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

NAR Genomics and Bioinformatics, vol. 2, pp. 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.

Authors 7

1. Gerard A. Bouland Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

2. Joline W. J. Beulens

   University Medical Center Utrecht · Amsterdam Public Health · Amsterdam UMC Location Vrije Universiteit Amsterdam

   Affiliation as printed

   Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute , Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands

   Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands

3. Joey Nap Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

4. Arno R. van der Slik Aachen Department of Immunohematology and Blood Transfusion

   Leiden University Medical Center

   Affiliation as printed

   Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

5. Arnaud Zaldumbide Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

6. Leen M. ‘t Hart Aachen Department of Cell and Chemical Biology Molecular Epidemiology Section Department of Biomedical Data Sciences

   Leiden University Medical Center · Amsterdam Public Health · Amsterdam UMC Location Vrije Universiteit Amsterdam

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

   Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute , Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands

   Molecular Epidemiology section, Department of Biomedical Data Sciences, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

7. Roderick C. Slieker corresponding Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center · Amsterdam Public Health · Amsterdam UMC Location Vrije Universiteit Amsterdam

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center , 2333 ZA, Leiden, The Netherlands

   Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute , Amsterdam UMC, location VUmc, 1081 HV, Amsterdam, The Netherlands