A validated heart-specific model for splice-disrupting variants in childhood heart disease
Abstract Background Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routine...
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2024-10-01
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| Online Access: | https://doi.org/10.1186/s13073-024-01383-8 |
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| author | Robert Lesurf Jeroen Breckpot Jade Bouwmeester Nour Hanafi Anjali Jain Yijing Liang Tanya Papaz Jane Lougheed Tapas Mondal Mahmoud Alsalehi Luis Altamirano-Diaz Erwin Oechslin Enrique Audain Gregor Dombrowsky Alex V. Postma Odilia I. Woudstra Berto J. Bouma Marc-Phillip Hitz Connie R. Bezzina Gillian M. Blue David S. Winlaw Seema Mital |
| author_facet | Robert Lesurf Jeroen Breckpot Jade Bouwmeester Nour Hanafi Anjali Jain Yijing Liang Tanya Papaz Jane Lougheed Tapas Mondal Mahmoud Alsalehi Luis Altamirano-Diaz Erwin Oechslin Enrique Audain Gregor Dombrowsky Alex V. Postma Odilia I. Woudstra Berto J. Bouma Marc-Phillip Hitz Connie R. Bezzina Gillian M. Blue David S. Winlaw Seema Mital |
| author_sort | Robert Lesurf |
| collection | DOAJ |
| description | Abstract Background Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routinely captured and/or evaluated by standard clinical genetic tests. Recent computational algorithms such as SpliceAI have shown an ability to predict such variants, but are not specific to cardiac-expressed genes and transcriptional isoforms. Methods We used genome sequencing (GS) (n = 1101 CHD probands) and myocardial RNA-Sequencing (RNA-Seq) (n = 154 CHD and n = 43 cardiomyopathy probands) to identify and validate splice disrupting variants, and to develop a heart-specific model for canonical and non-canonical splice variants that can be applied to patients with CHD and cardiomyopathy. Two thousand five hundred seventy GS samples from the Medical Genome Reference Bank were analyzed as healthy controls. Results Of 8583 rare DNA splice-disrupting variants initially identified using SpliceAI, 100 were associated with altered splice junctions in the corresponding patient myocardium affecting 95 genes. Using strength of myocardial gene expression and genome-wide DNA variant features that were confirmed to affect splicing in myocardial RNA, we trained a machine learning model for predicting cardiac-specific splice-disrupting variants (AUC 0.86 on internal validation). In a validation set of 48 CHD probands, the cardiac-specific model outperformed a SpliceAI model alone (AUC 0.94 vs 0.67 respectively). Application of this model to an additional 947 CHD probands with only GS data identified 1% patients with canonical and 11% patients with non-canonical splice-disrupting variants in CHD genes. Forty-nine percent of predicted splice-disrupting variants were intronic and > 10 bp from existing splice junctions. The burden of high-confidence splice-disrupting variants in CHD genes was 1.28-fold higher in CHD cases compared with healthy controls. Conclusions A new cardiac-specific in silico model was developed using complementary GS and RNA-Seq data that improved genetic yield by identifying a significant burden of non-canonical splice variants associated with CHD that would not be detectable through panel or exome sequencing. |
| format | Article |
| id | doaj-art-1d371c4ddd2340898e94f229a04d496b |
| institution | OA Journals |
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| language | English |
| publishDate | 2024-10-01 |
| publisher | BMC |
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| series | Genome Medicine |
| spelling | doaj-art-1d371c4ddd2340898e94f229a04d496b2025-08-20T02:17:48ZengBMCGenome Medicine1756-994X2024-10-0116112410.1186/s13073-024-01383-8A validated heart-specific model for splice-disrupting variants in childhood heart diseaseRobert Lesurf0Jeroen Breckpot1Jade Bouwmeester2Nour Hanafi3Anjali Jain4Yijing Liang5Tanya Papaz6Jane Lougheed7Tapas Mondal8Mahmoud Alsalehi9Luis Altamirano-Diaz10Erwin Oechslin11Enrique Audain12Gregor Dombrowsky13Alex V. Postma14Odilia I. Woudstra15Berto J. Bouma16Marc-Phillip Hitz17Connie R. Bezzina18Gillian M. Blue19David S. Winlaw20Seema Mital21Genetics and Genome Biology Program, The Hospital for Sick ChildrenCenter for Human Genetics, University Hospitals LeuvenGenetics and Genome Biology Program, The Hospital for Sick ChildrenThe Centre for Computational Medicine, The Hospital for Sick ChildrenThe Centre for Computational Medicine, The Hospital for Sick ChildrenThe Centre for Computational Medicine, The Hospital for Sick ChildrenGenetics and Genome Biology Program, The Hospital for Sick ChildrenDivision of Cardiology, Children’s Hospital of Eastern OntarioDivision of Cardiology, Department of Pediatrics, McMaster Children’s