Blog | Apr. 10, 2023
Liquid biopsy with Plasma-Safe-SeqS
Recently we published an OncoBEAM clinical milestones timeline infographic with the first paper stretching back over a decade analyzing various clinical cancer samples for liquid biopsy. Several of the important references can be found on our Publications page.
Here we review and summarize several concordance studies comparing RAS mutation status in colorectal cancer (CRC) patients as determined in tissue by Standard of Care (SoC) testing in plasma using OncoBEAM technology.
The OncoBEAM Colorectal Cancer Panel 1 tests for 34 mutations in the BRAF, KRAS and NRAS genes, and was used in these studies to test plasma and occasionally tissue. The stated limit of detection (LOD) of the OncoBEAM test used is 0.02% MAF.
In Schmiegel et al. (Molecular Oncology 2017), a retrospective concordance study was performed across 98 patients from Australia and Germany. A total of 98 metastatic colorectal cancer (mCRC) patients had tissue testing via Sanger sequencing, pyrosequencing or NGS depending on the established institutional protocol, and OncoBEAM was used on tissue where the SoC method was discordant from the plasma OncoBEAM result.
This study found RAS mutations in tissue from 53% of the patient samples, and in plasma from 51% of the samples. The Positive Percent Agreement (PPA) between tissue and plasma was 90.4%, the Negative Percent Agreement (NPA) was 93.5%, and Overall Percent Agreement (OPA) was 91.8%. The authors conclude “The high concordance of plasma and tissue results demonstrates that blood‐based RAS mutation testing is a viable alternative to tissue‐based RAS testing.”
In Vidal et al. (Annals Oncol. 2017), a retrospective concordance study was performed in two institutions in Spain. RAS mutation status was determined in tissue by each institution’s SoC method (either the QIAGEN Therascreen KRAS RGQ PCR kit or the Roche cobas KRAS Mutation Test, both real-time PCR assays).
RAS mutations were detected in tissue from 48% of the 115 patient samples tested, and in plasma from 51% of the samples. The PPA between tissue and plasma was 96.4%, the NPA was 90.0%, and the OPA was 93.0%. The authors conclude “The high overall agreement between baseline plasma and tissue RAS mutation status demonstrated in more than 100 patients evaluated in our study supports the use of blood-based testing with OncoBEAM™ RAS CRC as a viable alternative to tissue SoC for determining RAS mutation status in mCRC patients treated in routine clinical practice.”
Internally at Sysmex Inostics we have conducted our own verification studies, and with prospectively collected samples from throughout Europe (specifically Germany, France, Belgium and Spain) of 135 patient samples where the Overall Percent Agreement (OPA) compared to OncoBEAM was 93.3%, and the PPA was 92.6% and the NPA was 94.0%. This data was presented at CSCO in 2017 (Jones et al.).
Outside of the United States Sysmex Inostics offers the CE-marked OncoBEAM RAS CRC kit used in conjunction with a Sysmex readout platform. Two concordance studies were performed by individual laboratories using this OncoBEAM RAS CRC kit. (More information about this system can be found online here.)
In Grasselli et al. (Annals Oncol. 2017) a retrospective-prospective concordance study between tissue and plasma RAS mutation status was carried out in 146 metastatic CRC patients from three hospitals in Spain, as part of a Phase II TTD ULTRA clinical trial (NCT01704703). The SoC method was real-time PCR for tissue, and 130 of the 146 tissue samples were analyzed by OncoBEAM RAS CRC as well.
The investigators foundRAS mutations in tissue from 37.0% of the patient samples by real-time PCR, whereas RAS mutations were detected in plasma in 39.0% of the patient samples by OncoBEAM RAS CRC. Interestingly, when 130 of the tissue samples were analyzed by OncoBEAM, 46.1% of the tissue samples harbored RAS mutations. The researchers note that a full 48% of their samples harbored RAS mutations at less than 1% MAF.
Of the 146 samples tested, OncoBEAM had 89.7% Overall Percent Agreement, with a Positive Predicted Value (PPV) of 84% and a Negative Predictive Value (NPV) of 93%. Their abstract concludes: “Plasma RAS determination showed high overall agreement and captured a mCRC population responsive to anti-EGFR therapy with the same predictive level as SoC tissue testing. The feasibility and practicality of ctDNA analysis may translate into an alternative tool for anti-EGFR treatment selection.”
This table summarizes these four datasets along with three others, and when analyzed together the meta-analysis determines an Overall Percent Agreement of 90.3% (PPA 88.7% and NPA 91.8%) across a total of 913 clinical samples.
For more information about how OncoBEAM enhanced digital PCR can help in your liquid biopsy studies, please contact us here.