As the most comprehensively studied liquid biopsy analyte, circulating tumor DNA (ctDNA) has been demonstrated associated with tumor burden. The study of ctDNA can provide information on the molecular profile and biological properties of individual pancreatic ductal adenocarcinoma (PDAC) tumors, helping to identify new therapeutic targets, new risk variants, and markers of tumor response. Alfa Cytology is a leading provider of pancreatic cancer (PC) research services. Here, we are providing the most commonly used techniques for ctDNA analysis, including targeted gene sequencing and droplet digital PCR (ddPCR). We specialize in PC genetic/molecular research and are committed to providing reliable and flexible services for PC basic research and precision medicine.
The potential of ctDNA in PDAC
The highly sensitive and specific genetic profiles of plasma DNA have been proved in previous studies, suggesting that ctDNA as a liquid biopsy may significantly improve current tumor diagnosis, early detection, tumor progression monitoring, and targeted therapy. PDAC is one of the most lethal diseases with a poor prognosis that may be related to disease recurrence and lack of effective surveillance methods. Therefore, liquid biopsy-based on ctDNA analysis is more promising for this specific cancer type. Recent advances have demonstrated the potential of ctDNA as prognostic, diagnostic, pharmacodynamic, and predictive biomarkers for PDAC and their utility in the identification of therapeutically targeted molecular alterations within individual patients.
Fig. 1 Origins of circulating tumour DNA in the blood. (Sivapalan, L., et al.,2021)
The service offering at Alfa Cytology
Nowadays, there is a wide range of techniques for ctDNA analysis. Among them, ddPCR and targeted deep sequencing are the most widely explored. Each method has its advantages and disadvantages. We can offer the optimal strategies based on the specific needs of the client's project.
- ddPCR
PDAC has a unique mutational profile in that KRAS mutations can be observed in >90% of PDAC and are probably the clonal mutations present in most PC cells. Moreover, ddPCR is featured by high sensitivity. Therefore, ddPCR is an attractive tool to detect ctDNA in PDAC patients by interrogating some KRAS hotspots. Using ddPCR, we can effectively detect a limited number of specific target variants, including KRAS and other hotspot mutations in PC. It is worth pointing out that the detection of KRAS mutations in plasma using ddPCR often does not meet high expectations.
- Targeted deep sequencing
ctDNA sequencing analysis of broad genomic target regions helps monitor tumor burden, assess genetic heterogeneity within tumors, investigate clonal expansion during disease progression, and so on. Targeted deep sequencing (>10,000X) enables the interrogation of tumor variants across a relatively broad range of genomic regions. Therefore, detection of ctDNA by targeted deep sequencing of large genomic regions has diagnostic advantages, especially for PDACs that typically carry KRAS hotspot mutations. Based on advanced platforms, we can provide cost-effective and accurate targeted deep sequencing (~10,000X average sequencing depth) data for PC, involving KRAS mutation determination, single nucleotide variants (SNVs) detection across broad genomic target regions, tumor burden monitoring, and among others.
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References
- Park, Gahee, et al. "Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients." Scientific reports 8.1 (2018): 1-10.
- Sivapalan, L., et al. "Molecular profiling of ctDNA in pancreatic cancer: Opportunities and challenges for clinical application." Pancreatology 21.2 (2021): 363-378.