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A tunable filter for high molecular weight DNA selection and linked-read sequencing.

Nicolas Milon1, Juan-Luis Fuentes Rojas2, Adrien Castinel3

  • 1CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France. abancaud@laas.fr and Adelis Technologies, 478 Rue de la Découverte, 31670 Labège, France.

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This study introduces a novel capillary-based technology for size selection of long DNA molecules, crucial for high-quality third-generation sequencing data. The method achieves sharp cut-offs and high yields, significantly improving genomic DNA representation.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioengineering

Background:

  • Third-generation sequencing demands long DNA molecules (>20 kbp) for quality data.
  • Existing purification technologies often have size selection thresholds below this requirement.

Purpose of the Study:

  • To develop and validate a novel capillary-based technology for tunable size selection of long DNA molecules.
  • To demonstrate the effectiveness of this technology for improving genomic DNA quality for sequencing.

Main Methods:

  • A capillary-based system with an electric field-controlled tunable size selection threshold (3-40 kbp).
  • Demonstration of sharp selection cut-off, high purification yield, and scalable throughput.
  • Development of an analytical model for filter actuation settings.
  • Application to size selection of high molecular weight genomic DNA from Cucumis melo L.

Main Results:

  • The technology provides a sharp size selection cut-off.
  • High purification yield and scalable throughput were achieved.
  • Size selection of melon genomic DNA enhanced N50 phase block size by a factor of 2 in linked-read sequencing data.

Conclusions:

  • The developed technology offers a versatile and effective solution for size selection of long DNA molecules.
  • This method significantly improves the representation of genomic DNA, enhancing its utility for advanced sequencing applications.