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Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation.

Harrison Brand1, Ryan L Collins2, Carrie Hanscom2

  • 1Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02114, USA.

American Journal of Human Genetics
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Complex genomic rearrangements, like dupINVdups, are common in autism spectrum disorder (ASD) and missed by standard genetic tests. These structural variations highlight the need for advanced sequencing methods in genetic diagnostics.

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Area of Science:

  • Genomics
  • Human Genetics
  • Molecular Biology

Background:

  • Copy-number variants (CNVs) are the primary focus in genetic studies of structural variation.
  • Chromosomal microarray (CMA) is the recommended first-tier genetic screen for neurodevelopmental disorders.
  • Previous studies have primarily focused on CNVs, potentially overlooking complex structural variations.

Purpose of the Study:

  • To compare CNVs detected by CMA with structural variations identified by whole-genome sequencing in individuals with autism spectrum disorder (ASD).
  • To investigate the prevalence and mechanisms of complex duplications and inversions in the human genome.
  • To assess the clinical relevance of complex rearrangements cryptic to CMA.

Main Methods:

  • Whole-genome large-insert sequencing was performed on 259 individuals with ASD from the Simons Simplex Collection.
  • Comparison of structural variation detected by sequencing against CNVs identified by CMA.
  • Breakpoint analysis to determine the mechanism of formation for complex variants.
  • Analysis of inversion variation in 235 high-quality libraries.

Main Results:

  • A novel class of complex rearrangement, termed dupINVdup, involving paired duplications flanking an inversion, was identified in 8.1% of subjects.
  • Other paired-duplication signatures and duplication-mediated rearrangements were found in 15.8% of ASD subjects.
  • Microhomology-mediated repair was identified as the predominant mechanism for these complex variants.
  • A significant proportion of inversions (60.7%) were complex, not simple, rearrangements.

Conclusions:

  • Complex rearrangements, including dupINVdups, are common sources of genomic variation missed by CMA and low-depth sequencing.
  • These findings suggest that paired-duplication signatures detected by CMA may indicate clinically relevant complex rearrangements.
  • Advanced sequencing techniques are crucial for comprehensive genetic diagnostic testing, especially for neurodevelopmental disorders.