Nucleic acid-based biomarkers play a crucial role in precision medicine. They serve as indicators for various biological states, ranging from disease predisposition to the effectiveness of therapeutic interventions. The widespread application of DNA and RNA biomarkers in various diseases requires rigorous studies to identify them, understand their functional significance, and validate their applicability in clinical settings.
Molecular biomarkers in cancer and neurodegenerative diseases
Cancer can be diagnosed and monitored through genetic biomarkers that identify chromosomal aberrations, genetic variants, and epigenetic alterations. Tumor tissue is the most analyzed sample type for cancer biomarkers, but non-invasive liquid biopsies from blood, urine, stool, saliva/buccal swabs, cerebrospinal fluid (CNF), and other body fluids are increasingly used for biomarker analysis. The FDA has approved several genetic biomarker tests from liquid and tissue biopsies for various cancer types to guide treatment decisions (1–2).
Meaningful progress has been made in the discovery and validation of biomarkers for neurodegenerative diseases as well. The expansion of biomarker sources – from tissue biopsies to blood and CNF – and types – from imaging to nucleic acid biomarkers such as genetic variants, gene expression signatures, methylated DNA, and miRNAs – underscores the evolution of diagnostic and monitoring tools for neurological conditions (3–4).
Challenges in molecular biomarker analysis
Achieving high sensitivity and specificity in detecting biomarkers, especially those at low abundance, presents a multifaceted challenge. This complexity arises from several inherent issues associated with biological samples and the technical limitations of current detection methodologies.
Biomarker sources, such as blood, serum, and plasma, contain a myriad of molecules, among which the target biomarkers might be present only in minuscule amounts. For instance, the percentage of circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA) can be as low as 0.01%, which necessitates detection methods that can identify these biomarkers with high sensitivity and specificity (5).
Another challenge is the heterogeneity in biomarker concentration between individuals and within the same individual over time. Biomarkers may also degrade or change their molecular form in samples due to processing or storage conditions, complicating their detection and quantification.
Advances in analytical technologies to discover and probe nucleic acid biomarkers have the potential to enable us to overcome many of these challenges.
A comprehensive suite of technologies for biomarker research
Technologies for DNA and RNA-based biomarker analysis from Applied Biosystems™ facilitate a continuum of research from discovery to targeted detection of relevant mutations.
- For biomarker discovery, Ion AmpliSeq™ next-generation sequencing (NGS) workflows and Clariom™ and Axiom™ microarray solutions enable unbiased queries across the genome to uncover new sequences or gene relationships.
- Once sequences of interest are identified, researchers can focus on medium-throughput analyses such as Sanger sequencing for defined regions or use TaqMan™ panels on array cards for analyzing gene sets.
- In situations where a higher level of precision and sensitivity is warranted, such as identifying ultra-rare mutations in cancer research samples or analyzing circulating tumor DNA (ctDNA) in liquid biopsies, the QuantStudio™ Absolute Q Digital PCR System is an ideal option. The system employs TaqMan assays in a one-step workflow, mirroring the ease of qPCR but with enhanced precision.
This comprehensive suite of technologies supports a seamless transition from broad exploration to pinpointed analysis for identifying and verifying critical biomarkers for your research needs.
Explore tools for nucleic acid-based biomarker discovery and analytical validation
In this ebook, we explore the types and relevance of various molecular biomarkers and the relevant technologies to discover and evaluate them in cancer and neuroscience research.
What to expect:
- An introduction to nucleic acid-based biomarkers – learn about biomarker types and their sources
- In-depth case studies and research examples in cancer and neuroscience that showcase the latest methodologies – apply these learnings in your biomarker research
- Interviews with investigators working at the forefront of biomarker research – get inspired to solve your research challenges
- An overview of Applied Biosystems technologies for various types of biomarker analysis – find the right method for your analysis
Click here to download ebook.
For research use only. Not for use in diagnostic procedures.
References:
- Sarhadi VK, Armengol G. Molecular biomarkers in cancer. Biomolecules. 2022;12(8):1021.
- Martins I, et al. Liquid biopsies: Applications for cancer diagnosis and monitoring. Genes (Basel). 2021;12(3):349.
- Jeromin A, Bowser R. Biomarkers in neurodegenerative diseases. Adv Neurobiol. 2017;15:491-528.
- Doroszkiewicz J, Groblewska M, Mroczko B. Molecular biomarkers and their implications for the early diagnosis of selected neurodegenerative diseases. Int J Mol Sci. 2022;23(9):4610.
- Peng Y, Mei W, Ma K, Zeng C. Circulating tumor DNA and minimal residual disease (MRD) in solid tumors: Current horizons and future perspectives. Front Oncol. 2021;11:763790.
© 2024 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.
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