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Bouland GA, Beulens JWJ, Nap J, et al. CONQUER: an interactive toolbox to understand functional consequences of GWAS hits. NAR Genom Bioinform. 2020;2(4):lqaa085doi: 10.1093/nargab/lqaa085.
Bouland, G. A., Beulens, J. W. J., Nap, J., van der Slik, A. R., Zaldumbide, A., 't Hart, L. M., & Slieker, R. C. (2020). CONQUER: an interactive toolbox to understand functional consequences of GWAS hits. NAR genomics and bioinformatics, 2(4), lqaa085. https://doi.org/10.1093/nargab/lqaa085
Bouland, Gerard A, et al. "CONQUER: an interactive toolbox to understand functional consequences of GWAS hits." NAR genomics and bioinformatics vol. 2,4 (2020): lqaa085. doi: https://doi.org/10.1093/nargab/lqaa085
Bouland GA, Beulens JWJ, Nap J, van der Slik AR, Zaldumbide A, 't Hart LM, Slieker RC. CONQUER: an interactive toolbox to understand functional consequences of GWAS hits. NAR Genom Bioinform. 2020 Oct 27;2(4):lqaa085. doi: 10.1093/nargab/lqaa085. eCollection 2020 Dec. PMID: 33575630; PMCID: PMC7671384.
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NAR Genom Bioinform. 2020 Oct 27;2(4):lqaa085. doi: 10.1093/nargab/lqaa085. eCollection 2020 Dec.

CONQUER: an interactive toolbox to understand functional consequences of GWAS hits.

NAR genomics and bioinformatics

Gerard A Bouland, Joline W J Beulens, Joey Nap, Arno R van der Slik, Arnaud Zaldumbide, Leen M 't Hart, Roderick C Slieker

Affiliations

  1. Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands.
  2. Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands.
  3. Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands.

PMID: 33575630 PMCID: PMC7671384 DOI: 10.1093/nargab/lqaa085

Abstract

Numerous large genome-wide association studies have been performed to understand the influence of genetics on traits. Many identified risk loci are in non-coding and intergenic regions, which complicates understanding how genes and their downstream pathways are influenced. An integrative data approach is required to understand the mechanism and consequences of identified risk loci. Here, we developed the R-package CONQUER. Data for SNPs of interest are acquired from static- and dynamic repositories (build GRCh38/hg38), including GTExPortal, Epigenomics Project, 4D genome database and genome browsers. All visualizations are fully interactive so that the user can immediately access the underlying data. CONQUER is a user-friendly tool to perform an integrative approach on multiple SNPs where risk loci are not seen as individual risk factors but rather as a network of risk factors.

© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

References

  1. Nat Biotechnol. 2010 Oct;28(10):1045-8 - PubMed
  2. BMC Genomics. 2012 Nov 23;13:661 - PubMed
  3. Bioinformatics. 2016 Jun 1;32(11):1740-2 - PubMed
  4. Nat Genet. 2017 Jan;49(1):131-138 - PubMed
  5. Nat Genet. 2013 Nov;45(11):1274-1283 - PubMed
  6. Nat Commun. 2017 Dec 12;8(1):2084 - PubMed
  7. Nat Commun. 2015 Jan 19;6:5890 - PubMed
  8. Multivariate Behav Res. 1992 Jul 1;27(3):417-33 - PubMed
  9. PLoS One. 2018 Apr 4;13(4):e0193515 - PubMed
  10. Hum Mol Genet. 2012 Jun 15;21(12):2815-24 - PubMed
  11. Front Genet. 2020 May 13;11:424 - PubMed
  12. Brief Bioinform. 2013 Mar;14(2):144-61 - PubMed
  13. Am J Hum Genet. 2012 Jun 8;90(6):1046-63 - PubMed
  14. Nat Genet. 2015 Sep;47(9):979-986 - PubMed
  15. Genome Med. 2019 Mar 26;11(1):19 - PubMed
  16. Genome Biol. 2002 Jun 25;3(7):RESEARCH0036 - PubMed
  17. Lancet. 2012 Nov 3;380(9853):1590-605 - PubMed
  18. PLoS Genet. 2011 Jul;7(7):e1002193 - PubMed
  19. Nat Commun. 2017 Feb 27;8:14357 - PubMed
  20. Nat Commun. 2018 Aug 15;9(1):3268 - PubMed
  21. Bioinformatics. 2015 Aug 1;31(15):2560-4 - PubMed
  22. Nat Commun. 2019 Sep 24;10(1):4329 - PubMed
  23. Arthritis Rheumatol. 2018 Feb;70(2):255-265 - PubMed
  24. Nat Genet. 2013 Jun;45(6):580-5 - PubMed
  25. Lancet. 2017 Apr 29;389(10080):1741-1755 - PubMed
  26. PLoS Genet. 2010 Aug 12;6(8): - PubMed
  27. Science. 2012 Sep 7;337(6099):1190-5 - PubMed
  28. Database (Oxford). 2018 Jan 1;2018: - PubMed
  29. Cell Metab. 2013 Jul 2;18(1):130-43 - PubMed
  30. Nat Commun. 2015 Mar 20;6:6601 - PubMed
  31. Nature. 2013 Jul 4;499(7456):79-82 - PubMed
  32. Genome Res. 2011 Jan;21(1):68-73 - PubMed
  33. Bioinformatics. 2015 Nov 1;31(21):3555-7 - PubMed
  34. Nat Commun. 2019 Oct 21;10(1):4788 - PubMed
  35. Nucleic Acids Res. 2017 Jan 4;45(D1):D854-D859 - PubMed

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