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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

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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

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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

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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

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Supplementary Note

Rapid evaluation of phenotype, SNP and results through the dbGaP CHARGE Summary

site

Stephen S. Rich, Zeng Y. Wang, Anne Sturcke, Lora Ziyabari, Mike Feolo, Christopher

J. O’Donnell, Ken Rice, Joshua C. Bis, Bruce M. Psaty

Supplementary Information 1. Contributing results to the CHARGE dbGaP portal

CHARGE working groups are encouraged to post full disclosure analytic results from

published manuscripts to dbGaP. This mechanism satisfies many journal requirements

that data be posted publically, allows for broad sharing of association estimates to the

general public, and limites access to the full summary statistics to qualified investigators

via a dbGaP application.

Assemble the following files

§ the original manuscript and supplementary materials that describe all aspects of the study in detail. Be sure to include § Cohorts included, by sex § Genotyping platforms/arrays § Analytic plan § Phenotypes analyzed § The summary meta-analysis files (i.e., METAL output files) § Any additional documentation, typically a plain text README files

Upload files to CHARGE "Staging Area"

Once all files are assembled:

§ Contact the dbGaP deposit site at University of Virginia (UVA)

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§ Contributor will initiate a request to chargeco@uw.edu to provide access to the Google Drive "staging area"

§ Files can then be uploaded to the CHARGE shared folder § The UVA team will handle the transfer of files to dbGaP § Unless otherwise specified, results files may be retained in the Staging Area to

facilitate intra-CHARGE collaborations

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Supplementary Information 2. Example of a CHARGE Summary Data README file

CHARGE _________ GWAS Results README

Meta analysis results, in __ format:

§ phenotype.results.metal.txt.gz : single line description of trait analyzed § [list other files, phenotypes provided in upload]

For additional information, please see/cite: [Full citation]. PMID: ######; PMCID: PMC#####

Files include the following variables (edit as appropriate, required variables in bold):

§ MarkerName: rs# § Chromosome: Chromosome § Physical_Location: genome build position (e.g, , GRCH38) § Allele1: “coded” allele § Allele2: “noncoded” allele § Freq1: Frequency of Allele 1 § FreqSE: § MinFreq: § MaxFreq: § Effect: beta estimate § StdErr: SE(Beta) § P.value: p-value from inverse-variance meta-analysis § Direction: Direction of association from contributing studies* § HetISq**: I2 heterogeneity statistic § HetDf: degrees of freedom for heterogeneity test § HetPVal: heterogeneity p-value § TotalN: total sample size

Study order for Direction column (if provided):

§ Study 1 § Study 2 § Study 3 § ... § Study N

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