6
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Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2018; 51:117-127. [PMID: 30578417 PMCID: PMC6668343 DOI: 10.1038/s41588-018-0281-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3, and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.,Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Alejandra Perez
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Qingxue Liu
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - David A Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ekaterina Batourina
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Max Werth
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Charlly Kao
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Valentina P Capone
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Young-Ji Na
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dina Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alba Carrea
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Daniele Cusi
- National Research Council of Italy, Inst. Biomedical Technologies Milano Bio4dreams Scientific Unit, Milano, Italy
| | - Claudia Izzi
- Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST, Spedali Civili e Presidio di Montichiari, Brescia, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia, Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria "G. Martino", Messina, Italy
| | - Pasquale Zamboli
- Division of Nephrology, University of Campania "Luigi Vanvitell", Naples, Italy
| | - Hope White
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Anna Krakowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, Lublin, Poland
| | | | - Maria K Borszewska-Kornacka
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Robert Pawluch
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Mark G Dobson
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - John M Darlow
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Hospital Tallaght, Dublin, Ireland
| | - David E Barton
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,University College Dublin UCD School of Medicine, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Susan L Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Division of Nephrology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Bradley A Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Division of Nephrology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Zoran Gucev
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Vladimir J Lozanovski
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia.,University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Lida M Rodas
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M Campistol
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pasquale Casale
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Mount Sinai Medical Center, Kravis Children's Hospital, New York, NY, USA
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, NM, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Débora M Miranda
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo A Oliveira
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Cristina Simões-E-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jonathan M Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, all at Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
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8
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Takeda K, Kou I, Kawakami N, Iida A, Nakajima M, Ogura Y, Imagawa E, Miyake N, Matsumoto N, Yasuhiko Y, Sudo H, Kotani T, Nakamura M, Matsumoto M, Watanabe K, Ikegawa S. Compound Heterozygosity for Null Mutations and a Common Hypomorphic Risk Haplotype in TBX6 Causes Congenital Scoliosis. Hum Mutat 2017; 38:317-323. [PMID: 28054739 DOI: 10.1002/humu.23168] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/26/2016] [Indexed: 12/17/2022]
Abstract
Congenital scoliosis (CS) occurs as a result of vertebral malformations and has an incidence of 0.5-1/1,000 births. Recently, TBX6 on chromosome 16p11.2 was reported as a disease gene for CS; about 10% of Chinese CS patients were compound heterozygotes for rare null mutations and a common haplotype defined by three SNPs in TBX6. All patients had hemivertebrae. We recruited 94 Japanese CS patients, investigated the TBX6 locus for both mutations and the risk haplotype, examined transcriptional activities of mutant TBX6 in vitro, and evaluated clinical and radiographic features. We identified TBX6 null mutations in nine patients, including a missense mutation that had a loss of function in vitro. All had the risk haplotype in the opposite allele. One of the mutations showed dominant negative effect. Although all Chinese patients had one or more hemivertebrae, two Japanese patients did not have hemivertebra. The compound heterozygosity of null mutations and the common risk haplotype in TBX6 also causes CS in Japanese patients with similar incidence. Hemivertebra was not a specific type of spinal malformation in TBX6-associated CS (TACS). A heterozygous TBX6 loss-of-function mutation has been reported in a family with autosomal-dominant spondylocostal dysostosis, but it may represent a spectrum of the same disease with TACS.
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Affiliation(s)
- Kazuki Takeda
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, 108-8639, Japan
| | - Ikuyo Kou
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan
| | - Noriaki Kawakami
- Department of Orthopaedic Surgery, Meijo Hospital, Nagoya, 460-0001, Japan
| | - Aritoshi Iida
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan
| | - Masahiro Nakajima
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan
| | - Yoji Ogura
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, 108-8639, Japan
| | - Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Yukuto Yasuhiko
- Division of Cellular and Molecular Toxicology, National Institute of Health Sciences, Tokyo, 158-8501, Japan
| | - Hideki Sudo
- Department of Advanced Medicine for Spine and Spinal Cord Disorders, Hokkaido University Graduate School of Medicine, Sapporo, 060-8648, Japan
| | - Toshiaki Kotani
- Department of Orthopaedic Surgery, Seirei Sakura Citizen Hospital, Sakura, 285-0825, Japan
| | | | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, 108-8639, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, 108-8639, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, 108-8639, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 160-8582, Japan
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