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1. Human Genetics of Congenital Heart Defects

Author

Wilsdon, Anna, Loughna, Siobhan, Crusio, Wim E., Series Editor, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, Rickert-Sperling, Silke, editor, Kelly, Robert G., editor, and Haas, Nikolaus, editor

Published
2024
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2. Identifying novel genes that cause congenital heart disease

Author

Wilsdon, Anna

Subjects
QH426 Genetics
Abstract

Complex genetic networks underlie the development of the heart. Variants in some of these genes can lead to congenital heart disease (CHD). Despite the hundreds of genes that have been identified as causing CHD in humans, they only account for a small proportion of individuals with CHD. We carried out whole exome sequencing in the largest cohort of individuals with CHD reported at the time of publication, and identified three novel genome wide significant syndromic CHD genes; CDK13, PRKD1 and CHD4. Individuals with mutations in CHD4 show neurodevelopmental disability, genital abnormalities and share some phenotypic overlap with other chromatinopathies. Mutations in PRKD1 also cause syndromic CHD, but identification of further affected individuals is required to determine if there is a consistent phenotype. Prkd1 mouse models do not have a high incidence of CHD, but this gene may be important in future work as it plays a role in cardiac hypertrophy. Individuals with mutations in CDK13 show a recognisable phenotype and the mouse model shows embryonic lethality and atrioventricular canal defects. The precise mechanism by which heterozygous mutations cause disease in humans remains unclear. The phenotypic and genotypic spectrum has been expanded by subsequent reports of individuals with mutations in CKD13. We also identify a role for inherited variants with reduced penetrance in individuals with non-syndromic CHD. This is significant, as the vast majority of individuals with CHD have non-syndromic CHD. It is an important step in understanding the potential oligogenic pathogenesis of the majority of CHD. Ultimately we aim to increase our knowledge of the genes and networks that underlie CHD, to improve diagnostic yield in individuals affected with CHD. I was able to feedback pathogenic mutations in CHD genes to participants in this study locally. Following this unbiased approach of non-targeted testing in a cohort with multiple types of CHD, will improve our knowledge of genotype phenotype correlations. We also hope that understanding more about the genes involved in cardiogenesis and CHD might have relevance for the failing heart, and development of treatments in the future too.

Published
2021

3. Cyclin‐dependent kinase 13 is indispensable for normal mouse heart development.

Author

Waheed‐Ullah, Qazi, Wilsdon, Anna, Abbad, Aseel, Rochette, Sophie, Bu'Lock, Frances, Saed, Asma Ali, Hitz, Marc‐Phillip, Brook, J. David, and Loughna, Siobhan

Subjects
*CONGENITAL heart disease, *VENTRICULAR septal defects, *MITRAL valve, *HEART valves, *HEART development
Abstract

Congenital heart disease (CHD) has an incidence of approximately 1%. Over the last decade, sequencing studies including large cohorts of individuals with CHD have begun to unravel the genetic mechanisms underpinning CHD. This includes the identification of variants in cyclin‐dependent kinase 13 (CDK13), in individuals with syndromic CHD. CDK13 encodes a serine/threonine protein kinase. The cyclin partner of CDK13 is cyclin K; this complex is thought to be important in transcription and RNA processing. Pathogenic variants in CDK13 cause CDK13‐related disorder in humans, characterised by intellectual disability and developmental delay, recognisable facial features, feeding difficulties and structural brain defects, with 35% of individuals having CHD. To obtain a greater understanding for the role that this essential protein kinase plays in embryonic heart development, we have analysed a presumed loss of function Cdk13 transgenic mouse model (Cdk13tm1b). The homozygous mutants were embryonically lethal in most cases by E15.5. X‐gal staining showed Cdk13 expression localised to developing facial regions, heart and surrounding areas at E10.5, whereas at E12.5, it was more widely present. In the E15.5 heart, staining was seen throughout. RT‐qPCR showed significant reduction in Cdk13 transcript expression in homozygous compared with WT and heterozygous hearts at E10.5 and E12.5. Detailed morphological 3D analysis of embryonic and postnatal hearts was performed using high‐resolution episcopic microscopy, which affords a more detailed analysis of structures such as cardiac valve leaflets and endocardial cushions, compared with more traditional histological techniques. We show that both the homozygous and heterozygous Cdk13tm1b mutants exhibit a range of CHD, including ventricular septal defects, bicuspid aortic valve, double outlet right ventricle and atrioventricular septal defects. 100% (n = 4) of homozygous hearts displayed CHD. Differential expression was seen in Cdk13tm1b homozygous mutants for two genes known to be necessary for normal heart development. The types of defects, and the presence of CHD in heterozygous mice (17.02%, n = 8/47), are consistent with the CDK13‐related disorder phenotype in humans. This study provides important insights into the effects of reduced function of CDK13 in the mouse heart and contributes to our understanding of the mechanism behind this disorder as a cause of CHD. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Rare variants in KDR, encoding VEGF Receptor 2, are associated with tetralogy of Fallot

