Novel genetic susceptibility loci for diabetic end-stage renal disease identified through robust naive Bayes classification

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• 作者：Francesco Sambo (1)
  Alberto Malovini (2) (3)
  Niina Sandholm (4) (5) (6)
  Monica Stavarachi (4) (7)
  Carol Forsblom (4) (5)
  Ville-Petteri M?kinen (8) (9)
  Valma Harjutsalo (10) (4) (5)
  Raija Lithovius (4) (5)
  Daniel Gordin (4) (5)
  Maija Parkkonen (4) (5)
  Markku Saraheimo (4) (5)
  Lena M. Thorn (4) (5)
  Nina Tolonen (4) (5)
  Johan Wadén (4) (5)
  Bing He (11)
  Anne-May ?sterholm (11)
  Jaako Tuomilehto (10) (12) (13)
  Maria Lajer (14)
  Rany M. Salem (15) (16) (17)
  Amy Jayne McKnight (18)
  Lise Tarnow (20) (21)
  Nicolae M. Panduru (22) (4)
  Nicola Barbarini (2)
  Barbara Di Camillo (1)
  Gianna M. Toffolo (1)
  Karl Tryggvason (10)
  Riccardo Bellazzi (2)
  Claudio Cobelli (1)
  Per-Henrik Groop (23) (4) (5)
  
• 关键词：Bag of Naive Bayes ; Diabetic nephropathy ; End ; stage renal disease ; Susceptibility loci
• 刊名：Diabetologia
• 出版年：2014
• 出版时间：August 2014
• 年：2014
• 卷：57
• 期：8
• 页码：1611-1622
• 全文大小：519 KB
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• 作者单位：Francesco Sambo (1)
  Alberto Malovini (2) (3)
  Niina Sandholm (4) (5) (6)
  Monica Stavarachi (4) (7)
  Carol Forsblom (4) (5)
  Ville-Petteri M?kinen (8) (9)
  Valma Harjutsalo (10) (4) (5)
  Raija Lithovius (4) (5)
  Daniel Gordin (4) (5)
  Maija Parkkonen (4) (5)
  Markku Saraheimo (4) (5)
  Lena M. Thorn (4) (5)
  Nina Tolonen (4) (5)
  Johan Wadén (4) (5)
  Bing He (11)
  Anne-May ?sterholm (11)
  Jaako Tuomilehto (10) (12) (13)
  Maria Lajer (14)
  Rany M. Salem (15) (16) (17)
  Amy Jayne McKnight (18)
  Lise Tarnow (20) (21)
  Nicolae M. Panduru (22) (4)
  Nicola Barbarini (2)
  Barbara Di Camillo (1)
  Gianna M. Toffolo (1)
  Karl Tryggvason (10)
  Riccardo Bellazzi (2)
  Claudio Cobelli (1)
  Per-Henrik Groop (23) (4) (5)
  
  1. Department of Information Engineering, University of Padova, Padova, Italy
  2. Department of Industrial and Information Engineering, University of Pavia, Pavia, Italy
  3. IRCCS Fondazione Salvatore Maugeri, Pavia, Italy
  4. Folkh?lsan Institute of Genetics, Folkh?lsan Research Centre, Helsinki, Finland
  5. Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, PO Box 63, FI-00014, Helsinki, Finland
  6. Department of Biomedical Engineering and Computational Science, Aalto University, School of Science, Helsinki, Finland
  7. Department of Genetics, University of Bucharest, Bucharest, Romania
  8. Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
  9. South Australian Health and Medical Research Institute, Adelaide, Australia
  10. Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
  11. Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
  12. Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
  13. Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
  14. Clinical Research Department, Steno Diabetes Centre, Gentofte, Denmark
  15. Department of Genetics, Harvard Medical School, Boston, MA, USA
  16. Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
  17. Department of Endocrinology, Children’s Hospital Boston, Boston, MA, USA
  18. Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, UK
  20. Faculty of Health Sciences, University of Aarhus, Aarhus, Denmark
  21. Research Unit, Nordsjaellands Hospital, Hilleroed, Denmark
  22. Department of Pathophysiology, 2nd Clinical Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
  23. Baker IDI Heart & Diabetes Institute, Melbourne, Australia
  
• ISSN：1432-0428

文摘

Aims/hypothesis Diabetic nephropathy is a major diabetic complication, and diabetes is the leading cause of end-stage renal disease (ESRD). Family studies suggest a hereditary component for diabetic nephropathy. However, only a few genes have been associated with diabetic nephropathy or ESRD in diabetic patients. Our aim was to detect novel genetic variants associated with diabetic nephropathy and ESRD. Methods We exploited a novel algorithm, ‘Bag of Naive Bayes- whose marker selection strategy is complementary to that of conventional genome-wide association models based on univariate association tests. The analysis was performed on a genome-wide association study of 3,464 patients with type 1 diabetes from the Finnish Diabetic Nephropathy (FinnDiane) Study and subsequently replicated with 4,263 type 1 diabetes patients from the Steno Diabetes Centre, the All Ireland-Warren 3-Genetics of Kidneys in Diabetes UK collection (UK–Republic of Ireland) and the Genetics of Kidneys in Diabetes US Study (GoKinD US). Results Five genetic loci (WNT4/ZBTB40-rs12137135, RGMA/MCTP2-rs17709344, MAPRE1P2-rs1670754, SEMA6D/SLC24A5-rs12917114 and SIK1-rs2838302) were associated with ESRD in the FinnDiane study. An association between ESRD and rs17709344, tagging the previously identified rs12437854 and located between the RGMA and MCTP2 genes, was replicated in independent case–control cohorts. rs12917114 near SEMA6D was associated with ESRD in the replication cohorts under the genotypic model (p--.05), and rs12137135 upstream of WNT4 was associated with ESRD in Steno. Conclusions/interpretation This study supports the previously identified findings on the RGMA/MCTP2 region and suggests novel susceptibility loci for ESRD. This highlights the importance of applying complementary statistical methods to detect novel genetic variants in diabetic nephropathy and, in general, in complex diseases.