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Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E. Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Mol Genet Genomic Med 2023; 11:e2109. [PMID: 36468602 PMCID: PMC10009911 DOI: 10.1002/mgg3.2109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Sarah L Mehrem
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ariane C Fechtner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Ruth Raff
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.,Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Khalid Aldhorae
- Department of Orthodontics, College of Dentistry, Thamar University, Thamar, Yemen.,Department of Orthodontics, College of Dentistry, University of Ibn al-Nafis for Medical Sciences, Sanaa, Yemen
| | - Bert Braumann
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Teresa Kruse
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | | | - Gerrit Spanier
- Department of Cranio-Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Erlangen-Nürnberg, Erlangen, Germany.,Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,University Hospital Cologne, Cologne, Germany
| | - Tim Becker
- Institute of Community Medicine, University of Greifswald, Greifswald, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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