Liquid Biopsy – Circulating Tumor Cell Analysis at Single Cell Level

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

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. This panel has been validated by RareCyte, Mayo Clinic and Stanford University for single cell applications. 

In general, CleanPlex NGS Panels offer several advantages, such as the ability to directly amplify single cells without pre-amplification steps like whole genome amplification (WGA), and their ability to maintain high amplification uniformity while reducing biases and errors in variant calls. These features make CleanPlex especially suited for several high-precision applications, including:

1. Single-Cell Genomics: Since CleanPlex avoids WGA bias, it can accurately detect genetic variants at the single-cell level. This is crucial for studying rare cell populations or individual cells in heterogeneous samples, such as cancer research or developmental biology.
2. Cancer Research and Liquid Biopsies: CleanPlex can help detect low-frequency mutations and rare variants in circulating tumor cells (CTCs) or small subpopulations of cancer cells. It can also reduce false positives and false negatives, which is critical for early detection of cancer mutations and monitoring minimal residual disease (MRD).
3. Preimplantation Genetic Testing (PGT): The ability to directly amplify single cells makes CleanPlex useful in reproductive medicine for testing the genetic integrity of embryos. It can accurately detect aneuploidies or genetic mutations without the risk of introducing amplification biases, providing more reliable results for embryo selection.
4. Immunology and Autoimmune Disease Research: Single-cell analysis of immune cells, such as T-cells or B-cells, is often needed to understand immune responses. CleanPlex’s high amplification uniformity can enhance the detection of genetic variants involved in immune cell function, antigen receptor diversity, or clonal expansion.
5. Neuroscience and Brain Development Studies: Investigating the genetic makeup of individual neurons or glial cells in the brain can uncover insights into neurodevelopmental disorders or neurodegenerative diseases. CleanPlex’s accurate amplification from single cells supports studies on genetic mosaicism, somatic mutations, and neuronal diversity.
6. Rare Disease Research: For diseases caused by rare mutations or mosaicism, CleanPlex can offer higher sensitivity in detecting variants from single cells. This is particularly useful when studying rare genetic disorders where sample availability is limited or heterogeneity between cells needs to be precisely analyzed.
7. Forensic Analysis: CleanPlex’s ability to work with minimal DNA and avoid amplification biases makes it an excellent tool for forensic genomics, where DNA from single cells or low-quality samples is common. This can help in analyzing trace evidence with greater accuracy.