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Chan MMY, Sadeghi-Alavijeh O, Lopes FM, Hilger AC, Stanescu HC, Voinescu CD, Beaman GM, Newman WG, Zaniew M, Weber S, Ho YM, Connolly JO, Wood D, Maj C, Stuckey A, Kousathanas A, Kleta R, Woolf AS, Bockenhauer D, Levine AP, Gale DP. Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves. eLife 2022; 11:e74777. [PMID: 36124557 PMCID: PMC9512401 DOI: 10.7554/elife.74777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
Posterior urethral valves (PUV) are the commonest cause of end-stage renal disease in children, but the genetic architecture of this rare disorder remains unknown. We performed a sequencing-based genome-wide association study (seqGWAS) in 132 unrelated male PUV cases and 23,727 controls of diverse ancestry, identifying statistically significant associations with common variants at 12q24.21 (p=7.8 × 10-12; OR 0.4) and rare variants at 6p21.1 (p=2.0 × 10-8; OR 7.2), that were replicated in an independent European cohort of 395 cases and 4151 controls. Fine mapping and functional genomic data mapped these loci to the transcription factor TBX5 and planar cell polarity gene PTK7, respectively, the encoded proteins of which were detected in the developing urinary tract of human embryos. We also observed enrichment of rare structural variation intersecting with candidate cis-regulatory elements, particularly inversions predicted to affect chromatin looping (p=3.1 × 10-5). These findings represent the first robust genetic associations of PUV, providing novel insights into the underlying biology of this poorly understood disorder and demonstrate how a diverse ancestry seqGWAS can be used for disease locus discovery in a rare disease.
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Affiliation(s)
- Melanie MY Chan
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | | | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Alina C Hilger
- Children's Hospital, University of BonnBonnGermany
- Institute of Human Genetics, University of BonnBonnGermany
| | - Horia C Stanescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Catalin D Voinescu
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
| | - Glenda M Beaman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Evolution and Genomic Sciences, School of Biological Sciences, University of ManchesterManchesterUnited Kingdom
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona GóraZielona GoraPoland
| | - Stefanie Weber
- Department of Pediatric Nephrology, University of MarburgMarburgGermany
| | - Yee Mang Ho
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - John O Connolly
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Dan Wood
- Department of Adolescent Urology, University College London Hospitals NHS Foundation TrustLondonUnited Kingdom
| | - Carlo Maj
- Center for Human Genetics, University of MarburgMarburgGermany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of BonnBonnGermany
| | - Alexander Stuckey
- Genomics England, Queen Mary University of LondonLondonUnited Kingdom
| | | | - Robert Kleta
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Detlef Bockenhauer
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Nephrology Department, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUnited Kingdom
| | - Adam P Levine
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
- Research Department of Pathology, University College LondonLondonUnited Kingdom
| | - Daniel P Gale
- Department of Renal Medicine, University College LondonLondonUnited Kingdom
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Duffy KA, Cielo CM, Cohen JL, Gonzalez-Gandolfi CX, Griff JR, Hathaway ER, Kupa J, Taylor JA, Wang KH, Ganguly A, Deardorff MA, Kalish JM. Characterization of the Beckwith-Wiedemann spectrum: Diagnosis and management. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:693-708. [PMID: 31469230 DOI: 10.1002/ajmg.c.31740] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 01/20/2023]
Abstract
Beckwith-Wiedemann syndrome (BWS) is the most common epigenetic overgrowth and cancer predisposition disorder. Due to both varying molecular defects involving chromosome 11p15 and tissue mosaicism, patients can present with a variety of clinical features, leading to the newly defined Beckwith-Wiedemann spectrum (BWSp). The BWSp can be further divided into three subsets of patients: those presenting with classic features, those presenting with isolated lateralized overgrowth (ILO) and those not fitting into the previous two categories, termed atypical BWSp. Previous reports of patients with BWS have focused on those with the more recognizable, classic features, and limited information is available on those who fit into the atypical and ILO categories. Here, we present the first cohort of patients recruited across the entire BWSp, describe clinical features and molecular diagnostic characteristics, and provide insight into practical diagnosis and management recommendations that we have gained from this cohort.
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Affiliation(s)
- Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Christopher M Cielo
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer L Cohen
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Jessica R Griff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Evan R Hathaway
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jonida Kupa
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jesse A Taylor
- Division of Plastic and Reconstructive Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen H Wang
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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3
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Duffy KA, Sajorda BJ, Yu AC, Hathaway ER, Grand KL, Deardorff MA, Kalish JM. Beckwith-Wiedemann syndrome in diverse populations. Am J Med Genet A 2019; 179:525-533. [PMID: 30719840 DOI: 10.1002/ajmg.a.61053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 11/06/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) is the most common epigenetic overgrowth disorder and presents with patients affected by a variety of clinical features. Although genotype-phenotype correlations have been demonstrated in BWS and although BWS has been reported to occur equally among racial and ethnic backgrounds, no study to date has evaluated the frequency of findings in different backgrounds. In this study, we evaluated the incidence of clinical features and molecular diagnoses among patients with BWS in Caucasian, Mixed, and non-Caucasian groups. These results suggest that clinical features and molecular diagnoses differ between race/ethnicity groups and raise the possibility of race and ethnicity effects on genotype-phenotype correlations in BWS.
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Affiliation(s)
- Kelly A Duffy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Brian J Sajorda
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alice C Yu
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Evan R Hathaway
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katheryn L Grand
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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