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Published on: October 31, 2013
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Solid-State Nanopore Sizing for cfDNA Sample Quality Control in Point-of-Need Sequencing
Muhammad Asad Ullah Khalid1, Md Ahasan Ahamed1,2, Anthony J Politza3
1Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana 47408, United States.
ACS Sensors
|June 26, 2025
Summary
A novel solid-state nanopore device enables label-free quantification and qualification of cell-free DNA (cfDNA) outside the lab. This point-of-need quality control (QC) method shows high correlation with traditional assays, advancing personalized healthcare.
Area of Science:
- Biotechnology
- Genomics
- Analytical Chemistry
Background:
- DNA sequencing is crucial for disease diagnosis, but requires rigorous sample quality control (QC).
- Current QC methods are lab-bound, limiting the utility of portable sequencers for personalized healthcare.
- Cell-free DNA (cfDNA) analysis is vital for non-invasive diagnostics, necessitating accessible QC solutions.
Purpose of the Study:
- To develop and validate a solid-state nanopore device for label-free cfDNA quantification and qualification at the point of need.
- To assess the accuracy and reliability of the nanopore QC assay using a DNA marker and plasma samples.
- To demonstrate the potential of nanopore technology for on-site cfDNA assessment.
Main Methods:
- Utilized a solid-state nanopore device for label-free detection of cfDNA.
- Employed a 1 kbp double-stranded DNA internal marker for controlled quantification.
- Investigated nanopore diameters (6-19 nm) and acquisition times to optimize measurement consistency.
- Compared nanopore assay results with capillary electrophoresis (CE) for plasma cfDNA samples.
Main Results:
- Achieved consistent cfDNA measurements with a coefficient of variation (CV) below 15% across various nanopore sizes.
- Reduced measurement uncertainty to below 10% CV by analyzing data from multiple nanopores over extended periods.
- Demonstrated high correlation between the nanopore QC assay and traditional CE methods for plasma cfDNA.
- Validated the device's capability for controlled quantification and qualification of cfDNA.
Conclusions:
- The developed solid-state nanopore device offers a robust solution for on-site cfDNA quality control.
- This technology facilitates accurate and reliable cfDNA assessment at the point of need, enhancing personalized medicine.
- Nanopore-based QC assays hold significant promise for advancing accessible genomic diagnostics.
