Frontiers in Genetics (Sep 2020)
Genes and Pathways Implicated in Tetralogy of Fallot Revealed by Ultra-Rare Variant Burden Analysis in 231 Genome Sequences
- Roozbeh Manshaei,
- Daniele Merico,
- Daniele Merico,
- Miriam S. Reuter,
- Miriam S. Reuter,
- Worrawat Engchuan,
- Bahareh A. Mojarad,
- Rajiv Chaturvedi,
- Rajiv Chaturvedi,
- Tracy Heung,
- Tracy Heung,
- Giovanna Pellecchia,
- Mehdi Zarrei,
- Mehdi Zarrei,
- Thomas Nalpathamkalam,
- Reem Khan,
- John B. A. Okello,
- Eriskay Liston,
- Meredith Curtis,
- Ryan K. C. Yuen,
- Ryan K. C. Yuen,
- Ryan K. C. Yuen,
- Christian R. Marshall,
- Christian R. Marshall,
- Christian R. Marshall,
- Christian R. Marshall,
- Rebekah K. Jobling,
- Rebekah K. Jobling,
- Erwin Oechslin,
- Rachel M. Wald,
- Rachel M. Wald,
- Candice K. Silversides,
- Stephen W. Scherer,
- Stephen W. Scherer,
- Stephen W. Scherer,
- Stephen W. Scherer,
- Raymond H. Kim,
- Raymond H. Kim,
- Raymond H. Kim,
- Anne S. Bassett,
- Anne S. Bassett,
- Anne S. Bassett,
- Anne S. Bassett,
- Anne S. Bassett
Affiliations
- Roozbeh Manshaei
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Daniele Merico
- Deep Genomics Inc., Toronto, ON, Canada
- Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Miriam S. Reuter
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Miriam S. Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Bahareh A. Mojarad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Rajiv Chaturvedi
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Rajiv Chaturvedi
- Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada
- Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Tracy Heung
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
- Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Mehdi Zarrei
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Reem Khan
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- John B. A. Okello
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Eriskay Liston
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Meredith Curtis
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Ryan K. C. Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Ryan K. C. Yuen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Ryan K. C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Christian R. Marshall
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Christian R. Marshall
- 0Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Christian R. Marshall
- 1Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Rebekah K. Jobling
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Rebekah K. Jobling
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Erwin Oechslin
- 2Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
- Rachel M. Wald
- Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada
- Rachel M. Wald
- 2Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
- Candice K. Silversides
- 2Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
- Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Stephen W. Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Stephen W. Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Stephen W. Scherer
- 0Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Raymond H. Kim
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Raymond H. Kim
- 3Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Raymond H. Kim
- 4Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
- Anne S. Bassett
- 2Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
- Anne S. Bassett
- 5Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Anne S. Bassett
- 6Department of Mental Health, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- DOI
- https://doi.org/10.3389/fgene.2020.00957
- Journal volume & issue
-
Vol. 11
Abstract
Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF (n = 175) or related CHD. We adapted a burden test originally developed for de novo variants to assess ultra-rare variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets and for multiple testing. For truncating variants, the gene burden test confirmed significant burden in FLT4 (Bonferroni corrected p-value < 0.01). For missense variants, burden in NOTCH1 achieved genome-wide significance only when restricted to constrained genes (i.e., under negative selection, Bonferroni corrected p-value = 0.004), and showed enrichment for variants affecting the extracellular domain, especially those disrupting cysteine residues forming disulfide bonds (OR = 39.8 vs. gnomAD). Individuals with NOTCH1 ultra-rare missense variants, all with TOF, were enriched for positive family history of CHD. Other genes not previously implicated in CHD had more modest statistical support in gene burden tests. Gene-set burden tests for truncating variants identified a cluster of pathways corresponding to VEGF signaling (FDR = 0%), and of mouse phenotypes corresponding to abnormal vasculature (FDR = 0.8%); these suggested additional candidate genes not previously identified (e.g., WNT5A and ZFAND5). Results for the most promising genes were driven by the TOF subset of the cohort. The findings support the importance of ultra-rare variants disrupting genes involved in VEGF and NOTCH signaling in the genetic architecture of TOF, accounting for 11–14% of individuals in the TOF cohort. These proof-of-principle data indicate that this statistical methodology could assist in analyzing case-only sequencing data in which ultra-rare variants, whether de novo or inherited, contribute to the genetic etiopathogenesis of a complex disorder.
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