Author

Škorić-Milosavljević, Doris, Lahrouchi, Najim, Bosada, Fernanda M., Dombrowsky, Gregor, Williams, Simon G., Lesurf, Robert, Tjong, Fleur V.Y., Walsh, Roddy, El Bouchikhi, Ihssane, Breckpot, Jeroen, Audain, Enrique, Ilgun, Aho, Beekman, Leander, Ratbi, Ilham, Strong, Alanna, Muenke, Maximilian, Heide, Solveig, Muir, Alison M., Hababa, Mariam, Cross, Laura, Zhou, Dihong, Pastinen, Tomi, Hitz, Marc-Phillip, Abdul-Khaliq, Hashim, Berger, Felix, Dähnert, Ingo, Dittrich, Sven, Uebing, Anselm, Stiller, Brigitte, Zackai, Elaine, Atmani, Samir, Ouldim, Karim, Adadi, Najlae, Steindl, Katharina, Rauch, Anita, Brook, David, Wilsdon, Anna, Kuipers, Irene, Blom, Nico A., Mulder, Barbara J., Mefford, Heather C., Keren, Boris, Joset, Pascal, Kruszka, Paul, Thiffault, Isabelle, Sheppard, Sarah E., Roberts, Amy, Lodder, Elisabeth M., Keavney, Bernard D., Clur, Sally-Ann B., Mital, Seema, Hitz, Marc-Philip, Christoffels, Vincent M., Postma, Alex V., and Bezzina, Connie R.

Published
2021
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5. Effect of deletion of the protein kinase PRKD1 on development of the mouse embryonic heart.

Author

Waheed‐Ullah, Qazi, Wilsdon, Anna, Abbad, Aseel, Rochette, Sophie, Bu'Lock, Frances, Hitz, Marc‐Phillip, Dombrowsky, Gregor, Cuello, Friederike, Brook, J. David, and Loughna, Siobhan

Subjects
*PROTEIN kinases, *EMBRYOLOGY, *MITRAL valve, *PULMONARY valve, *CONGENITAL heart disease, *SERINE/THREONINE kinases
Abstract

Congenital heart disease (CHD) is the most common congenital anomaly, with an overall incidence of approximately 1% in the United Kingdom. Exome sequencing in large CHD cohorts has been performed to provide insights into the genetic aetiology of CHD. This includes a study of 1891 probands by our group in collaboration with others, which identified three novel genes—CDK13, PRKD1, and CHD4, in patients with syndromic CHD. PRKD1 encodes a serine/threonine protein kinase, which is important in a variety of fundamental cellular functions. Individuals with a heterozygous mutation in PRKD1 may have facial dysmorphism, ectodermal dysplasia and may have CHDs such as pulmonary stenosis, atrioventricular septal defects, coarctation of the aorta and bicuspid aortic valve. To obtain a greater appreciation for the role that this essential protein kinase plays in cardiogenesis and CHD, we have analysed a Prkd1 transgenic mouse model (Prkd1em1) carrying deletion of exon 2, causing loss of function. High‐resolution episcopic microscopy affords detailed morphological 3D analysis of the developing heart and provides evidence for an essential role of Prkd1 in both normal cardiac development and CHD. We show that homozygous deletion of Prkd1 is associated with complex forms of CHD such as atrioventricular septal defects, and bicuspid aortic and pulmonary valves, and is lethal. Even in heterozygotes, cardiac differences occur. However, given that 97% of Prkd1 heterozygous mice display normal heart development, it is likely that one normal allele is sufficient, with the defects seen most likely to represent sporadic events. Moreover, mRNA and protein expression levels were investigated by RT‐qPCR and western immunoblotting, respectively. A significant reduction in Prkd1 mRNA levels was seen in homozygotes, but not heterozygotes, compared to WT littermates. While a trend towards lower PRKD1 protein expression was seen in the heterozygotes, the difference was only significant in the homozygotes. There was no compensation by the related Prkd2 and Prkd3 at transcript level, as evidenced by RT‐qPCR. Overall, we demonstrate a vital role of Prkd1 in heart development and the aetiology of CHD. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

Author

van Walree, Eva S., Dombrowsky, Gregor, Jansen, Iris E., Mirkov, Maša Umićević, Zwart, Rob, Ilgun, Aho, Guo, Dongchuan, Clur, Sally-Ann B., Amin, Ahmed S., Savage, Jeanne E., van der Wal, Allard C., Waisfisz, Quinten, Maugeri, Alessandra, Wilsdon, Anna, Bu’Lock, Frances A., Hurles, Matthew E., Dittrich, Sven, Berger, Felix, Audain Martinez, Enrique, Christoffels, Vincent M., Hitz, Marc-Philip, Milewicz, Dianna M., Posthuma, Daniëlle, Meijers-Heijboer, Hanne, Postma, Alex V., and Mathijssen, Inge B.

Published
2021
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7. Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project.

Author

Moore, A. Rachel, Jing Yu, Yang Pei, Cheng, Emily W. Y., Taylor Tavares, Ana Lisa, Walker, Woolf T., Thomas, N. Simon, Kamath, Arveen, Ibitoye, Rita, Josifova, Dragana, Wilsdon, Anna, Ross, Alison, Calder, Alistair D., Offiah, Amaka C., Wilkie, Andrew O. M., Taylor, Jenny C., and Pagnamenta, Alistair T.

