MRD Detection Methodology
Assessment of minimal residual disease (MRD) is becoming an increasingly important tool for early detection of tumor recurrence and guiding treatment decisions in the management of solid tumors. Building on the insights of our previous article, which explored the unique challenges of detecting MRD in solid tumors and how recent genetic advances are addressing them, this article provides a more in-depth overview of the analytical flexibility of current MRD detection approaches.
Target Genes for MRD Detection
The landscape of genetic analysis for MRD detection is as diverse as the solid tumors themselves. Public databases such as the Genomic Data Commons (GDC) and the Catalogue Of Somatic Mutations In Cancer (COSMIC) compile mutation data from numerous studies, including both tumor cell culture models and patient-derived samples. These resources help identify key genes and recurrent genetic alterations specific to different tumor types, which can then be targeted through liquid biopsy approaches for MRD detection.
These genetic alterations can generally be classified into two major categories:
- Common driver mutations: Several genes are frequently mutated in solid tumors, particularly those involved in pathways that regulate tumor growth and survival. These cancer-related pathways are perfect targets for monitoring and therapy [1]. The probably most famous gene in this respect is TP53, which is considered one of the main genes with cancer driver mutations [2].
- Epigenetic alterations: Altered DNA methylation is a key indicator of epigenetic changes, as it involves modifications to the DNA that affect gene expression without altering the DNA sequence itself [3]. This process is crucial for regulating various biological functions and can be influenced by both genetic and environmental factors. Cancer-related epigenetic changes in genes can therefore be investigated via altered methylation patterns of circulating tumor DNA (ctDNA) [1,4].
NGS Panels for MRD Detection
ctDNA is a non-invasive biomarker used in liquid biopsy to assess MRD in solid tumors [5]. Released into the bloodstream as tumor-derived cell-free DNA, ctDNA carries tumor-specific mutations that can be detected and monitored using next-generation sequencing (NGS).
In NGS, a panel refers to a targeted set of genes or genomic regions that are sequenced with high sensitivity. These panels are designed to detect genetic mutations, structural variants, or other tumor-related alterations in a patient’s blood. The two main strategies for panel design are tumor-informed and fixed-panel approaches [6,7].
- Personalized (tumor-informed) assays utilize a patient’s specific tumor mutation profile to increase the sensitivity and specificity of MRD detection. By comparing a patient’s blood sample with the genetic profile of their primary tumor, these assays can detect even small traces of residual disease.
- Tumor-naïve, or fixed-panel assays provide a cost-effective and standardized alternative, targeting a predefined set of common cancer-associated mutations. While less personalized than tumor-informed approaches, fixed panels are broadly applicable and easier to implement across multiple patients.
NGS Sequencing Depth
In addition to panel design, sequencing depth is a critical factor in liquid biopsy and MRD assessment, as it directly affects the sensitivity and thoroughness of the analysis. At one end of the spectrum is deep sequencing of hotspot mutations, which provides high sensitivity for detecting low-frequency variants. At the other end is broad sequencing of marker genes, which provides a more comprehensive genetic overview. The optimal approach depends on the clinical context, such as tumor type, the desired balance between sensitivity and breadth, and resource availability.
- Broad sequencing coverage of wide gene range: Methods like whole genome sequencing (WGS) or whole exome sequencing (WES) capture a wide range of genetic alterations, providing a comprehensive view of tumor evolution and MRD. These methods identify not only single nucleotide variants but also structural variations, such as indels, copy number alterations and fusions, which can be clinically relevant [8].
- Deep sequencing of hotspot mutations: This targeted approach focuses on known oncogenic hotspots, allowing the detection of low-frequency mutations with high sensitivity (as low as 0.78 parts per million) [9,10]. By focusing on a limited number of well-characterized oncogenic mutations, it ensures high accuracy and minimal false positives. However, it may miss alterations outside the targeted regions [9].
In the recent development of personalized assays, both approaches actually complement each other [6,11]. There, broad sequencing methods can be used to gather a patient’s mutation profile. Once this profile is established, a personalized assay can apply deep sequencing to detect low-frequency ctDNA mutations, offering a more sensitive and targeted analysis of residual disease.
Conclusion
Incorporating MRD detection into the monitoring and treatment of solid tumors is a rapidly advancing field that holds great promise for improving patient outcomes. As highlighted in this article, genetic analysis via ctDNA, particularly through the use of NGS, is at the forefront of MRD detection. With ongoing advancements in technology and methodology, MRD detection in solid tumors could become a key component in precision oncology, helping to guide more personalized treatment strategies.
LIQOMICS & Our Services
At LIQOMICS, we support precision oncology with advanced MRD monitoring solutions based on ctDNA analysis and next-generation sequencing. We offer LymphoVista, a highly sensitive and specific ctDNA-based MRD test for lymphomas, along with an MRD monitoring assay for solid tumors, enabling precise, non-invasive disease tracking. Both tests use ctDNA analysis with NGS. Learn more about our services here, and get in touch to explore how we can support your needs.
Author: Lisa Baum, PhD, Bioinformatician and Data Scientist, LIQOMICS
Literature
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