Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan dPCR Liquid Biopsy Assays
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This document discusses the use of Next Generation Sequencing (NGS) and Digital PCR (dpcr) for detecting cancer-causing mutations in liquid biopsies, highlighting their complementary roles. The study confirms that both methods can accurately detect mutations at a frequency of 0.1%, enhancing the precision of cancer genotyping and monitoring. The findings suggest that integrating these techniques can lead to more effective and cost-efficient cancer treatment strategies.
Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan dPCR Liquid Biopsy Assays
- 1. 1Vidya Venkatesh, 2Yanchun Li, 2Kelli Bramlett, 1Dalia Dhingra, 1Richard Chien, 1Kamini Varma, 1Marion Laig 1Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080 2Thermo Fisher Scientific, 2130 Woodward, Austin, TX 78744 RESULTS Figure 1. Example of orthogonal Validation of KRAS G12D A. Next generation sequencing data generated with the Oncomine Lung cfDNAAssay was analyzed with the Torrent Suite Variant Caller Software. In this example, the data was visualized using the Integrative Genomics Viewer (IGV, Broad Institute) Software. B. Using the same sample, sequencing results were confirmed by digital PCR with TaqMan dPCR Liquid Biopsy Assays. The FAM cluster (blue) contains the mutant allele, the VIC cluster (red) contains the wild-type allele, and the yellow cluster represents no target in the reaction. Table 1. Variant Detection with OncomineTM cfDNA Assays and Digital PCR TaqMan dPCR Liquid Biopsy Assays were used for orthogonal validation of results obtained with three Oncomine cfDNA panels. Acrometrix plasmid controls spiked into wild-type genomic DNA were used as mutant template for testing. The template was fragmented to mimick cfDNA. *N/A: This mutation is not represented in the Oncomine Assay listed Figure 3. TaqMan Rare Mutation AnalysisFigure 2. Oncomine cfDNA Assays The Oncomine cfDNAAssays include targets identified by the OncomineTM Knowledgebase, a cancer genomics data resource, and reviewed by our trained professionals. Optimized analysis with variant caller removes PCR errors to increase sensitivity and specificity. Figure 4. Sample to Variant Data in Liquid Biopsy Clinical Research Thermo Fisher offers a unique value by combining the Ion sequencing platform with the QS3D dPCR system. It provides all the necessary tools to research cancer subjects throughout all the clinical stages: • Sequence and identify somatic mutations on primary tumors with Ion sequencing platforms • Perform orthogonal validation of low frequency somatic mutations with QS3D dPCR system. The QS3D system and our TaqMan validated assays provide unmatched sensitivity that confirms the validity of low frequency mutations obtained by sequencing • Quantifying the % of DNA containing the mutation in cell free DNA (cfDNA) in plasma with the QS3D system to study the efficacy of the targeted drug • Sequence metastatic samples, identify new driver mutations and repeat the steps described above NGS with Oncomine cfDNAAssays is used in the discovery step to identify mutations present in a sample. Digital PCR with TaqMan dPCR Liquid Biopsy Assaysis used for orthogonal verification and monitoring. Figure 5. WorkflowABSTRACT & INTRODUCTION The discovery of circulating tumor DNA (ctDNA) in blood, urine and other bodily fluids has led to a new type of non-invasive method of characterizing cancer-causing mutations, the liquid biopsy. With NGS technologies becoming increasingly sensitive, down to a Limit of Detection (LOD) of 0.1%, they are rapidly gaining traction as a valid assay for cancer genotyping and have potential to direct cancer treatment plans. The wide- angle view provided by NGS panels, combined with digital PCR’s zoomed-in precision detection of DNA provide a comprehensive picture of a cancer’s genetic makeup. By applying these complementary techniques at the appropriate time based on the disease type and stage, cancer treatment becomes quicker, more precise and more cost-effective in the future. NGS and digital PCR (dPCR) together provide a complete picture of the cancer genome. As part of our research, we wet-lab tested a subset of TaqMan dPCR Liquid Biopsy Assays corresponding to three Oncomine cfDNA panels. Synthetic plasmid (GeneArt® Gene Synthesis) carrying the mutation was spiked into wild-types genomic DNA to reflect a mutation rate of 0.1%. Wild-type genomic DNA was used as negative control. Thermal cycling was performed according to protocol for digital PCR using the QuantStudio 3D Digital PCR System (QS3D). In this study, we tested a pilot set of samples using AcroMetrix Oncology Hotspot Control and Horizon cfDNA Reference Standard with both NGS using Oncomine cfDNAAssays and digital PCR with TaqMan dPCR Liquid Biopsy Assays. Comparison of NGS and digital PCR results for the same sample showed excellent correlation in the low mutation range around 0.1%. This study confirms that digital PCR using QuantStudio 3D and TaqMan dPCR Liquid Biopsy Assays is effective as a method for orthogonal verification of NGS data using the Oncomine cfDNAAssays. Additionally, these assays offer a sensitive and precise solution for downstream mutation tracking over a time course. MATERIALS AND METHODS TaqMan dPCR Liquid Biopsy Assays were wet-lab tested using mutant plasmid (GeneArt® Gene Synthesis) spiked into wild-type genomic DNA as proof of principle that the assay detect 0.1% mutation frequency. For orthogonal verification experiments, input samples for sequencing and digital PCR were Horizon cfDNA Standard (0.1%) or AcroMetrix™ Oncology Hotspot Control (0.1%) spiked into genomic DNA. Input amount for sequencing was 20ng and input amount for digital PCR was 15ng. Reactions were performed according to protocol. Sequencing data was analyzed using Torrent Suite™ version 5.2 variant caller. dPCR data was analyzed using QuantStudio 3D AnalysisSuite Cloud Software. CONCLUSIONS In the present work, we tested Oncomine cfDNAAssays and TaqMan dPCR Liquid Biopsy Assays to detect mutations at a frequency of 0.1%. We showed that both Oncomine next generation sequencing and rare mutation analysis by digital PCR successfully detect 0.1% mutation frequency and can be used as complementary approaches. ACKNOWLEDGEMENTS We thank Christie Fakete, Lawreen Asuncion, Tom Bittick, Jared Solomon, Kerry Colligan and Rachel Formosa for reviewing this document. TRADEMARKS/LICENSING © 2017 Thermo Fisher Scientific Inc. All rights reserved All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. For Research Use OnIy. Not for use in diagnostic procedures. Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan dPCR Liquid Biopsy Assays Thermo Fisher Scientific • 5791 Van Allen Way • Carlsbad, CA 92008 • www.lifetechnologies.com A B Wet-lab tested TaqMan Assays for key somatic mutations plus the power of digital PCR on the QuantStudio 3D Digital PCR system combined with AnalysisSuite Cloud Software are an optimal workflow solution to routinely quantify cancer mutations at a frequency less than or equal to 0.1%. NGS verification Wet-lab verified dPCR Rare Mutation Analysis TaqMan Assays