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Huth EA, Zhao X, Owen N, Luna PN, Vogel I, Dorf ILH, Joss S, Clayton-Smith J, Parker MJ, Louw JJ, Gewillig M, Breckpot J, Kraus A, Sasaki E, Kini U, Burgess T, Tan TY, Armstrong R, Neas K, Ferrero GB, Brusco A, Kerstjens-Frederikse WS, Rankin J, Helvaty LR, Landis BJ, Geddes GC, McBride KL, Ware SM, Shaw CA, Lalani SR, Rosenfeld JA, Scott DA. Clinical exome sequencing efficacy and phenotypic expansions involving anomalous pulmonary venous return. Eur J Hum Genet 2023; 31:1430-1439. [PMID: 37673932 PMCID: PMC10689790 DOI: 10.1038/s41431-023-01451-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Anomalous pulmonary venous return (APVR) frequently occurs with other congenital heart defects (CHDs) or extra-cardiac anomalies. While some genetic causes have been identified, the optimal approach to genetic testing in individuals with APVR remains uncertain, and the etiology of most cases of APVR is unclear. Here, we analyzed molecular data from 49 individuals to determine the diagnostic yield of clinical exome sequencing (ES) for non-isolated APVR. A definitive or probable diagnosis was made for 8 of those individuals yielding a diagnostic efficacy rate of 16.3%. We then analyzed molecular data from 62 individuals with APVR accrued from three databases to identify novel APVR genes. Based on data from this analysis, published case reports, mouse models, and/or similarity to known APVR genes as revealed by a machine learning algorithm, we identified 3 genes-EFTUD2, NAA15, and NKX2-1-for which there is sufficient evidence to support phenotypic expansion to include APVR. We also provide evidence that 3 recurrent copy number variants contribute to the development of APVR: proximal 1q21.1 microdeletions involving RBM8A and PDZK1, recurrent BP1-BP2 15q11.2 deletions, and central 22q11.2 deletions involving CRKL. Our results suggest that ES and chromosomal microarray analysis (or genome sequencing) should be considered for individuals with non-isolated APVR for whom a genetic etiology has not been identified, and that genetic testing to identify an independent genetic etiology of APVR is not warranted in individuals with EFTUD2-, NAA15-, and NKX2-1-related disorders.
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Affiliation(s)
- Emily A Huth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Nichole Owen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ida Vogel
- Department of Clinical Medicine, Aarhus University, 8000, Aarhus, C, Denmark
| | - Inger L H Dorf
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Shelagh Joss
- West of Scotland Genomics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, Manchester University Hospitals, Manchester, M13 9WL, UK
- University of Manchester, Manchester, M13 9PL, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield, Children's Hospital, UK
| | - Jacoba J Louw
- Pediatric Cardiology Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marc Gewillig
- Department of Cardiovascular Sciences KU Leuven, Leuven, Belgium
- Pediatric Cardiology University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Catholic University, Leuven, Belgium
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Giovanni B Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | | | | | | | - Gabrielle C Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kim L McBride
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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