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DNA Isolation

DNA Isolation

DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.

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Updated: Sep 13, 2025

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Rescue of Low-Yield DNA Samples for Next-Generation Sequencing Using Vacuum Centrifugal Concentration in a Clinical

Lau K Vestergaard¹, Nicolai S Mikkelsen¹, Douglas V N P Oliveira¹

¹Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, DK-2730 Herlev, Denmark.

|July 29, 2025

Summary

Concentrating low-yield DNA from clinical samples using vacuum centrifugation is effective for next-generation sequencing (NGS) cancer diagnostics. This method ensures sufficient DNA levels without altering the crucial mutational profile for accurate disease management.

Keywords:

cancer clinical diagnosis linear regression models low-yield DNA next-generation sequencing targeted therapeutics vacuum centrifugation

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Last Updated: Sep 13, 2025

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

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Published on: November 10, 2009

DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation

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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

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Published on: July 28, 2017

Area of Science:

Oncology
Molecular Diagnostics
Genomics

Background:

Next-generation sequencing (NGS) is vital for cancer diagnostics and treatment selection.
Low DNA yield from clinical samples (e.g., FFPE, biopsies) poses challenges for accurate mutational profiling.
Standardized DNA extraction protocols can further reduce DNA concentration, complicating molecular analysis.

Purpose of the Study:

To evaluate the efficacy of vacuum centrifugation for concentrating low-yield DNA from formalin-fixed paraffin-embedded (FFPE) tissues.
To determine if DNA concentration via vacuum centrifugation impacts the mutational profile obtained through NGS.
To establish a method for improving DNA suitability for NGS in challenging clinical samples.

Main Methods:

DNA was extracted from five FFPE tissue blocks with initial concentrations below 0.2 ng/µL.
Vacuum centrifugation was employed to concentrate the extracted low-yield DNA samples.
Next-generation sequencing (NGS) analysis was performed on the concentrated DNA to assess mutational profiles.

Main Results:

Vacuum centrifugation successfully concentrated DNA from low-yield FFPE samples to sufficient levels for analysis.
NGS analysis of concentrated DNA revealed no compromise in the detected mutational profile.
The method demonstrated the feasibility of obtaining reliable mutational data from previously challenging samples.

Conclusions:

Vacuum centrifugation is a viable and effective technique for concentrating low-yield DNA in clinical oncology.
This method enhances the utility of NGS for cancer diagnostics, particularly with limited or degraded DNA samples.
The approach preserves the integrity of the mutational profile, ensuring accurate diagnostic and therapeutic insights.