HospitalDivision of Cardiology, Department of Pediatrics, Kingston Health Sciences CentreDivision of Cardiology, Department of Pediatrics, London Health Sciences CentreDivision of Cardiology, Department of Medicine, Toronto Adult Congenital Heart Disease Program at Peter Munk Cardiac Centre, University Health Network, and University of TorontoInstitute of Medical Genetics, University Medicine Oldenburg, Carl von Ossietzky UniversityInstitute of Medical Genetics, University Medicine Oldenburg, Carl von Ossietzky UniversityDepartment of Medical Biology, Amsterdam University Medical CenterDepartment of Internal Medicine, Amsterdam University Medical CenterDepartment of Cardiology, Amsterdam University Medical CenterInstitute of Medical Genetics, University Medicine Oldenburg, Carl von Ossietzky UniversityDepartment of Clinical and Experimental Cardiology, Amsterdam University Medical CenterHeart Centre for Children, The Children’s Hospital at WestmeadHeart Center, Ann and Robert H. Lurie Children’s Hospital of Chicago and Feinberg School of Medicine, Northwestern UniversityGenetics and Genome Biology Program, The Hospital for Sick ChildrenAbstract Background Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routinely captured and/or evaluated by standard clinical genetic tests. Recent computational algorithms such as SpliceAI have shown an ability to predict such variants, but are not specific to cardiac-expressed genes and transcriptional isoforms. Methods We used genome sequencing (GS) (n = 1101 CHD probands) and myocardial RNA-Sequencing (RNA-Seq) (n = 154 CHD and n = 43 cardiomyopathy probands) to identify and validate splice disrupting variants, and to develop a heart-specific model for canonical and non-canonical splice variants that can be applied to patients with CHD and cardiomyopathy. Two thousand five hundred seventy GS samples from the Medical Genome Reference Bank were analyzed as healthy controls. Results Of 8583 rare DNA splice-disrupting variants initially identified using SpliceAI, 100 were associated with altered splice junctions in the corresponding patient myocardium affecting 95 genes. Using strength of myocardial gene expression and genome-wide DNA variant features that were confirmed to affect splicing in myocardial RNA, we trained a machine learning model for predicting cardiac-specific splice-disrupting variants (AUC 0.86 on internal validation). In a validation set of 48 CHD probands, the cardiac-specific model outperformed a SpliceAI model alone (AUC 0.94 vs 0.67 respectively). Application of this model to an additional 947 CHD probands with only GS data identified 1% patients with canonical and 11% patients with non-canonical splice-disrupting variants in CHD genes. Forty-nine percent of predicted splice-disrupting variants were intronic and > 10 bp from existing splice junctions. The burden of high-confidence splice-disrupting variants in CHD genes was 1.28-fold higher in CHD cases compared with healthy controls. Conclusions A new cardiac-specific in silico model was developed using complementary GS and RNA-Seq data that improved genetic yield by identifying a significant burden of non-canonical splice variants associated with CHD that would not be detectable through panel or exome sequencing.https://doi.org/10.1186/s13073-024-01383-8Congenital Heart DiseaseGenomicsRNA splicingNon-canonicalMachine Learning |
| spellingShingle | Robert Lesurf Jeroen Breckpot Jade Bouwmeester Nour Hanafi Anjali Jain Yijing Liang Tanya Papaz Jane Lougheed Tapas Mondal Mahmoud Alsalehi Luis Altamirano-Diaz Erwin Oechslin Enrique Audain Gregor Dombrowsky Alex V. Postma Odilia I. Woudstra Berto J. Bouma Marc-Phillip Hitz Connie R. Bezzina Gillian M. Blue David S. Winlaw Seema Mital A validated heart-specific model for splice-disrupting variants in childhood heart disease Genome Medicine Congenital Heart Disease Genomics RNA splicing Non-canonical Machine Learning |
| title | A validated heart-specific model for splice-disrupting variants in childhood heart disease |
| title_full | A validated heart-specific model for splice-disrupting variants in childhood heart disease |
| title_fullStr | A validated heart-specific model for splice-disrupting variants in childhood heart disease |
| title_full_unstemmed | A validated heart-specific model for splice-disrupting variants in childhood heart disease |
| title_short | A validated heart-specific model for splice-disrupting variants in childhood heart disease |
| title_sort | validated heart specific model for splice disrupting variants in childhood heart disease |
| topic | Congenital Heart Disease Genomics RNA splicing Non-canonical Machine Learning |
| url | https://doi.org/10.1186/s13073-024-01383-8 |
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