Abstract

Background Current clinical testing methods used to uncover the genetic basis of rare disease have inherent limitations, which can lead to causative pathogenic variants being missed. Within the rare disease arm of the 100 000 Genomes Project (100kGP), families were recruited under the clinical indication ’single autosomal recessive mutation in rare disease’. These participants presented with strong clinical suspicion for a specific autosomal recessive disorder, but only one suspected pathogenic variant had been identified through standard-of-care testing. Whole genome sequencing (WGS) aimed to identify cryptic ’second-hit’ variants. Methods To investigate the 31 families with available data that remained unsolved following formal review within the 100kGP, SVRare was used to aggregate structural variants present in <1% of 100kGP participants. Small variants were assessed using population allele frequency data and SpliceAI. Literature searches and publicly available online tools were used for further annotation of pathogenicity. Results Using these strategies, 8/31 cases were solved, increasing the overall diagnostic yield of this cohort from 10/41 (24.4%) to 18/41 (43.9%). Exemplar cases include a patient with cystic fibrosis harbouring a novel exonic LINE1 insertion in CFTR and a patient with generalised arterial calcification of infancy with complex interlinked duplications involving exons 2–6 of ENPP1. Although ambiguous by short-read WGS, the ENPP1 variant structure was resolved using optical genome mapping and RNA analysis. Conclusion Systematic examination of cryptic variants across a multi-disease cohort successfully identifies additional pathogenic variants. WGS data analysis in autosomal recessive rare disease should consider complex structural and small intronic variants as potentially pathogenic second hits. [ABSTRACT FROM AUTHOR]

Published
2023
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9. 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))

Author

van Walree, Eva S., Dombrowsky, Gregor, Jansen, Iris E., Umićević Mirkov, Maša, Zwart, Rob, Ilgun, Aho, Guo, Dongchuan, Clur, Sally-Ann B., Amin, Ahmed S., Savage, Jeanne E., van der Wal, Allard C., Waisfisz, Quinten, Maugeri, Alessandra, Wilsdon, Anna, Bu'Lock, Frances A., Hurles, Matthew E., Dittrich, Sven, Berger, Felix, Audain Martinez, Enrique, Christoffels, Vincent M., Hitz, Marc-Philip, Milewicz, Dianna M., Posthuma, Daniëlle, Meijers-Heijboer, Hanne, Postma, Alex V., Mathijssen, Inge B., Pediatric surgery, Human genetics, ACS - Atherosclerosis & ischemic syndromes, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Reproduction & Development (AR&D), AII - Cancer immunology, Graduate School, Human Genetics, ACS - Heart failure & arrhythmias, Medical Biology, Amsterdam Cardiovascular Sciences, Paediatric Cardiology, Cardiology, Pathology, and ACS - Pulmonary hypertension & thrombosis

Abstract

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.”

Published
2022
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10. Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

Author

van Walree, Eva S, Dombrowsky, Gregor, Jansen, Iris E, Umićević Mirkov, Maša, Zwart, Rob, Ilgun, Aho, Guo, Dongchuan, Clur, Sally-Ann B, Amin, Ahmed S, Savage, Jeanne E, van der Wal, Allard C, Waisfisz, Quinten, Maugeri, Alessandra, Wilsdon, Anna, Bu'Lock, Frances A, Hurles, Matthew E, Dittrich, Sven, Berger, Felix, Audain Martinez, Enrique, Christoffels, Vincent M, Hitz, Marc-Philip, Milewicz, Dianna M, Posthuma, Daniëlle, Meijers-Heijboer, Hanne, Postma, Alex V, Mathijssen, Inge B, van Walree, Eva S, Dombrowsky, Gregor, Jansen, Iris E, Umićević Mirkov, Maša, Zwart, Rob, Ilgun, Aho, Guo, Dongchuan, Clur, Sally-Ann B, Amin, Ahmed S, Savage, Jeanne E, van der Wal, Allard C, Waisfisz, Quinten, Maugeri, Alessandra, Wilsdon, Anna, Bu'Lock, Frances A, Hurles, Matthew E, Dittrich, Sven, Berger, Felix, Audain Martinez, Enrique, Christoffels, Vincent M, Hitz, Marc-Philip, Milewicz, Dianna M, Posthuma, Daniëlle, Meijers-Heijboer, Hanne, Postma, Alex V, and Mathijssen, Inge B

Published
2022
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11. Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms

Author

van Walree, Eva S., primary, Dombrowsky, Gregor, additional, Jansen, Iris E., additional, Umićević Mirkov, Maša, additional, Zwart, Rob, additional, Ilgun, Aho, additional, Guo, Dongchuan, additional, Clur, Sally-Ann B., additional, Amin, Ahmed S., additional, Savage, Jeanne E., additional, van der Wal, Allard C., additional, Waisfisz, Quinten, additional, Maugeri, Alessandra, additional, Wilsdon, Anna, additional, Bu'Lock, Frances A., additional, Hurles, Matthew E., additional, Dittrich, Sven, additional, Berger, Felix, additional, Audain Martinez, Enrique, additional, Christoffels, Vincent M., additional, Hitz, Marc-Philip, additional, Milewicz, Dianna M., additional, Posthuma, Daniëlle, additional, Meijers-Heijboer, Hanne, additional, Postma, Alex V., additional, and Mathijssen, Inge B., additional

Published
2022
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12. Correction to: Rare variants in KDR, encoding VEGF Receptor 2, are associated with tetralogy of Fallot (Genetics in Medicine, (2021), 23, 10, (1952-1960), 10.1038/s41436-021-01212-y)

