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Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices

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Published on: March 26, 2018

Hydrogel beads for enhanced nucleic acid analysis in complex fluid matrices.

Lokman Alpsoy^1,2, Stephan Tieu¹, Sina Dehestanizad¹

¹Department of Microsystems Engineering (IMTEK), Chemistry & Physics of Interfaces, University of Freiburg, 79110 Freiburg im Breisgau, Germany. ruehe@imtek.de.

|July 23, 2025

Summary

We developed a hydrogel bead platform to capture cell-free DNA (cfDNA) for cancer detection. This sensitive method achieves a low detection limit, offering a promising tool for disease diagnosis.

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Area of Science:

Biomaterials Science
Molecular Diagnostics
Cancer Research

Background:

Cell-free DNA (cfDNA) released from tumors is a valuable biomarker for cancer detection.
Existing methods for cfDNA analysis often require complex purification steps and lack sufficient sensitivity.
A need exists for a simplified and highly sensitive platform for cfDNA biomarker detection.

Purpose of the Study:

To develop a functionalized hydrogel bead platform for efficient capture of cfDNA.
To utilize this platform for sensitive detection of cancer-associated mutations in biological samples.
To establish a novel approach for early cancer diagnosis using cfDNA biomarkers.

Main Methods:

Fabrication of hydrogel beads with incorporated probes, magnetic nanoparticles, and oligonucleotide barcodes via photo-cross-linking in a microfluidic system.
Utilized C, H-insertion cross-linking (CHic) for bead generation.
Demonstrated detection of a specific breast cancer mutation (c.1633G>A) in MCF-7 cells using fluorescently labeled DNA in various biological matrices (PBS, serum, whole blood).
Employed polymerase chain reaction (PCR) for amplification of captured cfDNA sequences.

Main Results:

Successfully developed hydrogel beads with covalently incorporated probes (HBP) for cfDNA capture.
Demonstrated the detection of a target mutation sequence in phosphate-buffered saline, serum, and whole blood.
Achieved a highly sensitive detection limit as low as 0.36 ng mL⁻¹, surpassing existing literature values.
Showcased direct PCR amplification from captured DNA on beads, eliminating purification steps.

Conclusions:

The functionalized hydrogel bead platform offers a sensitive and simplified approach for cfDNA detection.
This technology holds significant promise for non-invasive cancer diagnosis and monitoring.
The platform's versatility and high sensitivity suggest potential applications in diagnosing various diseases.