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Rapid evaluation of phenotypes, SNPs and results through the dbGaP CHARGE Summary Results site

Nature Genetics volume 48, pages 702–703 (2016)Cite this article

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To the Editor:

The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium was established to conduct prospective meta-analyses for discovery of SNPs associated with phenotypes critical to heart, lung and blood disorders through genome-wide association studies (GWAS)1,2. The CHARGE Principles of Collaboration committed to broad sharing of GWAS results. It was reported, however, that public posting of summary results could, under certain conditions, be used to identify individuals in contributing studies3,4,5. In response, the US National Institutes of Health (NIH) moved large-scale GWAS summary results under the institutional review board (IRB) protection of the National Center for Biotechnology Information (NCBI) database of Genotypes and Phenotypes (dbGaP)6. Although association P values could be safely released, public posting of detailed GWAS results decreased dramatically. This decreased posting of GWAS results led to investigators requesting 'lookups' of analytical results from the authors of studies, a tedious process for both authors and investigators.

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Acknowledgements

The authors wish to thank all CHARGE investigators who have generated the analyses and manuscripts that constitute the summary statistics provided in the dbGaP portal. This work was generated without funding for the project. The CHARGE Consortium infrastructure grant to support meetings, working groups and young investigators was provided to B.M.P. (5 R01 HL105756) from the NIH. This research was also supported in part by the Intramural Research Program of the NIH, National Library of Medicine.

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Authors and Affiliations

  1. Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA

    Stephen S Rich

  2. National Center for Biotechnology Information, National Library of Medicine, US National Institutes of Health, Bethesda, Maryland, USA

    Zeng Y Wang, Anne Sturcke, Lora Ziyabari & Mike Feolo

  3. Division of Intramural Research, Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, Massachusetts, USA

    Christopher J O'Donnell

  4. Division of Cardiology, Massachusetts General Hospital, Boston, Massachusetts, USA

    Christopher J O'Donnell

  5. Department of Biostatistics, University of Washington, Seattle, Washington, USA

    Ken Rice

  6. Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA

    Joshua C Bis & Bruce M Psaty

  7. Department of Epidemiology, University of Washington, Seattle, Washington, USA

    Bruce M Psaty

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  1. Stephen S Rich
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  2. Zeng Y Wang
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  3. Anne Sturcke
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  7. Ken Rice
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  8. Joshua C Bis
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  9. Bruce M Psaty
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Corresponding author

Correspondence to Stephen S Rich.

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Integrated supplementary information

Supplementary Figure 1 CHARGE dbGaP Summary Statistics site portal entry.

CHARGE consortium summary results "study page" in dbGaP; click on the "Analyses" tab (Supplementary Figure 2) to browse for analyses of interest.

Supplementary Figure 2 CHARGE analysis description for alpha-linoleic acid GWAS.

Analysis view shows details for each analysis and provides a link to the genome browser, using the selected box on the right to change the analysis shown.

Supplementary Figure 3 Ideogram view of alpha-linoleic acid GWAS results (p < 10-4).

Ideogram is a graphical heat map showing association signals across 2Mb bins.

Supplementary Figure 4 Detailed view of the associated region on chromosome 11 for GWAS of alpha-linoleic acid (ALA).

dbGaP Genome Browser focused on the GWAS region for alpha-linoleic acid (ALA) on chromosome 11.

Supplementary information

Supplementary Figures and Texts

Supplementary Figures 1–4 and Supplementary Note. (PDF 985 kb)

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Rich, S., Wang, Z., Sturcke, A. et al. Rapid evaluation of phenotypes, SNPs and results through the dbGaP CHARGE Summary Results site. Nat Genet 48, 702–703 (2016). https://doi.org/10.1038/ng.3582

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