Liquid Biopsies for Pancreatic Cancer: A Step Towards Early Detection
Surinder K. Batra, Moorthy P. Ponnusamy in Gene Regulation and Therapeutics for Cancer, 2021
Circulating cell-free DNA (cfDNA) are degraded DNA fragments released into the blood plasma. cfDNA can be used to describe various forms of DNA which are freely circulating in the bloodstream, such as circulating tumor DNA (ctDNA) and cell-free fetal DNA (cffDNA) [3]. Circulating tumor DNA (ctDNA) originates specifically from tumor cells and potentially harbors tumor-associated genetic mutations that inherently provide a marker for disease progression and/or therapeutic response [4]. Many cell death mechanisms including apoptosis, necrosis, oncosis, and phagocytosis release cfDNA/ctDNA into the bloodstream. These molecules can be present in their free form circulating by themselves or in the intravesicular compartment of various cell-derived vesicles [4]. They can also be bound to a DNA binding protein (specific or nonspecific) and the multi-nucleosome complex during vascular transport [4, 5].
Great strides in precision medicine: Personalized oncology and molecular diagnostics
Priya Hays in Advancing Healthcare Through Personalized Medicine, 2017
Tissue biopsy has long served as the mainstay of cancer diagnosis, staging, and therapeutic decisions, with its role evolving from simple histologic examination to complex genetic analysis. Despite its utility, biopsy represents only a single time point from a single location, often proving inadequate at fully characterizing a malignancy and its evolution because nearby tissue might contain additional genetic information that would affect staging or treatment. Unfortunately, the invasive nature and inherent selection bias of biopsy limit its usefulness as a real-time monitoring tool. Newer technologies seeking to transcend this shortcoming include analysis of circulating tumor cells and their fragments, such as exosomes and DNA, in peripheral blood. A recent feature in Nature highlights advancements in the detection of circulating tumor DNA (ctDNA) for this purpose. This emerging methodology enables sequencing of DNA originating from lysed tumor cells present in a blood sample to follow tumor recurrence and to characterize genetic abnormalities that confer resistance (Ryder and Schmotzer, 2015, 443).
The Precision Medicine Approach in Oncology
David E. Thurston, Ilona Pysz in Chemistry and Pharmacology of Anticancer Drugs, 2021
The use of Circulating Tumor DNA (ctDNA) as a biomarker of cancer is another important concept, as it is assumed that free circulating DNA of this type must originate in a primary tumor somewhere in the body. ctDNA typically contains somatic mutations specific to a particular tumor type, and the exact sequence can provide useful information about the molecular state and stage of the disease. Such mutations include epigenetic changes such as DNA hypermethylation and also point mutations, which can all be quantified. As these DNA alterations are disease specific, it is possible to use ctDNA as a biomarker to diagnose and assess the prognosis of patients with cancer. Similarly, exosomes have emerged as a promising biomarker both in cancer diagnostics and treatment monitoring. Compared to CTCs they are abundant in bodily fluids, and the molecular information they carry makes them a potentially useful tool in providing information on the primary tumor. One of the most prominent uses of detecting circulating nucleic acids is in the identification of epigenetic changes, and this is covered in more detail in the section below.
Trends in molecular diagnostics: 12th European Meeting on Molecular Diagnostics, Noordwijk aan Zee, the Netherlands, 12-14 October 2022
Published in Expert Review of Molecular Diagnostics, 2023
Anne J.M. Loonen, Rob Schuurman, Adriaan J.C. van den Brule
The second day of the meeting covered topics in the areas of liquid biopsies, quality management, and automation and the role of molecular diagnostics in preventive medicine. The first session was opened by Ellen Heitzer (Medical University of Graz, Austria) who provided an overview of liquid biopsy diagnostics by focusing on technologies and applications in cancer. An interdisciplinary molecular tumor board was suggested in which specialists from pathology and genetics are combined for therapy decisions. Circulating tumor DNA 1) can serve as a response to therapy marker and 2) a marker to (de)escalate adjuvant treatment, and 3) recurrence is predictive for relapse. Interesting discussion followed with questions from the infectious disease specialists. In sepsis (bloodstream infection) targeted testing to detect microorganisms in blood is very difficult. Why does it work for tumors? Possibly it has a relation to the amount of target DNA present in the liquid sample. Liquid biopsy mutation detection is more successful in higher-stage cancer. Jaap Jan Boelens (Memorial Sloan Kettering Cancer Center, New York, U.S.A) discussed ways toward a predictable optimal immune reconstitution after stem cell transplantation (SCT). One size does not fit all, and results showed that CD4+ T-cell reconstitution is crucial in survival chances. Furthermore, it turned out that pulmonary microbiome (respiratory viruses) can predict outcome after SCT. Microbiome analysis should gain more attention in the clinic.
Genetic testing for the clinician in prostate cancer
Published in Expert Review of Molecular Diagnostics, 2020
Fernando López-Campos, Estefanía Linares-Espinós, Xavier Maldonado Pijoan, Gemma Sancho Pardo, Todd Mathew Morgan, Claudio Martínez-Ballesteros, Juan Martínez-Salamanca, Felipe Couñago
Molecular analysis of plasma DNA has gained prominence in recent years due to the noninvasive nature of this technique, which provides a dynamic image of molecular changes taking place in the tumor. The potential clinical applications for circulating tumor DNA (ctDNA) analysis are numerous, including risk stratification, determination of possible causes of treatment resistance, and selection of the most appropriate treatment, among other applications. Different platforms can also be used for ctDNA detection, including BEAMing, ddPCR, and next-generation sequencing (NGS), with excellent concordance between platforms [108], highlighting the potential value of ddPCR, a recently developed technology that utilizes Taq polymerase in a standard PCR reaction to amplify a target DNA fragment from a complex sample using pre-validated primer or primer/probe assays. In turn, the PCR reaction can be partitioned into thousands of individual reaction vessels prior to amplification and data acquisition at the reaction end point [109].
Progress in determining response to treatment in gastrointestinal stromal tumor
Published in Expert Review of Anticancer Therapy, 2020
Junaid Arshad, Jibran Ahmed, Ty Subhawong, Jonathan C Trent
Tissue-based molecular diagnostic testing for a targeted mutation is considered an integral part of the diagnosis and management of GIST. Detection of various mutations including KIT and PDGFRA can be performed by various methods including Sanger sequencing, next-generation sequencing (NGS), high-resolution melting analysis (HRM), allele-specific PCR, and pyrosequencing [78]. Although the tissue-based molecular testing is very effective and the current gold standard, it is invasive and expensive and requires a certain amount of tissue with an adequate percentage of tumor cells to produce a measurable yield [79]. The tissue-based testing involves the localized sampling of the tissue specimen, thus providing limited information about the intra-tumor (spatial) as well as inter-tumor heterogeneity (temporal). Tumor accessibility for various invasive procedures creates a risk of clinical complications, making repetitive biopsy an unfavorable option especially in patients with poor performance status and comorbid conditions. Moreover, the tissue-based samples obtained prior to the initial treatment are genetically different from the growing tumors on active treatment and may not harbor resistance mutations [80]. This has led to exploring other options of molecular testing such as circulating tumor DNA often referred to as ctDNA.
Related Knowledge Centers
- Apoptotic DNA Fragmentation
- Circulating Tumor Cell
- DNA
- Genome
- Lymph
- Necrosis
- Neoplasm
- Apoptosis
- Liquid Biopsy
- Nucleosome