Author

Škorić-Milosavljević, Doris, Lahrouchi, Najim, Bosada, Fernanda M., Dombrowsky, Gregor, Williams, Simon G., Lesurf, Robert, Tjong, Fleur V. Y., Walsh, Roddy, el Bouchikhi, Ihssane, Breckpot, Jeroen, Audain, Enrique, Ilgun, Aho, Beekman, Leander, Ratbi, Ilham, Strong, Alanna, Muenke, Maximilian, Heide, Solveig, Muir, Alison M., Hababa, Mariam, Cross, Laura, Zhou, Dihong, Pastinen, Tomi, Hitz, Marc-Phillip, Abdul-Khaliq, Hashim, Berger, Felix, Dähnert, Ingo, Dittrich, Sven, Uebing, Anselm, Stiller, Brigitte, Zackai, Elaine, Atmani, Samir, Ouldim, Karim, Adadi, Najlae, Steindl, Katharina, Rauch, Anita, Brook, David, Wilsdon, Anna, Kuipers, Irene, Blom, Nico A., Mulder, Barbara J., Mefford, Heather C., Keren, Boris, Joset, Pascal, Kruszka, Paul, Thiffault, Isabelle, Lodder, Elisabeth M., Clur, Sally-Ann B., Christoffels, Vincent M., Postma, Alex V., Bezzina, Connie R., Cardiology, ACS - Heart failure & arrhythmias, Medical Biology, Amsterdam Cardiovascular Sciences, Paediatric Cardiology, APH - Methodology, APH - Quality of Care, APH - Aging & Later Life, APH - Personalized Medicine, Human Genetics, Amsterdam Reproduction & Development (AR&D), and ACS - Pulmonary hypertension & thrombosis

Abstract

Due to a processing error the author’s Doris Škorić-Milosavljević, Najim Lahrouchi, Alex V. Postma, Connie R. Bezzina were assigned to affiliation 38. However, affiliation 38 does not exist. In addition, the affiliations of Najim Lahrouchi, Elisabeth M. Lodder, and Connie R. Bezzina should be number 1 instead of number 2. The correct affiliation is Department of Clinical and Experimental Cardiology, Amsterdam University Medical Center, Amsterdam, The Netherlands. The original article has been corrected.

Published
2021

13. Erratum: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease (PLoS Genetics (2021) 17:7 (e1009679) DOI: 10.1371/journal.pgen.1009679)

Author

Audain, Enrique, Wilsdon, Anna, Breckpot, Jeroen, Izarzugaza, Jose M. G., Fitzgerald, Tomas W., Kahlert, Anne-Karin, Sifrim, Alejandro, Wunnemann, Florian, Perez-Riverol, Yasset, Abdul-Khaliq, Hashim, Bak, Mads, Bassett, Anne S., Benson, D. Woodrow, Berger, Felix, Daehnert, Ingo, Devriendt, Koenraad, Dittrich, Sven, Daubeney, Piers Ef, Garg, Vidu, Hackmann, Karl, Hoff, Kirstin, Hofmann, Philipp, Dombrowsky, Gregor, Pickardt, Thomas, Bauer, Ulrike, Keavney, Bernard D., Klaassen, Sabine, Kramer, Hans-Heiner, Marshall, Christian R., Milewicz, Dianna M., Lemaire, Scott, Coselli, Joseph S., Mitchell, Michael E., Tomita-Mitchell, Aoy, Prakash, Siddharth K., Stamm, Karl, Stewart, Alexandre F. R., Silversides, Candice K., Siebert, Reiner, Stiller, Brigitte, Rosenfeld, Jill A., Vater, Inga, Postma, Alex V., Caliebe, Almuth, Brook, J. David, Andelfinger, Gregor, Hurles, Matthew E., Thienpont, Bernard, Larsen, Lars Allan, Hitz, Marc-Phillip, Human Genetics, Medical Biology, ACS - Heart failure & arrhythmias, ACS - Pulmonary hypertension & thrombosis, Amsterdam Cardiovascular Sciences, and Amsterdam Reproduction & Development (AR&D)

Abstract

The thirteenth author's name is spelled incorrectly. The correct name is: D. Woodrow Benson.

Published
2021

14. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

Author

Audain, Enrique, primary, Wilsdon, Anna, additional, Breckpot, Jeroen, additional, Izarzugaza, Jose M. G., additional, Fitzgerald, Tomas W., additional, Kahlert, Anne-Karin, additional, Sifrim, Alejandro, additional, Wünnemann, Florian, additional, Perez-Riverol, Yasset, additional, Abdul-Khaliq, Hashim, additional, Bak, Mads, additional, Bassett, Anne S., additional, Benson, D. Woodrow, additional, Berger, Felix, additional, Daehnert, Ingo, additional, Devriendt, Koenraad, additional, Dittrich, Sven, additional, Daubeney, Piers EF, additional, Garg, Vidu, additional, Hackmann, Karl, additional, Hoff, Kirstin, additional, Hofmann, Philipp, additional, Dombrowsky, Gregor, additional, Pickardt, Thomas, additional, Bauer, Ulrike, additional, Keavney, Bernard D., additional, Klaassen, Sabine, additional, Kramer, Hans-Heiner, additional, Marshall, Christian R., additional, Milewicz, Dianna M., additional, Lemaire, Scott, additional, Coselli, Joseph S., additional, Mitchell, Michael E., additional, Tomita-Mitchell, Aoy, additional, Prakash, Siddharth K., additional, Stamm, Karl, additional, Stewart, Alexandre F. R., additional, Silversides, Candice K., additional, Siebert, Reiner, additional, Stiller, Brigitte, additional, Rosenfeld, Jill A., additional, Vater, Inga, additional, Postma, Alex V., additional, Caliebe, Almuth, additional, Brook, J. David, additional, Andelfinger, Gregor, additional, Hurles, Matthew E., additional, Thienpont, Bernard, additional, Larsen, Lars Allan, additional, and Hitz, Marc-Phillip, additional

