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Pers TH, Karjalainen JM, Chan Y, et al. Biological interpretation of genome-wide association studies using predicted gene functions. Nat Commun. 2015;6:5890doi: 10.1038/ncomms6890.
Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H. J., Wood, A. R., Yang, J., Lui, J. C., Vedantam, S., Gustafsson, S., Esko, T., Frayling, T., Speliotes, E. K., Boehnke, M., Raychaudhuri, S., Fehrmann, R. S., Hirschhorn, J. N., & Franke, L. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature communications, 65890. https://doi.org/10.1038/ncomms6890
Pers, Tune H, et al. "Biological interpretation of genome-wide association studies using predicted gene functions." Nature communications vol. 6 (2015): 5890. doi: https://doi.org/10.1038/ncomms6890
Pers TH, Karjalainen JM, Chan Y, Westra HJ, Wood AR, Yang J, Lui JC, Vedantam S, Gustafsson S, Esko T, Frayling T, Speliotes EK, Boehnke M, Raychaudhuri S, Fehrmann RS, Hirschhorn JN, Franke L. Biological interpretation of genome-wide association studies using predicted gene functions. Nat Commun. 2015 Jan 19;6:5890. doi: 10.1038/ncomms6890. PMID: 25597830; PMCID: PMC4420238.
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Nat Commun. 2015 Jan 19;6:5890. doi: 10.1038/ncomms6890.

Biological interpretation of genome-wide association studies using predicted gene functions.

Nature communications

Tune H Pers, Juha M Karjalainen, Yingleong Chan, Harm-Jan Westra, Andrew R Wood, Jian Yang, Julian C Lui, Sailaja Vedantam, Stefan Gustafsson, Tonu Esko, Tim Frayling, Elizabeth K Speliotes, Michael Boehnke, Soumya Raychaudhuri, Rudolf S N Fehrmann, Joel N Hirschhorn, Lude Franke

Affiliations

  1. 1] Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 2142, USA.
  2. Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen 9711, The Netherlands.
  3. 1] Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 2142, USA [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
  4. Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
  5. Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK.
  6. 1] Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia [2] The University of Queensland Diamantina Institute, The Translation Research Institute, Brisbane, Queensland 4012, Australia.
  7. Section on Growth and Development, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
  8. Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala 75185, Sweden.
  9. 1] Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA [2] Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 2142, USA [3] Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
  10. Department of Internal Medicine, Division of Gastroenterology, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.
  11. Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
  12. 1] Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 2142, USA [2] Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [3] Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts 02115, USA [4] Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [5] Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.

PMID: 25597830 PMCID: PMC4420238 DOI: 10.1038/ncomms6890

Abstract

The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

References

  1. Nature. 2010 Aug 5;466(7307):707-13 - PubMed
  2. PLoS Genet. 2009 Jun;5(6):e1000534 - PubMed
  3. Nature. 2015 Feb 12;518(7538):187-96 - PubMed
  4. PLoS Genet. 2010 Aug;6(8). pii: e1001058. doi: 10.1371/journal.pgen.1001058 - PubMed
  5. Nat Genet. 2000 May;25(1):25-9 - PubMed
  6. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7 - PubMed
  7. Bioinformatics. 2005 Oct 15;21(20):3940-1 - PubMed
  8. Am J Hum Genet. 2006 Jun;78(6):1011-25 - PubMed
  9. Science. 2007 Feb 16;315(5814):972-6 - PubMed
  10. Nat Biotechnol. 2007 Mar;25(3):309-16 - PubMed
  11. Science. 2007 Jun 1;316(5829):1331-6 - PubMed
  12. Am J Hum Genet. 2007 Sep;81(3):559-75 - PubMed
  13. Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9362-7 - PubMed
  14. Nature. 2010 Sep 2;467(7311):52-8 - PubMed
  15. PLoS Genet. 2010 Sep;6(9):e1001097 - PubMed
  16. Nature. 2010 Oct 14;467(7317):832-8 - PubMed
  17. Nat Rev Genet. 2010 Dec;11(12):843-54 - PubMed
  18. Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7 - PubMed
  19. Genet Epidemiol. 2011 Jul;35(5):318-32 - PubMed
  20. Genome Res. 2011 Jul;21(7):1109-21 - PubMed
  21. Bioinformatics. 2011 Aug 15;27(16):2304-5 - PubMed
  22. Bioinformatics. 2011 Sep 1;27(17):2463-4 - PubMed
  23. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14 - PubMed
  24. PLoS Comput Biol. 2012;8(2):e1002386 - PubMed
  25. Nat Rev Genet. 2012 Aug;13(8):523-36 - PubMed
  26. Nature. 2012 Nov 1;491(7422):56-65 - PubMed
  27. Nature. 2012 Nov 1;491(7422):119-24 - PubMed
  28. Hum Mol Genet. 2012 Dec 1;21(23):5193-201 - PubMed
  29. Nat Methods. 2012 Nov;9(11):1069-76 - PubMed
  30. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5 - PubMed
  31. Nat Genet. 2013 Oct;45(10):1238-43 - PubMed
  32. Curr Opin Genet Dev. 2013 Dec;23(6):602-10 - PubMed
  33. Nucleic Acids Res. 2014 Jan;42(Database issue):D810-7 - PubMed
  34. Nucleic Acids Res. 2014 Jan;42(Database issue):D749-55 - PubMed
  35. Nat Genet. 2014 Sep;46(9):957-63 - PubMed
  36. Nat Genet. 2014 Nov;46(11):1173-86 - PubMed
  37. Hum Mol Genet. 2015 Feb 15;24(4):1155-68 - PubMed
  38. Nat Genet. 2015 Feb;47(2):115-25 - PubMed

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