DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome

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• 作者：Judy Savige (1) (11)
  Elisabet Ars (2)
  Richard G. H. Cotton (3)
  David Crockett (4)
  Hayat Dagher (1)
  Constantinos Deltas (5)
  Jie Ding (6)
  Frances Flinter (7)
  Genevieve Pont-Kingdon (4)
  Nizar Smaoui (8)
  Roser Torra (9)
  Helen Storey (10)
  
• 关键词：Alport syndrome ; Gene variant ; DNA database ; Genetic testing ; Inherited renal disease
• 刊名：Pediatric Nephrology
• 出版年：2014
• 出版时间：June 2014
• 年：2014
• 卷：29
• 期：6
• 页码：971-977
• 全文大小：
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• 作者单位：Judy Savige (1) (11)
  Elisabet Ars (2)
  Richard G. H. Cotton (3)
  David Crockett (4)
  Hayat Dagher (1)
  Constantinos Deltas (5)
  Jie Ding (6)
  Frances Flinter (7)
  Genevieve Pont-Kingdon (4)
  Nizar Smaoui (8)
  Roser Torra (9)
  Helen Storey (10)
  
  1. Department of Medicine (Northern Health), The University of Melbourne, Epping, VIC, Australia
  11. The University of Melbourne (AH/NH), The Northern Hospital, Cooper, Epping, VIC, 3076, Australia
  2. Nephrology Department, Fundacio Puigvert, Barcelona, Spain
  3. Human Variome Project, The University of Melbourne, Parkville, VIC, Australia
  4. ARUP Laboratories, ARUP Institute of Clinical and Experimental Pathology, Salt Lake City, UT, USA
  5. Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
  6. Pediatric Department, Peking University First Hospital, Beijing, China
  7. Department of Clinical Genetics, Guy’s and St Thomas-NHS Trust Foundation, London, UK
  8. GeneDx, Gaithersburg, MD, USA
  9. Molecular Biology Laboratory, Fundacio Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
  10. GSTS Pathology, Guy’s and St Thomas-NHS Trust Foundation, London, UK
  
• ISSN：1432-198X

文摘

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants (https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases.