Abstract 18657: Diagnostic Yield of Whole Genome Sequencing in Congenital Heart Disease: Data From the UK 100,000 Genomes Project

Abstract

Congenital heart disease (CHD) is the most common birth defect affecting around 1% global live births. The aetiology of CHD is poorly understood: while a number genetic loci have already been identified, the majority of cases remain unexplained. Many CHD cases occur with additional abnormalities, or as part of a defined syndrome (eg. Noonan or CHARGE syndromes). The 100,000 Genomes Project conducted whole genome sequencing for patients with a range of rare diseases and cancers in partnership with the UK National Health Service. We analysed clinical and genetic data from the project in 2638 participants with CHD, including both primary CHD cases and secondary cases who have CHD as part of a syndromic presentation but were recruited under other disease categories. Both cohorts are primarily composed of patients with CHD accompanied by additional extra-cardiac abnormalities without a prior diagnosis of a defined syndrome. We found that families recruited as primary CHD cases were significantly less likely to have been classed as “solved cases” (indicating a pathogenic variant has been identified) than phenotypically similar secondary CHD cases (5.4% primary, 16.2% secondary; p = 6.78х -11 ). This is primarily due to differences in the gene lists used in analysis, with the majority of diagnoses in both groups due to genes not included in the CHD gene panel (83% primary and 97% secondary cases). Expanding standard CHD screening to include a wider range of syndromic CHD genes is likely to increase the diagnostic yield for the primary CHD cohort by more than two-fold. Copy number variants (CNVs) also contribute to CHD, especially in cases with additional abnormalities. CHD cases have a significantly higher burden of both deletions (p = 1.00х10 -5 ) and duplications (p = 0.009) than an ethnically-matched control cohort. However, only 7 of 2638 participants have CNVs in known CHD-causative regions such as the 22q11.2 or Williams-Beuren syndrome regions indicating novel CNVs are likely to contribute to a significant number of cases. Wider screening of syndromic CHD genes and novel copy number variants is likely significantly increase the diagnostic yield for CHD both within the 100,000 Genomes Project and in healthcare settings, and potentially yield novel CHD-associated loci.