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Abstract 2276: Performance and cost comparison of circulating tumor DNA detection platforms. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose
The field of circulating cell free DNA (cfDNA) testing is quickly developing. Multiple platforms to detect hotspot mutations in ctDNA are available, including Bio-Rad droplet digital PCR (ddPCR), BioCartis Idylla, Roche COBAS z480 and Sysmex BEAMing. These platforms vary in the amount of plasma required, the method of ctDNA isolation, the number of hotspots analyzed, and the costs per sample. These factors can impact the applicability of a specific platform in the analysis of ctDNA.
In this study we compared these platforms in terms of sensitivity and total costs per sample.
Methods
The platform comparison was performed as follows:
1. Plasma from six metastatic colorectal cancer (mCRC) patients with known tissue KRAS mutation status was analyzed according to the manufacturers’ protocols.
2. Sensitivity was tested using six constructed reference samples with seven KRAS hotspot mutations at various total input (10ng, 50ng) and mutant allele frequencies (0%, 0.04%, 0.50%); each in four replicates.
3. Twelve mCRC patients were analyzed using equal amounts of ctDNA for each platform.
4. Total costs per sample were evaluated, including costs for consumables, technician hands-on time, equipment and maintenance.
Results
1. In six mCRC samples BEAMing (3ml plasma) detected 5/6 mutations, ddPCR and Idylla (both 1ml plasma) 4/6 mutations and COBAS z480 (2ml plasma) 3/6 mutations.
2. In constructed reference samples ddPCR (65%) and BEAMing (46%) yielded the highest sensitivity. With 10ng input BEAMing and COBAS z480 produced “Too little DNA” errors in 60% and 100% of cases, respectively.
3. In twelve mCRC samples, eight had more than 10ng ctDNA and four had less. All platforms were fully concordant for samples with more than 10ng input. Detection rate across twelve samples: Idylla detected 7/11 detectable mutations, COBAS z480 and BEAMing both detected 5/11, ddPCR detected 4/10.
4. BEAMing has the highest cost per sample (€486-€821) whereas ddPCR has the lowest cost per sample (€39-€298).
Conclusions
A direct comparison of ctDNA mutation detection platforms is complex and should take into account the differences in input and output specifications of the platforms.
Factors such as complexity of analysis (Idylla is a low complexity platform, whereas BEAMing requires more specialized training), total costs (varying from ddPCR to BEAMing), sensitivity (ddPCR and BEAMing yielded the highest sensitivity) and the number of mutations evaluated vary greatly between the platforms. All these factors influence ctDNA analysis and will have to be considered when choosing a specific platform for a specific (clinical) question, or when comparing results between studies.
Our data provide insight in the comparative performance of four commercial ctDNA analysis platforms, allowing future users to make an informed decision regarding a platform.
Acknowledgement
Powered by Health~Holland, Top Sector Life Sciences & Health, grant LSHM16047-H005.
Citation Format: Daan C. Vessies, Marjolein J. Greuter, Karlijn L. van Rooijen, Theodora C. Linders, Mirthe Lanfermeijer, Kalpana L. Ramkisoensing, Flore E. Grijseels, Boris van Doorn, Gerrit A. Meijer, Miriam Koopman, Veerle M. Coupé, Geraldine R. Vink, Remond J. Fijneman, Daan van den Broek. Performance and cost comparison of circulating tumor DNA detection platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2276.
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Abstract
Abstract
Purpose
Circulating cell-free tumor DNA (ctDNA) is rapidly gaining attention as a valuable biosource for the detection and diagnosis of multiple types of cancer. ctDNA can be easily obtained through a minimally invasive liquid biopsy. Multiple NGS-based methods have been developed specifically for application in liquid biopsies.
Before such methods can be implemented in clinical care, they need to be technically validated through measurement of independent reference standards. In the current project we technically validated the Roche AVENIO ctDNA Assay, which is based on the CAPP-seq technology [Newman AM, et al. Nat Biotechnol. 2016;34:547-55]. Its Targeted Kit interrogates 17 genes for Single Nucleotide Variants (SNVs), Insertions and Deletions (InDels), Copy Number Variations (CNVs) and gene fusions in a single workflow.
Methods
The detection of SNVs, CNVs, Indels and gene fusions was evaluated as follows:
- SeraCare Seraseq ctDNA Complete was analyzed in four replicates at 2.5%, 0.5% and 0.1% mutant allele frequency (AF), and at 50ng and 10ng input. This material contains SNVs, InDels, CNVs and gene fusions.
- An in-house characterized reference pool of patient plasma, containing SNVs and InDels at various AF (0.07% - 5.51%), was analyzed in four replicates at 50ng and 10ng input.
- Plasma and serum samples obtained from patients with tissue confirmed presence of CNV were used to validate the robustness of CNV detection. Twelve samples were selected to represent a range of background DNA (serum had 2-4 times higher wildtype DNA levels compared to plasma), amplification levels (CNV levels 1.4-fold to 4.2-fold by ddPCR) and total input (10-50ng cfDNA input).
- Plasma obtained from five patients with EML4-ALK gene fusion confirmed on tissue was used to further validate fusion detection.
Sequencing was performed on an Illumina NextSeq on High Output mode with sixteen samples per run (20-33M read pairs per sample).
Results
Sensitivity for detection of SNVs and InDels was 100% for all variants down to 0.18% AF when using 50ng input, and 50% for variants at 0.10% AF. For 10ng input the variants were detected down to 0.60% AF with sensitivity of 92%. For variants with AF between 0.07% and 0.53%, sensitivity was 67%.
Results from twelve plasma and serum samples obtained from patients with EGFR CNV were 100% concordant with ddPCR results. These results were confirmed in SeraCare samples at 10ng and 50ng input.
Sensitivity of fusion detection in SeraCare material was 100% for AF of 0.5% and 50ng input, and 38% for input of 10ng. No fusions were detected at 50ng or 10ng input for AF of 0.1%. We furthermore confirmed 3 out of the 5 fusions found in tissue.
Conclusions
We have determined the lower limits of detection for SNVs, CNVs and gene fusions. Sensitivity was dependent on DNA input with performance optimized at 50ng.
Our results confirm the feasibility of in-house use of the AVENIO ctDNA Targeted Kit for broad molecular profiling in liquid biopsies.
Citation Format: Daan C. Vessies, Theodora C. Linders, Kalpana L. Ramkisoensing, Petra M. Nederlof, Gerrit A. Meijer, Kim Monkhorst, Daan van den Broek. Technical validation of Roche AVENIO sequencing platform for liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1381.
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