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Resolving structural variations missed by short-read sequencing uncovers their pathogenicity.

Caroline Schluth-Bolard1,2, Laïla El Khattabi3, Pierre-Antoine Rollat-Farnier4,5

  • 1Service de Génétique, Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Unversité Lyon 1, Centre Hospitalier Universitaire de Lyon, Bron, France caroline.schluth-bolard@chru-strasbourg.fr.

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|August 20, 2025
PubMed
Summary
This summary is machine-generated.

Short-read genome sequencing struggles to detect apparently balanced chromosomal rearrangements (ABCRs) in repetitive regions. Using the T2T-CHM13 V.2.0 genome and advanced analysis improved breakpoint resolution, aiding patient diagnosis.

Keywords:
chromosome aberrationsin situ hybridization, fluorescencenanopore sequencing

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Area of Science:

  • Genomics
  • Human Genetics
  • Molecular Biology

Background:

  • Short-read genome sequencing (sr-GS) is effective for characterizing apparently balanced chromosomal rearrangements (ABCRs).
  • However, sr-GS fails to detect breakpoints in 9%-11% of ABCR cases.
  • These undetected cases often involve complex genomic regions.

Purpose of the Study:

  • To investigate the reasons for sr-GS failure in detecting ABCR breakpoints.
  • To improve the detection and characterization of ABCRs using advanced genomic analysis.
  • To assess the clinical impact of resolving these complex rearrangements.

Main Methods:

  • Studied 117 ABCRs in patients with abnormal phenotypes, focusing on 14 undetectable by standard sr-GS and GRCh38 alignment.
  • Re-aligned sequencing data against the T2T-CHM13 V.2.0 reference genome and employed multiple structural variant (SV) callers.
  • Utilized complementary methods like FISH, linked-read, long-read sequencing, and optical genome mapping for further characterization.

Main Results:

  • Successfully characterized breakpoints at the base-pair level for 12 translocations previously undetectable by sr-GS.
  • Identified that at least one breakpoint in each translocation involved highly repetitive elements (e.g., alpha-satellites, segmental duplications).
  • Determined that in 50% of cases, the resolved breakpoint explained the patient's phenotype through gene disruption or position effects.

Conclusions:

  • Failure of sr-GS in detecting ABCRs is attributed to breakpoints within highly repetitive genomic regions.
  • The T2T-CHM13 V.2.0 reference genome and advanced SV callers enhance the resolution of complex rearrangements.
  • Accurate characterization of ABCRs is crucial for diagnosing pathogenic variants and informing patient care.