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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Flexible and rapid validation of structural variation using adaptive sampling.

Aida Paivandy1, Felix Lenner1,2, Jesper Eisfeldt3

  • 1Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

European Journal of Human Genetics : EJHG
|February 23, 2026
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Summary
This summary is machine-generated.

Oxford Nanopore long-read adaptive sampling rapidly confirms complex genomic rearrangements. This method accurately characterizes structural variants and offers advantages over current diagnostic assays.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Microarrays and short-read sequencing have limitations in characterizing complex genomic rearrangements and structural variants (SVs).
  • Independent verification of SVs using custom assays is time-consuming and labor-intensive, hindering clinical application.

Purpose of the Study:

  • To evaluate Oxford Nanopore long-read adaptive sampling for rapid and flexible confirmation and characterization of complex genomic rearrangements.
  • To assess the utility of adaptive sampling for identifying structural variants in clinical samples.

Main Methods:

  • Utilized Oxford Nanopore long-read adaptive sampling to target 10 genomic regions with diverse structural variant types.
  • Performed sequencing on MinION or PromethION flow-cells, generating substantial data with high on-target coverage.
  • Analyzed sequencing data to verify rearrangements, resolve architecture, and identify breakpoint-spanning reads.

Main Results:

  • Successfully verified all 10 targeted genomic rearrangements, including deletions, translocations, and complex rearrangements.
  • Achieved full resolution of the architecture for nine out of ten regions, with breakpoint-spanning reads for nine.
  • Demonstrated the capability to detect structural variants in non-targeted genomic regions using background reads.

Conclusions:

  • Long-read adaptive sampling provides a flexible and rapid strategy for confirming and characterizing clinically relevant genomic rearrangements.
  • This approach offers advantages over existing assays by providing sequence, read depth, and methylation data for variant confirmation in diagnostic settings.