Cell-free DNA (cfDNA) is currently trending as a biomarker for liquid biopsy in several clinical applications, including oncology, organ and transplant medicine, and non-invasive prenatal testing (NIPT). cfDNA comprises various forms of unencapsulated DNA freely circulating the bloodstream, including circulating tumor DNA (ctDNA) and cell-free fetal DNA (cffDNA). Due to the small amount of cfDNA found in circulation, there is need to use efficient, highly sensitive technologies, such as NGS, to detect these biomarkers. However, the NGS workflow—isolation, library preparation, and sequencing—can present its own sensitivity challenges in clinical application. For example, with cfDNA extraction, the release of genomic DNA from lysed or apoptotic cells contaminates the limited amount of cfDNA in a sample, thereby diluting the concentration of the cfDNA used in an assay. This white paper discusses some of these challenges and opportunities to measure cfDNA and ctDNA from blood.
Nucleic acid isolation and purification is a fundamental requirement in biological research. High-quality DNA is essential for enabling scientists across a plethora of fields to conduct life science and medical research. Automation and technological advances in DNA isolation and purification have lowered the cost and time needed for DNA sequencing and diagnostics. This is driving extensive changes through those specialties where the utilization of nucleic acids has gone far beyond just the storage of genetic information and protein synthesis.
The ability to identify tumor genotype variations between patients, called interpatient heterogeneity, has driven recent therapeutic advances in oncology. The process can help predict the clinical response and guide both conventional and novel treatments. It can also inform clinical trial enrolment. Researchers and clinicians are now able to identify intratumoral heterogeneity: subpopulations of cancer cells with distinct genomes in different regions of tumor. These subpopulations can arise during tumor growth due to microenvironmental pressures such as nutrient availability, a reduced oxygen supply (hypoxia), or radio-, chemo-, or immune-therapy treatment (1).
Sequencing technologies provide the ability to characterize intratumor heterogeneity at diagnosis, monitor subpopulation dynamics during treatment, and identify the emergence of resistant cells during disease progression. However, interpatient and intratumor heterogeneity can pose challenges for the design and enrolment of patients onto clinical trials that use genomic selection criteria. These criteria can include the presence or absence of a specific mutation, for example, EGFR amplification (2).
>> Download the Full Application Note as a PDF
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