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De Novo Variants Predominate in Autism Spectrum Disorder.

Richard G Boles1,2, Omri Bar1, Philip T Boles1

  • 1Mitochondrial & Molecular Medicine, Pasadena, CA 91108, USA.

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|September 27, 2025
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Summary
This summary is machine-generated.

De novo variants (DNVs) are new mutations found in 47% of autism spectrum disorder (ASD) patients, suggesting environmental factors may influence ASD's rising prevalence. These DNVs, along with inherited variants, contribute to ASD pathogenesis.

Keywords:
DNA sequencingautismdiagnostic yielddisease modelmissensepolygenic inheritancesilent variantssynonymous variantswhole genome sequencing

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Area of Science:

  • Genetics
  • Neurodevelopmental Disorders
  • Genomic Medicine

Background:

  • Autism spectrum disorder (ASD) presents significant lifelong challenges.
  • While genetics play a role (~80%), rapidly increasing ASD prevalence suggests environmental influences.
  • De novo variants (DNVs), or new mutations, are a potential explanation for this paradox.

Purpose of the Study:

  • To validate previous findings on DNVs in ASD using trio whole-genome sequencing (trio-WGS).
  • To investigate the association of both de novo and inherited variants with ASD.
  • To explore the role of silent variants in ASD etiology.

Main Methods:

  • Conducted trio-WGS on 100 additional unrelated ASD patients.
  • Analyzed de novo variants (DNVs) and inherited variants, including missense and silent types.
  • Utilized non-transcribed variants as controls to assess DNV-PDV association with ASD-related genes.

Main Results:

  • Identified de novo Principal Diagnostic Variants (DNV-PDVs) in 47% of ASD cases.
  • DNV-PDVs were significantly more likely to be in SFARI-listed ASD-associated genes (p < 0.0001).
  • Both inherited and de novo silent variants showed statistical association with ASD (p < 0.0001 and p < 0.007, respectively).
  • Inherited silent variants were more associated with ASD than inherited missense variants (p < 0.0001).
  • Inclusion of silent DNVs increased the proportion of subjects with at least one DNV-PDV to 55%.

Conclusions:

  • A model incorporating prominent DNVs explains ASD pathogenesis and prevalence.
  • Environmental factors like nutrient deficiencies or toxicant exposures may interact with genetic predispositions.
  • Further research is needed for functional validation and inclusion of diverse patient populations.