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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
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
cell-free DNAnanopore, sequencingplasmapoint-of-needquality control

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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.