Large-scale data-driven analysis to understand the genetics of Congenital Heart Disease

Congenital Heart Disease (CHD) delineates a large group of structural defects, which can occur due to perturbations at some stage in the cardiac embryogenesis process. With a global incidence ranging from 7 to 9 cases per 1000 live births, CHD accounts for a significant fraction of new-borns deaths worldwide. Different studies have identified genetics as an essential factor underlying CHD, along with environmental factors. The technological advances within the last years have helped improve CHD diagnosis and understand its genetic causes. Nevertheless, despite the advances in our understanding of the disease, many molecular mechanisms underlying CHD remain uncertain. Herein I present my efforts focused on discovering new genes and biological pathways altered in patients with CHD. The work is based on large CHD patient cohorts, collected and analysed as part of an international collaboration. The adopted integrative data-driven approach in this work can roughly be grouped into two principal aims: i) the development of statistical frameworks and bioinformatics tools to analyse high-dimensional data and ii) the meta-analysis of large-scale exome sequencing data to elucidate variants and genes conferring risk of CHD. By meta-analysing copy number variations and de novo variants in CHD probands, we implicated novel genes reaching genome-wide significant association with CHD and strengthened previously described associations. We also explored the differences between non-syndromic and syndromic CHD by analysing a large-scale exome cohort of patients. In summary, our integrative approach, supported by the data analysis of ~15,000 CHD patients, allowed us to gain new insights into the genetic origin of CHD. Consequently, we present here a valuable resource to continue investigating the causes of CHD and pave the way to promote new studies in this area

Erratum: Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms(Genet Med (2021)23(103-110)(s41436020009394)(10.1038/s41436-020-00939-4))

Correction to: Genetics in Medicine 2021; https://doi.org/10.1038/s41436-020-00939-4 In the article “Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms” by van Walree ES et al (Genet Med 2021;23:103-110), there was an error in a sentence in the Methods section of the abstract. This sentence should read “To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370 controls, and the other 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls.

Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

Purpose: In this study we aimed to establish the genetic cause of a myriad of cardiovascular defects prevalent in individuals from a genetically isolated population, who were found to share a common ancestor in 1728. Methods: Trio genome sequencing was carried out in an index patient with critical congenital heart disease (CHD); family members had either exome or Sanger sequencing. To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370. These controls were also ancestry-matched (same as FTAA controls), and the other with 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls. Functional consequences of identified variants were evaluated using expression studies. Results: We identified a loss-of-function variant in the Notch target transcription factor-encoding gene HEY2. The homozygous state (n = 3) causes life-threatening congenital heart defects, while 80% of heterozygous carriers (n = 20) had cardiovascular defects, mainly CHD and FTAA of the ascending aorta. We confirm enrichment of rare risk variants in HEY2 functional domains after meta-analysis (MetaSKAT p = 0.018). Furthermore, we show that several identified variants lead to dysregulation of repression by HEY2. Conclusion: A homozygous germline loss-of-function variant in HEY2 leads to critical CHD. The majority of heterozygotes show a myriad of cardiovascular defects

Erratum: Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms(Genet Med (2021)23(103-110)(s41436020009394)(10.1038/s41436-020-00939-4))

Correction to: Genetics in Medicine 2021; https://doi.org/10.1038/s41436-020-00939-4 In the article “Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms” by van Walree ES et al (Genet Med 2021;23:103-110), there was an error in a sentence in the Methods section of the abstract. This sentence should read “To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370 controls, and the other 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls.

Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

Purpose: In this study we aimed to establish the genetic cause of a myriad of cardiovascular defects prevalent in individuals from a genetically isolated population, who were found to share a common ancestor in 1728. Methods: Trio genome sequencing was carried out in an index patient with critical congenital heart disease (CHD); family members had either exome or Sanger sequencing. To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370. These controls were also ancestry-matched (same as FTAA controls), and the other with 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls. Functional consequences of identified variants were evaluated using expression studies. Results: We identified a loss-of-function variant in the Notch target transcription factor-encoding gene HEY2. The homozygous state (n = 3) causes life-threatening congenital heart defects, while 80% of heterozygous carriers (n = 20) had cardiovascular defects, mainly CHD and FTAA of the ascending aorta. We confirm enrichment of rare risk variants in HEY2 functional domains after meta-analysis (MetaSKAT p = 0.018). Furthermore, we show that several identified variants lead to dysregulation of repression by HEY2. Conclusion: A homozygous germline loss-of-function variant in HEY2 leads to critical CHD. The majority of heterozygotes show a myriad of cardiovascular defects