Published
2021
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15. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

Author

Audain, Enrique, primary, Wilsdon, Anna, additional, Breckpot, Jeroen, additional, Izarzugaza, Jose M. G., additional, Fitzgerald, Tomas W., additional, Kahlert, Anne-Karin, additional, Sifrim, Alejandro, additional, Wünnemann, Florian, additional, Perez-Riverol, Yasset, additional, Abdul-Khaliq, Hashim, additional, Bak, Mads, additional, Bassett, Anne S., additional, Benson, Woodrow D., additional, Berger, Felix, additional, Daehnert, Ingo, additional, Devriendt, Koenraad, additional, Dittrich, Sven, additional, Daubeney, Piers EF, additional, Garg, Vidu, additional, Hackmann, Karl, additional, Hoff, Kirstin, additional, Hofmann, Philipp, additional, Dombrowsky, Gregor, additional, Pickardt, Thomas, additional, Bauer, Ulrike, additional, Keavney, Bernard D., additional, Klaassen, Sabine, additional, Kramer, Hans-Heiner, additional, Marshall, Christian R., additional, Milewicz, Dianna M., additional, Lemaire, Scott, additional, Coselli, Joseph S., additional, Mitchell, Michael E., additional, Tomita-Mitchell, Aoy, additional, Prakash, Siddharth K., additional, Stamm, Karl, additional, Stewart, Alexandre F. R., additional, Silversides, Candice K., additional, Siebert, Reiner, additional, Stiller, Brigitte, additional, Rosenfeld, Jill A., additional, Vater, Inga, additional, Postma, Alex V., additional, Caliebe, Almuth, additional, Brook, J. David, additional, Andelfinger, Gregor, additional, Hurles, Matthew E., additional, Thienpont, Bernard, additional, Larsen, Lars Allan, additional, and Hitz, Marc-Phillip, additional

Published
2021
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16. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

Author

Audain, Enrique, Wilsdon, Anna, Breckpot, Jeroen, Izarzugaza, Jose M.G., Fitzgerald, Tomas W., Kahlert, Anne Karin, Sifrim, Alejandro, Wünnemann, Florian, Perez-Riverol, Yasset, Abdul-Khaliq, Hashim, Bak, Mads, Bassett, Anne S., Benson, Woodrow D., Berger, Felix, Daehnert, Ingo, Devriendt, Koenraad, Dittrich, Sven, Daubeney, Piers E.F., Garg, Vidu, Hackmann, Karl, Hoff, Kirstin, Hofmann, Philipp, Dombrowsky, Gregor, Pickardt, Thomas, Bauer, Ulrike, Keavney, Bernard D., Klaassen, Sabine, Kramer, Hans Heiner, Marshall, Christian R., Milewicz, Dianna M., Lemaire, Scott, Coselli, Joseph S., Mitchell, Michael E., Tomita-Mitchell, Aoy, Prakash, Siddharth K., Stamm, Karl, Stewart, Alexandre F.R., Silversides, Candice K., Siebert, Reiner, Stiller, Brigitte, Rosenfeld, Jill A., Vater, Inga, Postma, Alex V., Caliebe, Almuth, Brook, J. David, Andelfinger, Gregor, Hurles, Matthew E., Thienpont, Bernard, Larsen, Lars Allan, Hitz, Marc Phillip, Audain, Enrique, Wilsdon, Anna, Breckpot, Jeroen, Izarzugaza, Jose M.G., Fitzgerald, Tomas W., Kahlert, Anne Karin, Sifrim, Alejandro, Wünnemann, Florian, Perez-Riverol, Yasset, Abdul-Khaliq, Hashim, Bak, Mads, Bassett, Anne S., Benson, Woodrow D., Berger, Felix, Daehnert, Ingo, Devriendt, Koenraad, Dittrich, Sven, Daubeney, Piers E.F., Garg, Vidu, Hackmann, Karl, Hoff, Kirstin, Hofmann, Philipp, Dombrowsky, Gregor, Pickardt, Thomas, Bauer, Ulrike, Keavney, Bernard D., Klaassen, Sabine, Kramer, Hans Heiner, Marshall, Christian R., Milewicz, Dianna M., Lemaire, Scott, Coselli, Joseph S., Mitchell, Michael E., Tomita-Mitchell, Aoy, Prakash, Siddharth K., Stamm, Karl, Stewart, Alexandre F.R., Silversides, Candice K., Siebert, Reiner, Stiller, Brigitte, Rosenfeld, Jill A., Vater, Inga, Postma, Alex V., Caliebe, Almuth, Brook, J. David, Andelfinger, Gregor, Hurles, Matthew E., Thienpont, Bernard, Larsen, Lars Allan, and Hitz, Marc Phillip

Abstract

Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parentoffspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Published
2021

17. Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease

Author

Izarzugaza, Jose M.G., Ellesøe, Sabrina G., Doganli, Canan, Ehlers, Natasja Spring, Dalgaard, Marlene D., Audain, Enrique, Dombrowsky, Gregor, Banasik, Karina, Sifrim, Alejandro, Wilsdon, Anna, Thienpont, Bernard, Breckpot, Jeroen, Gewillig, Marc, Brook, J. David, Hitz, Marc Phillip, Larsen, Lars A., Brunak, Søren, Izarzugaza, Jose M.G., Ellesøe, Sabrina G., Doganli, Canan, Ehlers, Natasja Spring, Dalgaard, Marlene D., Audain, Enrique, Dombrowsky, Gregor, Banasik, Karina, Sifrim, Alejandro, Wilsdon, Anna, Thienpont, Bernard, Breckpot, Jeroen, Gewillig, Marc, Brook, J. David, Hitz, Marc Phillip, Larsen, Lars A., and Brunak, Søren

Abstract

Background: Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD. Methods: We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model. Results: We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2, and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes. Conclusions: The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.

