CleanPlex NGS Panels – The Most Sensitive Solution for Genomic Profiling of CTCs

Circulating tumor cells (CTCs) are released into the bloodstream from primary cancer, metastasis, and even from a disseminated tumor cell reservoir. Since CTCs can give rise to new metastatic lesions and metastases are responsible for most cancer-related deaths, analysis of CTCs is important and allows investigation of cancer cell biomarkers and mutational status using a non-invasive approach.

There are a wide range of instruments and methods for capturing, enriching, and enumerating CTCs. Once isolated, CTCs can be studied using next-generation sequencing (NGS) to obtain their genomic profiles. Targeted sequencing of CTCs using amplicon-based NGS panels is an ideal approach because the workflow is simple to implement and requires little amount of input DNA.

The CleanPlex® OncoZoom® Cancer Hotspot Panel is a multiplex PCR-based targeted sequencing assay designed for rapid detection of somatic mutations across 2,900+ hotspot regions of 65 oncogenes and tumor suppressor genes. Sequencing-ready libraries can be prepared using a single-tube workflow in just 3 hours. The panel is optimized to deliver data with high on-target performance and high coverage uniformity to ensure efficient use of sequencing reads.

Case Studies of Single-Cell Applications

RareCyte & Mayo Clinic:


In collaboration with the expert teams at RareCyte and Mayo Clinic, CTCs were visually identified using the CyteFinder® Instrument and were mechanically retrieved with the CytePicker® Module for genomics analysis. Cells were lysed in a PCR-compatible lysis buffer without whole genome amplification, and the lysate were used to prepare targeted NGS libraries using the CleanPlex OncoZoom Cancer Hotspot Panel. This approach resulted in libraries with excellent and consistent coverage and low error frequencies, enabling efficient and accurate assessment of somatic mutations in CTCs.

The Complete Picture: Cell free and single CTC sequencing from a single tube

Download the RareCyte and Paragon Genomics flyer for using RareCyte’s CTC assays and CyteFinder Instrument paired with Paragon’s CleanPlex NGS Technology to reliably measure somatic mutations from single circulating tumor cells (CTCs) and plasma.

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Stanford University & RareCyte

Prof. Lowe from Stanford University along with colleagues from RareCyte, Inc performed a study to identify and characterize Effusion Tumor Cells (ETCs) from malignant pleural effusions in patients with metastatic lung adenocarcinoma. In this study, researchers modified and applied a CTC testing method to examine malignancies from pleural effusion specimens. To generate Next-Generation Sequencing libraries, cell lysates were used as template with the CleanPlex OncoZoom Cancer Hotspot NGS Panel. They retrieved high-quality sequencing results with great coverage uniformity and high per variant sensitivity. In this study, the authors developed a novel ETC-testing assay that detected epithelial malignancies in pleural effusions with 89.5% sensitivity and 100% specificity. Molecular profiling of ETCs showed promising concordance with their respective clinical molecular findings.

Identification and Characterization of Effusion Tumor Cells (ETCs) From Remnant Pleural Effusion Specimens

Download publication from Cancer Cytopathology demonstrating CleanPlex OncoZoom Cancer Hotspot Panel’s single-cell application with body fluids from pleural effusion

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Technical Note

A High-Performance Solution Combining CleanPlex® OncoZoom® Cancer Hotspot Panel and SOPHiA AI for Rapid Characterization of Somatic Mutations

Download our joint technical note with SOPHiA GENETICS to see the full dataset demonstrating CleanPlex’s superior performance.

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Amplicon-based targeted sequencing of single circulating tumor cells

Download RareCyte poster at AMP 2019 demonstrating CleanPlex OncoZoom Cancer Hotspot Panel’s superior single cell level sensitivity.

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User Guide

CleanPlex® OncoZoom® NGS Panel for Single Cell User Guide

Download the User Guide specifically designed for running our Oncozoom Panel with Single Cell level input

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Interested in Custom Panels? 

CleanPlex Custom NGS Panels offer excellent performance and high level of customization to help you build smarter NGS assays. To create a custom panel for single cell applications, schedule a free consultation below.

Request a Custom Panel Consultation for your Circulating Tumor Cell targeted sequencing projects.