Genome-Wide DNA Methylation Profiling Solves Uncertainty in Classifying NSD1 Variants

Area of Science:

• Genetics
• Epigenetics
• Molecular Biology

Background:

• Sotos syndrome is linked to NSD1 mutations and a distinct DNA methylation pattern.
• Phenotypic overlap with other overgrowth syndromes complicates Sotos syndrome diagnosis.
• Variants of unknown significance (VoUS) in NSD1 further challenge accurate diagnosis.

Purpose of the Study:

• To resolve diagnostic uncertainty for Sotos syndrome in individuals with NSD1 variants of unknown significance (VoUS).
• To assess the utility of genome-wide DNA methylation (DNAm) profiling for diagnosing Sotos syndrome.
• To evaluate the impact of training cohort size on classifier performance for DNAm analysis.

Main Methods:

• Microarray DNA methylation (DNAm) profiling was performed on individuals with suspected Sotos syndrome and NSD1 variants.
• A Sotos syndrome-specific DNAm signature was developed and validated.
• Classifier performance was assessed using varying training cohort sizes and a data balancing strategy.

Main Results:

• DNAm profiling confirmed pathogenicity in 8/11 individuals with NSD1 variants and excluded it in 3.
• The Sotos syndrome DNAm signature successfully validated in patients with pathogenic NSD1 variants.
• Classifier sensitivity and prediction confidence remained stable across different training set sizes, with improvement via data balancing.

Conclusions:

• DNA methylation profiling effectively resolves diagnostic uncertainty for NSD1 variants of unknown significance (VoUS).
• This approach demonstrates significant clinical utility in diagnosing Sotos syndrome.
• Epigenetic signatures provide valuable diagnostic information for genetic disorders.