Whole genome sequencing in the 100,000 Genomes project identifies a RYR2 variant associating with dilated cardiomyopathy and sudden unexpected death in the young

Abstract

Abstract Funding Acknowledgements Type of funding sources: None. Background Previous studies have shown genetic testing in sudden unexpected death in the young (SUDY) cases identify a pathogenic variant in 13-27% of cases. This diagnostic yield increased up to 39% when genetic testing was combined with family evaluation. The 100,000 Genomes Project was launched to investigate the role of whole genome sequencing (WGS) as a diagnostic tool for cancers and rare diseases in a national health care system. Young sudden death victims with no finding on postmortem testing were enrolled to the SUDY cohort. Purpose We aimed to analyse WGS data in the SUDY cohort of 100,000 Genomes Project with panel analysis and trio studies in order to examine the yield of WGS in this population. Methods Sudden death victims, aged 40 or younger, without pre-existing condition that would explain the event and with no diagnosis established on postmortem examination were enrolled between 2017 and 2019 at different Genomic Medicine Centres (GMCs) across the UK. Parents were recruited in all paediatric cases. DNA sequencing was performed by Illumina. The platform's automated pipeline was used for variant calling. Panel based and hypothesis free approaches were used for data analysis. Variant analysis was performed with focus on variants with combined annotation-dependent depletion (CADD) score >15 and American College of Medical Genetics and Genomics (ACMG) classification of pathogenic (P), likely pathogenic (LP), or variant of unknown significance (VUS). Results A total of 15 participants, including 6 trios, were included in the study. Participants had a median age of 18 [IQR 1-29.5] and two thirds were male. Following assessment of all protein coding and intronic variants identified, only the missense variant RYR2:c.10046C>T (p.Ser3349Leu) was thought to be suitable for investigation for upgrade to likely pathogenic, giving a diagnostic yield of 6.67% for WGS in SUDY cases. This variant was detected in a 24-year-old sudden death victim. Family evaluation led to the diagnosis of dilated cardiomyopathy (DCM) in four family members and segregation testing confirmed affected family members harboured the variant. Further investigation in 100,000 Genomes Project, laboratory data, and our inherited cardiac conditions database as well as previous publications, identified additional cases of this variant in association with DCM and sudden cardiac death (see table and figure). Conclusion WGS with targeted gene analysis can be an effective diagnostic tool for SUDY. The study’s findings show the importance of large population databases and collaboration in the research community, allowing reclassification of a RYR2 VUS as a LP variant, the strongest genetic data so far to associate a missense variant with familial DCM and the risk for SCD. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project.