Published
2020

21. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike MM, Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances, Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, INTERVAL Study, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J, Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P, Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H, Park, Soo-Mi, Parker, Michael J, Pickardt, Thomas, Pollard, Martin O, Robert, Leema, Roberts, David J, Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Chris, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers EF, Keavney, Bernard, Goodship, Judith, UK10K Consortium, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F, Firth, Helen V, Barrett, Jeffrey C, Devriendt, Koenraad, FitzPatrick, David R, Brook, J David, Deciphering Developmental Disorders Study, Hurles, Matthew E, Sifrim, Alejandro [0000-0001-8247-4020], Thienpont, Bernard [0000-0002-8772-6845], Banka, Siddharth [0000-0002-8527-2210], Pollard, Martin O [0000-0001-8738-0920], Mital, Seema [0000-0002-7643-4484], Keavney, Bernard [0000-0001-9573-0812], Barrett, Jeffrey C [0000-0002-1152-370X], and Apollo - University of Cambridge Repository

Subjects
Heart Defects, Congenital, Male, Protein Conformation, Syndrome, Autoantigens, CDC2 Protein Kinase, Mutation, Humans, Exome, Female, cardiovascular diseases, Protein Kinase C, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Sequence Deletion
Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2). Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (∼2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Published
2016

22. Germline variants in HEY2functional domains lead to congenital heart defects and thoracic aortic aneurysms

Author

van Walree, Eva S., Dombrowsky, Gregor, Jansen, Iris E., Mirkov, Maša Umićević, Zwart, Rob, Ilgun, Aho, Guo, Dongchuan, Clur, Sally-Ann B., Amin, Ahmed S., Savage, Jeanne E., van der Wal, Allard C., Waisfisz, Quinten, Maugeri, Alessandra, Wilsdon, Anna, Bu’Lock, Frances A., Hurles, Matthew E., Dittrich, Sven, Berger, Felix, Audain Martinez, Enrique, Christoffels, Vincent M., Hitz, Marc-Philip, Milewicz, Dianna M., Posthuma, Daniëlle, Meijers-Heijboer, Hanne, Postma, Alex V., and Mathijssen, Inge B.

Abstract

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.

Published
2021
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24. An emerging phenotype of Xq22 microdeletions in females with severe intellectual disability, hypotonia and behavioral abnormalities

Author

Yamamoto, Toshiyuki, Wilsdon, Anna, Joss, Shelagh, Isidor, Bertrand, Erlandsson, Anna, Suri, Mohnish, Sangu, Noriko, Shimada, Shino, Shimojima, Keiko, Le Caignec, Cedric, Samuelsson, Lena, Stefanova, Margarita, Yamamoto, Toshiyuki, Wilsdon, Anna, Joss, Shelagh, Isidor, Bertrand, Erlandsson, Anna, Suri, Mohnish, Sangu, Noriko, Shimada, Shino, Shimojima, Keiko, Le Caignec, Cedric, Samuelsson, Lena, and Stefanova, Margarita

Abstract

The majority of Xq22 duplications seen in patients with Pelizaeus-Merzbacher disease (PMD) include proteolipid protein 1 (PLP1), the gene responsible for PMD, and neighboring genes. Some cases result from larger duplications up to 7 Mb in size. In comparison, the deletions including PLP1 seen in PMD patients are small. In this study, we present the genetic and clinical information for five female patients with deletions involving the Xq22 region, and review the correlation between the genotype and phenotype. Three of the five patients show similar large deletions (greater than3 Mb) ranging from Xq22.1 to Xq22.3 and all manifest severe intellectual disability, hypotonia and behavioral abnormalities. The most striking similarity among them are the behavioral problems, including poor eye contact and sleep disturbance. We propose that this represents an emerging distinctive microdeletion syndrome encompassing PLP1 in female patients. The possible candidate region responsible for such distinctive features has been narrowed down to the neighboring region for PLP1, including the interleukin 1 receptor accessory protein-like 2 (IL1RAPL2) gene and the clustered brain expressed X-linked (BEX) genes. The gene(s) responsible for severe neurological features in the patients in this study would be located in the regions proximate to PLP1; thus, males with the deletions involving the gene(s) would be lethal, and finally, the sizes of the deletions in PMD patients would be smaller than those of the duplications.

