Complimentary Episignature Testing for Variant Reclassification: Case Reports with Variant Classification Guideline...

Variants of uncertain significance (VUS) are being increasingly encountered in contemporary clinical genetics practice. Peripheral blood derived global DNA methylation pattern or Episignatures have been established for several Mendelian disorders.

We describe in detail the phenotype, genotype and episignature analysis of two children with atypical presentations of Rubinstein-Taybi and Cornelia de Lange syndromes. Whole exome sequencing showed missense VUS (CREBBP:c.3503A>G p.(Asn1168Ser) and NIPBL:c.6535T>G p.(Tyr2179Asp). Infinium Human Methylation 935 (EPICv2 array) was performed followed by methylation analysis using the EpiSign^™ METRIC (Methylation based Episignature Testing and Reference based Interpretation and Classification) V5 assay. METRIC score of 1 suggesting high confidence concordance with the episignature pattern associated with pathogenic variants in CREBBP and NIPBL was obtained.

We introduce the METRIC scoring component of the EpiSign^™ assay, which provides an integrated assessment of concordance between a patient's methylation profile and established episignatures, representing an evolution from earlier approaches using Methylation Variant Probability (MVP) scoring. While formal guidance for Bayesian point-based use of episignature results is not yet established, this functional evidence has clear potential for future incorporation and may enhance variant interpretation when combined with genomic data.