Four applications of dPCR fundamental to cancer genomics

Genomic technologies are a driving force shaping the evolution of cancer genomics (1). More and more, researchers need revolutionary tools that help them comprehensively understand material genetic and epigenetic changes that cause cancer and develop more effective and personalized diagnosis and treatment approaches (2).

Although in recent years scientists have made significant progress in cancer genomics, further research is needed to:

• Understand the role of genomic diversity observed in cancers
• Analyze the stages of cancer development and changes that initiate this development
• Identify prognostic or predictive actionable variants for potential use in cancer predisposition screening or therapy management

To make progress in these areas, scientists have used various PCR technologies to analyze cancer-causing changes better. Digital PCR has, so far, proved superior to the rest in the accurate detection and absolute quantification of cancer-specific gene alterations while speeding up time to insight. Unsurprisingly, researchers are beginning to recognize and embrace its abundant potential for unlocking answers to complex and everyday research questions in various applications.

Digital PCR in a nutshell

This third-generation PCR method enables precise detection and absolute quantification of nucleic acid, including DNA, cell-free DNA (cDNA), and RNA, using limiting dilution and Poisson distribution analysis, and end-point PCR (3). Designed to overcome conventional PCR technologies' limitations, it offers several advantages over older PCR generations, with greater sensitivity, reproducibility, precision, accuracy, and resistance to inhibitors while being simple, fast, and cost-effective.

Using dPCR in cancer genomics

Applications of dPCR in mutation and copy number variation (CNV) analysis, fusion gene analysis, and DNA methylation analysis makes dPCR a powerful technology and an invaluable tool that you can rely on at critical stages of cancer genomic research. The method is suitable for finding genetic changes in the tumor genome, identifying the role of cancer-specific fusion genes, and understanding cancer-related epigenetic changes.

Four research areas in cancer genomics that are ideal for dPCR analysis

1. Mutation and CNV analysis for detecting genetic variants that matter: dPCR supports quick and accurate detection of cancer-causing somatic mutations and CNVs, in turn, helping with mutation and copy number profiling to provide insights into changes that result in cancer starting and progressing.
2. Fusion gene analysis for identifying the role of cancer-specific fusion genes: dPCR performs reliably well at the accurate, specific, and sensitive detection of fusion genes, making it requisite for investigating cancer-driver genes.
3. DNA methylation analysis for understanding cancer-related epigenetic changes: dPCR enables the accurate detection and absolute quantification of methylated DNA, highlighting its utility in evaluating epigenetic mechanisms of cancer.
4. Quality control of next-generation sequencing (NGS) data: dPCR can be employed as a complementary technique to validate and calibrate NGS data, particularly for quantifying genetic alterations accurately and assessing the sensitivity and specificity of NGS assays.

How can you get the most out of your dPCR in cancer genomics?

dPCR tools with a fully integrated system and high-degree multiplexing capabilities bring greater simplicity, efficiency, and speed into your cancer genomics workflows.

In addition, for precisely, accurately, and rapidly detecting and quantifying cancer-related DNA mutations and gene analysis, you can rely on commercially available dPCR assays that serve this function with superior specificity, sensitivity, and multiplexing functions for a seamless workflow.

Likewise, you can consider dPCR assays that support the accurate and rapid detection of copy number alterations and mutations for applications in CNV analysis in understanding cancer genomes. 

With a focus on hallmark mutations within specific genes, dPCR allows researchers to investigate samples in multiplex reactions, providing faster and more efficient analysis of the most important cancer-related genes.

With these capabilities, researchers can, in turn, address crucial questions surrounding biomarker validation, orthogonal validation of next-generation sequencing, resistance monitoring, drug monitoring, tumor characterization, and more. The good news is that we’ll add new pan-cancer assays to our digital PCR portfolio in 2024.

The future of cancer genomics relies on today’s laboratory technologies, one of which every researcher looking to ramp up their cancer research efforts should prioritize is dPCR. Find the dPCR tools to support your cancer genomics workflow needs here.

Reference:

1. Tran B, Dancey JE, Kamel-Reid S, et al. Cancer genomics: technology, discovery, and translation [published correction appears in J Clin Oncol. 2012 Apr 1;30(10):1149]. J Clin Oncol. 2012;30(6):647-660. Published 2012 April 1.
2. “Cancer Genomics Overview” National Cancer Institute. n.d. 
3. Crucitta S et al. Comparison of digital PCR systems for the analysis of liquid biopsy samples of patients affected by lung and colorectal cancer. Clinica Chimica Acta 2023; 541: 117239.