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Updated: Jan 27, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
Published on: March 15, 2011
Considerations and quality controls when analyzing cell-free tumor DNA.
Gustav Johansson1,2,3, Daniel Andersson1, Stefan Filges1
1Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden.
Optimizing the liquid biopsy workflow is crucial for reliable circulating tumor DNA (ctDNA) detection. Quantitative PCR assays ensure robust ctDNA analysis for improved cancer diagnostics.
Area of Science:
- Oncology
- Molecular Biology
- Biochemistry
Background:
- Circulating cell-free tumor DNA (ctDNA) shows promise as a cancer biomarker.
- Ultrasensitive technologies allow detection of low mutant allele frequencies (<0.1%).
- Optimizing the entire liquid biopsy workflow is essential for reliable ctDNA analysis.
Purpose of the Study:
- To discuss key considerations for ctDNA detection in plasma.
- To demonstrate the utility of quantitative PCR (qPCR) for evaluating each step of the liquid biopsy workflow.
- To highlight the importance of quality control for robust and standardized ctDNA analysis.
Main Methods:
- Utilizing quantitative PCR (qPCR) assays to evaluate experimental steps.
- Assessing cellular DNA contamination and PCR inhibition.
- Analyzing the impact of DNA fragmentation and target sequence on ctDNA assay performance.
Main Results:
- qPCR effectively evaluates each step of the liquid biopsy workflow.
- Cellular DNA contamination and PCR inhibition can be detected.
- DNA fragmentation and target sequence influence ctDNA assay performance.
- qPCR aids in estimating sequencing depth and monitoring DNA loss.
Conclusions:
- Quality control assays are vital for developing robust and standardized ctDNA workflows.
- Optimized workflows facilitate the clinical implementation of ctDNA analysis.
- Reliable ctDNA detection enhances cancer diagnostics.
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