A multi-tiered analysis platform for genome sequencing: design and initial findings of the Australian Genomics Cardiovascular Disorders Flagship

Background The Australian Genomics Cardiovascular Disorders Flagship was a national multidisciplinary collaboration. It aimed to investigate the feasibility of genome sequencing (GS) and functional genomics to resolve variants of uncertain significance (VUS) in the clinical management of patients and families with cardiomyopathies, primary arrhythmias and congenital heart disease (CHD). Methods Between April 2019 and December 2021, 600 probands meeting cardiovascular disorder criteria from 17 cardiology and genetics clinics across Australia were enrolled in the Flagship and underwent GS. The Flagship adopted a tiered approach to GS analysis: Tier 1 analysis assessed genes with established clinical validity for each cardiovascular condition; Tier 2 analysis assessed lesser-evidenced research-based genes. Tier 3 analysis assessed the functional impact of VUS that remained after Tier 1 and Tier 2 analysis. Results Overall, a pathogenic (P) or likely pathogenic (LP) variant was identified in 41% of participants with a cardiomyopathy, 40% with an arrhythmia syndrome and 15% with a familial CHD/CHD+ Extra Cardiac Anomalies (ECA). A VUS outcome ranged from 13% for arrhythmias to 34% for CHD/CHD+ECA participants. Tier 2 research analysis identified an LP/P variant for a further 15 participants and a VUS for an additional 15 participants. Conclusion The Flagship successfully facilitated a model of care that harnesses clinical GS and functional genomics for the resolution of VUS in the clinical setting. This valuable dataset can be utilised to inform clinical practice and facilitate research into the future.