Deep intronic NIPBL variants underlie unresolved Cornelia de Lange syndrome revealed by integrated epigenomic and transcriptomic analysis - Nature
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AbstractCornelia de Lange syndrome (CdLS) is a rare congenital disorder characterised by craniofacial features, growth retardation, limb anomalies, and intellectual disability. The condition arises from pathogenic variants in genes encoding cohesin complex components or regulators, most frequently NIPBL. Despite advances in genomic testing, approximately 30% of clinically diagnosed cases remain unresolved, suggesting the presence of non-coding variants. We investigated 10 classical CdLS patients negative for pathogenic variants in NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Genome-wide methylation profiling was performed to identify CdLS-specific epigenetic signatures. Episignature-positive cases underwent trio-based deep sequencing of the entire NIPBL locus while targeted NIPBL RNA sequencing was used to assess splicing. Whole-genome sequencing (WGS) was performed in episignature-negative individuals. Five of ten patients exhibited a positive CdLS episignature in blood, saliva, or skin. Deep sequencing identified de novo deep intronic NIPBL variants in all cases, and two additional variants in episignature-negative patients.
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