Concordance of whole-genome long-read sequencing with standard clinical testing for Prader-Willi and Angelman syndromes

Current clinical testing approaches for individuals with suspected imprinting disorders are complex, often requiring multiple tests performed in a stepwise fashion to make a precise molecular diagnosis. We investigated whether whole-genome long-read sequencing (LRS) could be used as a single data source to simultaneously evaluate copy number variants (CNVs), single nucleotide variants (SNVs), structural variants (SVs), and differences in methylation in a cohort of individuals known to have either Prader-Willi or Angelman syndrome. We evaluated 25 individuals sequenced to an average depth of coverage of 36x on an Oxford Nanopore PromethION. A custom one-page report was generated that could be used to assess copy number, SNVs, and methylation patterns at select CpG sites within the 15q11.2-q13.1 region and prioritize candidate pathogenic variants in UBE3A. After training with three positive controls, three analysts blinded to the known clinical diagnosis arrived at the correct molecular diagnosis for 22 out of 22 cases (20 true positive, 2 negative controls). Our findings demonstrate the utility of LRS as a single, comprehensive data source for complex clinical testing, offering potential benefits such as reduced testing costs, increased diagnostic yield, and shorter turnaround times in the clinical laboratory. ### Competing Interest Statement DEM is on a scientific advisory board at ONT and is engaged in a research agreement with them. CRP, MPGZ, and DEM have received travel funds from ONT. DEM holds stock options in MyOme. ### Funding Statement This work was supported by Seattle Childrens Hospital through an academic enrichment grant to CRP and AEB. Sequencing was subsidized by the Brotman Baty Institute for Precision Medicine. DEM is supported by the National Institutes of Health through the NIH Directors Early Independence Award DP5OD033357. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Use of residual samples for testing was approved by the Seattle Childrens Hospital IRB, study #00003536. Individuals recruited from an imprinting disorder clinic were recruited using protocol 7064 (University of Washington Repository for Mendelian Disorders) for which all participants or their legal guardian provided written consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Original sequencing data used in this study cannot be made publicly available. Summary methylation data is available on request.