Published
2014
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25. An emerging phenotype of Xq22 microdeletions in females with severe intellectual disability, hypotonia and behavioral abnormalities

Author

Yamamoto, Toshiyuki, primary, Wilsdon, Anna, additional, Joss, Shelagh, additional, Isidor, Bertrand, additional, Erlandsson, Anna, additional, Suri, Mohnish, additional, Sangu, Noriko, additional, Shimada, Shino, additional, Shimojima, Keiko, additional, Le Caignec, Cédric, additional, Samuelsson, Lena, additional, and Stefanova, Margarita, additional

Published
2014
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26. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Al Turki, Saeed H., Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M. M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances, Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Chris, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E. F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, and Hurles, Matthew

Abstract

Congenital Heart Defects (CHD) have a neonatal incidence of 0.8-1%1,2. Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (~2.7%)3, suggesting a considerable role for de novo mutations (DNM), and/or incomplete penetrance4,5. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of ‘syndromic’ patients with extra-cardiac manifestations6,7. We exome sequenced 1,891 probands, including both syndromic (S-CHD, n=610) and non-syndromic cases (NS-CHD, n=1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs, but not inherited PTVs, in known CHD-associated genes, consistent with recent findings8. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three novel genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study reveals distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Published
2018
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27. Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease.

Author

Izarzugaza, Jose M. G., Ellesøe, Sabrina G., Doganli, Canan, Ehlers, Natasja Spring, Dalgaard, Marlene D., Audain, Enrique, Dombrowsky, Gregor, Banasik, Karina, Sifrim, Alejandro, Wilsdon, Anna, Thienpont, Bernard, Breckpot, Jeroen, Gewillig, Marc, Competence Network for Congenital Heart Defects, Germany, Abdul-Khaliq, Hashim, Kramer, Hans-Heiner, Berger, Felix, Stiller, Brigitte, Bauer, Ulrike, and Pickardt, Thomas

Subjects
CONGENITAL heart disease, SYSTEM analysis, SYSTEMS biology, ETIOLOGY of diseases, HEART disease related mortality, GENE silencing, EXOMES
Abstract

Background: Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD. Methods: We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model. Results: We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1, PLCB2, and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes. Conclusions: The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD. [ABSTRACT FROM AUTHOR]

Published
2020
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28. Identifying novel genes that cause congenital heart disease

Author

Wilsdon, Anna

Subjects
cardiovascular diseases
Abstract

Complex genetic networks underlie the development of the heart. Variants in some of these genes can lead to congenital heart disease (CHD). Despite the hundreds of genes that have been identified as causing CHD in humans, they only account for a small proportion of individuals with CHD. We carried out whole exome sequencing in the largest cohort of individuals with CHD reported at the time of publication, and identified three novel genome wide significant syndromic CHD genes; CDK13, PRKD1 and CHD4. \ud \ud Individuals with mutations in CHD4 show neurodevelopmental disability, genital abnormalities and share some phenotypic overlap with other chromatinopathies. Mutations in PRKD1 also cause syndromic CHD, but identification of further affected individuals is required to determine if there is a consistent phenotype. Prkd1 mouse models do not have a high incidence of CHD, but this gene may be important in future work as it plays a role in cardiac hypertrophy. \ud \ud Individuals with mutations in CDK13 show a recognisable phenotype and the mouse model shows embryonic lethality and atrioventricular canal defects. The precise mechanism by which heterozygous mutations cause disease in humans remains unclear. The phenotypic and genotypic spectrum has been expanded by subsequent reports of individuals with mutations in CKD13. \ud \ud We also identify a role for inherited variants with reduced penetrance in individuals with non-syndromic CHD. This is significant, as the vast majority of individuals with CHD have non-syndromic CHD. It is an important step in understanding the potential oligogenic pathogenesis of the majority of CHD.\ud \ud Ultimately we aim to increase our knowledge of the genes and networks that underlie CHD, to improve diagnostic yield in individuals affected with CHD. I was able to feedback pathogenic mutations in CHD genes to participants in this study locally. Following this unbiased approach of non-targeted testing in a cohort with multiple types of CHD, will improve our knowledge of genotype phenotype correlations. We also hope that understanding more about the genes involved in cardiogenesis and CHD might have relevance for the failing heart, and development of treatments in the future too.

29. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, Hurles, Matthew E., Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, and Hurles, Matthew E.

Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8–1%. Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (~2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Full Text
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30. Identifying novel genes that cause congenital heart disease

Author

Wilsdon, Anna and Wilsdon, Anna

Abstract

Complex genetic networks underlie the development of the heart. Variants in some of these genes can lead to congenital heart disease (CHD). Despite the hundreds of genes that have been identified as causing CHD in humans, they only account for a small proportion of individuals with CHD. We carried out whole exome sequencing in the largest cohort of individuals with CHD reported at the time of publication, and identified three novel genome wide significant syndromic CHD genes; CDK13, PRKD1 and CHD4. Individuals with mutations in CHD4 show neurodevelopmental disability, genital abnormalities and share some phenotypic overlap with other chromatinopathies. Mutations in PRKD1 also cause syndromic CHD, but identification of further affected individuals is required to determine if there is a consistent phenotype. Prkd1 mouse models do not have a high incidence of CHD, but this gene may be important in future work as it plays a role in cardiac hypertrophy. Individuals with mutations in CDK13 show a recognisable phenotype and the mouse model shows embryonic lethality and atrioventricular canal defects. The precise mechanism by which heterozygous mutations cause disease in humans remains unclear. The phenotypic and genotypic spectrum has been expanded by subsequent reports of individuals with mutations in CKD13. We also identify a role for inherited variants with reduced penetrance in individuals with non-syndromic CHD. This is significant, as the vast majority of individuals with CHD have non-syndromic CHD. It is an important step in understanding the potential oligogenic pathogenesis of the majority of CHD. Ultimately we aim to increase our knowledge of the genes and networks that underlie CHD, to improve diagnostic yield in individuals affected with CHD. I was able to feedback pathogenic mutations in CHD genes to participants in this study locally. Following this unbiased approach of non-targeted testing in a cohort with multiple types of CHD, will improve our knowledge of

31. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, Hurles, Matthew E., Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, and Hurles, Matthew E.

Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8–1%. Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (~2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Full Text
View/download PDF

32. Identifying novel genes that cause congenital heart disease

Author

Wilsdon, Anna and Wilsdon, Anna

Abstract

Complex genetic networks underlie the development of the heart. Variants in some of these genes can lead to congenital heart disease (CHD). Despite the hundreds of genes that have been identified as causing CHD in humans, they only account for a small proportion of individuals with CHD. We carried out whole exome sequencing in the largest cohort of individuals with CHD reported at the time of publication, and identified three novel genome wide significant syndromic CHD genes; CDK13, PRKD1 and CHD4. Individuals with mutations in CHD4 show neurodevelopmental disability, genital abnormalities and share some phenotypic overlap with other chromatinopathies. Mutations in PRKD1 also cause syndromic CHD, but identification of further affected individuals is required to determine if there is a consistent phenotype. Prkd1 mouse models do not have a high incidence of CHD, but this gene may be important in future work as it plays a role in cardiac hypertrophy. Individuals with mutations in CDK13 show a recognisable phenotype and the mouse model shows embryonic lethality and atrioventricular canal defects. The precise mechanism by which heterozygous mutations cause disease in humans remains unclear. The phenotypic and genotypic spectrum has been expanded by subsequent reports of individuals with mutations in CKD13. We also identify a role for inherited variants with reduced penetrance in individuals with non-syndromic CHD. This is significant, as the vast majority of individuals with CHD have non-syndromic CHD. It is an important step in understanding the potential oligogenic pathogenesis of the majority of CHD. Ultimately we aim to increase our knowledge of the genes and networks that underlie CHD, to improve diagnostic yield in individuals affected with CHD. I was able to feedback pathogenic mutations in CHD genes to participants in this study locally. Following this unbiased approach of non-targeted testing in a cohort with multiple types of CHD, will improve our knowledge of

33. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, Hurles, Matthew E., Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, and Hurles, Matthew E.

Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8–1%. Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (~2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

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34. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing

Author

Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, Hurles, Matthew E., Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike M.M., Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances A., Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J., Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P., Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H., Park, Soo-Mi, Parker, Michael J., Pickardt, Thomas, Pollard, Martin O., Robert, Leema, Roberts, David J., Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Christopher, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers E.F., Keavney, Bernard, Goodship, Judith, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F., Firth, Helen V., Barrett, Jeffrey C., Devriendt, Koenraad, FitzPatrick, David R., Brook, J. David, and Hurles, Matthew E.

Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8–1%. Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (~2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

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35. Correction to: Rare variants in KDR, encoding VEGF Receptor 2, are associated with tetralogy of Fallot.

Author

Škorić-Milosavljević D, Lahrouchi N, Bosada FM, Dombrowsky G, Williams SG, Lesurf R, Tjong FVY, Walsh R, El Bouchikhi I, Breckpot J, Audain E, Ilgun A, Beekman L, Ratbi I, Strong A, Muenke M, Heide S, Muir AM, Hababa M, Cross L, Zhou D, Pastinen T, Zackai E, Atmani S, Ouldim K, Adadi N, Steindl K, Rauch A, Brook D, Wilsdon A, Kuipers I, Blom NA, Mulder BJ, Mefford HC, Keren B, Joset P, Kruszka P, Thiffault I, Sheppard SE, Roberts A, Lodder EM, Keavney BD, Clur SB, Mital S, Hitz MP, Christoffels VM, Postma AV, and Bezzina CR

Published
2021
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36. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing.

Author

Sifrim A, Hitz MP, Wilsdon A, Breckpot J, Turki SH, Thienpont B, McRae J, Fitzgerald TW, Singh T, Swaminathan GJ, Prigmore E, Rajan D, Abdul-Khaliq H, Banka S, Bauer UM, Bentham J, Berger F, Bhattacharya S, Bu'Lock F, Canham N, Colgiu IG, Cosgrove C, Cox H, Daehnert I, Daly A, Danesh J, Fryer A, Gewillig M, Hobson E, Hoff K, Homfray T, Kahlert AK, Ketley A, Kramer HH, Lachlan K, Lampe AK, Louw JJ, Manickara AK, Manase D, McCarthy KP, Metcalfe K, Moore C, Newbury-Ecob R, Omer SO, Ouwehand WH, Park SM, Parker MJ, Pickardt T, Pollard MO, Robert L, Roberts DJ, Sambrook J, Setchfield K, Stiller B, Thornborough C, Toka O, Watkins H, Williams D, Wright M, Mital S, Daubeney PE, Keavney B, Goodship J, Abu-Sulaiman RM, Klaassen S, Wright CF, Firth HV, Barrett JC, Devriendt K, FitzPatrick DR, Brook JD, and Hurles ME

Subjects
CDC2 Protein Kinase chemistry, Exome genetics, Female, Humans, Male, Protein Conformation, Sequence Deletion, Syndrome, Autoantigens genetics, CDC2 Protein Kinase genetics, Heart Defects, Congenital genetics, Mi-2 Nucleosome Remodeling and Deacetylase Complex genetics, Mutation genetics, Protein Kinase C genetics
Abstract

Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2). Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (∼2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.

Published
2016
Full Text
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