 70%. The cfDNA–cfRNA paired test is suitable for implementation in routine clinical decision‐making to maximize the benefit without delay.

Keywords

• cell‐free DNA
• cell‐free RNA
• liquid biopsy
• NGS
• RT‐qPCR
• time to treatment initiation