A Streamlined Approach to Prader-Willi and Angelman Syndrome Molecular Diagnostics

Abstract

Establishing or ruling out a molecular diagnosis of Prader–Willi or Angelman syndrome (PWS/AS) presents unique challenges due to the variety of different genetic alterations that can lead to these conditions. Point mutations, copy number changes, uniparental isodisomy (i-UPD) 15 of two subclasses (segmental or total isodisomy), uniparental heterodisomy (h-UPD), and defects in the chromosome 15 imprinting center can all cause PWS/AS. Here, we outline a combined approach using whole-exome sequencing (WES) and DNA methylation data with methylation-sensitive multiplex ligation-dependent probe amplification (MLPA) to establish both the disease diagnosis and the mechanism of disease with high sensitivity using current standard of care technology and improved efficiency compared to serial methods. The authors encourage the use of this approach in the clinical setting to confirm and establish the diagnosis and genetic defect which may account for the secondary genetic conditions that may be seen in those with isodisomy 15, impacting surveillance and counseling with more accurate recurrence risks. Other similarly affected individuals due to other gene disorders or cytogenetic anomalies such as Rett syndrome or microdeletions would also be identified with this streamlined approach.

Behavioral and Psychiatric Disorders in Syndromic Autism

“…The remaining affected individuals have either a defect in the imprinting center controlling the imprinted genes in the PWCR or chromosome 15 translocations or inversions [60][61][62]. The diagnosis and molecular cause of PWS can be identified using high-resolution chromosome microarrays [61] or, more precisely, with a streamlined molecular approach including whole-exome sequencing with a deletion or duplication status, and DNA methylation analysis with methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) [63].…”

Epilepsy Genetics and Precision Medicine in Adults: A New Landscape for Developmental and Epileptic Encephalopathies

“…Firstly, analysis of nucleotide repeat expansions would require a different specific study (triplet-primed polymerase chain reaction –PCR- with specific primers) ( 35 ), although further bioinformatic tools are under development to allow their analysis basing on next generation sequencing (NGS) techniques [gene panels, whole exome sequencing (WES) and whole genome sequencing -WGS] ( 32 ). Examination of non-coding regions or intronic regions would also require distinct procedures within gene panels or WES, or a WGS ( 17 ), except variants present in intron-exon boundaries, whose detection would not require additional processing Analysis of epigenetic variations would as well involve a separated technique ( 34 , 36 ). Besides, detection of mosaicism when employing NGS techniques would necessitate a deep sequencing approach (coverage > 100x) when suspected (inferior coverages would probably lead to misdetection of the mosaic variant and, for instance, a mistaken label of de novo in segregation studies) ( 37 , 38 ).…”

Developmental and Epileptic Encephalopathy 76: Case Report and Review of Literature

“…However, combined with the clinical presentation and auxiliary examination results, the possibility of a hereditary etiology was still considered. At 2 years and 5 months, the trio of sequencing was completed, and we used the whole-exon next-generation sequencing (NGS) data analysis method to analyze the deletion duplication of all exons (more than 190,000 exons) in the whole exon group [ 6 ]. The genomic DNA was extracted from the peripheral blood of the proband and its parents.…”