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Detection of Complex Genomic Rearrangements Using Short-Read Whole Genome Sequencing in C. elegans.

Tatiana Maroilley1,2, Maja Tarailo-Graovac3,4

  • 1Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|August 30, 2025
PubMed
Summary

This study introduces a new workflow using short-read whole genome sequencing (srWGS) to detect complex genomic rearrangements (CGRs). The Caenorhabditis elegans (C. elegans) model organism aids in validating this cost-efficient method for genomic analysis.

Keywords:
C. elegansChromoanagenesisShort-readStructural variantWhole genome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Clinical diagnostics often miss complex genomic rearrangements (CGRs) due to focus on exome sequencing and small variants.
  • Detecting CGRs necessitates whole genome sequencing and advanced analytical tools, which are often costly and complex.
  • Short-read whole genome sequencing (srWGS) offers a cost-efficient approach for comprehensive variant detection.

Purpose of the Study:

  • To develop and validate a novel workflow for accurate CGR detection using srWGS.
  • To establish guidelines for interpreting CGR structures identified through srWGS.
  • To leverage Caenorhabditis elegans (C. elegans) balancer strains as a model system for CGR analysis.

Main Methods:

  • Utilized srWGS on C. elegans balancer strains known to harbor CGRs.
  • Developed and implemented a complete bioinformatics workflow for CGR breakpoint detection.
  • Established experimental validation procedures for identified CGR breakpoints and structures.

Main Results:

  • Successfully detected and validated CGR breakpoints within C. elegans balancer strains.
  • Demonstrated the capability of the srWGS workflow to identify a spectrum of CGRs.
  • Provided a framework for interpreting the structural complexity of detected CGRs.

Conclusions:

  • The developed srWGS workflow provides an accurate and efficient method for detecting CGRs.
  • C. elegans balancer strains serve as an effective model for assessing and validating genomic analysis tools.
  • This approach has the potential to improve diagnostic capabilities for complex genetic variations.