Quick-start-guide - Duke H2P2 GWAS Project

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Use this portal to explore summary data or to query your favorite SNP, gene, or phenotype! Read the H2P2 paper at Cell Host & Microbe Quick Start Guide Click the links below to review example queries If you have a favorite SNP or gene and want to determine if it is associated with any H2P2 phenotypes, on the Phenotypic Associations page:

Specify phenotype, SNP, gene, and/or position
1. Default: All phenotypes. If you want to look only at the association of your SNP/gene with a particular phenotype, select it from the Phenotype pull-down list.
2. Enter SNP ID (rs2869462), gene name (ART3), or both (rs2869462 and ART3).
Filter
1. Default SNP Sub-types: All. To focus on more functionally relevant SNPs, select exonic or eQTL or other categories.
2. Default –log10(p) lower bound: 3. This will return SNP-phenotype associations that have p < 10-3 and can be made more or less stringent. Note that the common threshold for genome-wide significance is p < 5x10-8 (–log10(p) > 7.3). True associations can still be found with less stringent p-value thresholds but false positives will also become more common.
3. Default Results to return: 1000 (though for the sample SNP query, above, only two are returned).
Review
1. Click Query and Review. If instead you would like a CSV file of the associations, click Query and Save.
2. Using the example SNP, from above, two associations will be returned. The entry with the lowest p-value is the association of rs2869462 with Chlamydia-infected levels of CXCL10 (also known as IP-10) (IP10_Chlamydia; p = 2x10-9). The output can be sorted by clicking on any of the column headings.
3. Click on a row to see a plot of phenotypic response X genotype for LCLs in the selected phenotype and SNP. The default is to plot all populations combined, but individual populations can be selected to generate a paneled plot. n (LCLs in sample) and median response are given for each population and genotype. The log-2 transform option transforms response values to their log2 values. This is particularly useful for cytokine level phenotypes.
4. Click the Results: Individual LCL Data tab to see individual LCL IDs, genotypes, and phenotype values. Click the Download button to download a CSV file with this information for further analysis.
5. Click Results: SNP Details or Query/Filter tabs to examine other associations or change query parameters.

If you have a favorite cellular phenotype and want to determine which SNPs are associated with it, on the Phenotypic Associations page:

Select the cellular phenotype you are interested in (IP10_Chlamydia).
Leave the SNP and gene entries blank. Filter based on –log10(p) lower bound (8) and/or based on functional categories (eQTL) as described in step 2, above (IP10_Chlamydia, –log10(p) > 8, and eQTL).
Review as in step 3, above.

To review summary plots for individual cellular phenotypes, on the GWAS Summary page:

Select the cellular phenotype you are interested in (IP10_Chlamydia).
Select either Manhattan or QQ plot.

If you would like access to the complete dataset, please click here: Bulk Data Download Happy querying! Feel free to email with any questions or interesting results.