GWAS

Genome-wide Association Studies (GWAS) is a statistical test that helps detect genetic markers (SNPs) associated with a particular phenotypic trait. The result of this analysis is presented as a “Manhattan plot” which maps each marker on the x-axis to the results of the corresponding test (as –log10(p-value)) on the y-axis.

Create a GWAS analysis

What you need:

a. Genotype file
b. Phenotype file

Steps:

1. On the sidebar to your left, click GWAS

   

2. On the GWAS page, click Fit

   

   

3. Create GWAS page will be displayed, requiring you the following inputs:

   a. GWAS Name - name of your GWAS analysis
   b. Genotype file - reference genotype file
   c. Phenotype file - reference phenotype file
   d. Trait - the trait you want to analyze
   e. Parameters - statistical parameters to be applied in the analysis
       

   

4. Enter GWAS Name

   

5. Click Select Genotype to upload a Genotype file.

   

6. Click Select Phenotype to upload a Phenotype file.

   

7. Click Select Trait and select the trait you want to analyze.

   

   

8. Adjust the statistical parameters of your analysis (optional)

   a. Multi-testing P-Value correction method - Value can either be: bonferroni, holm, hochberg, BH, BY, FDR (false discovery rate), or none.
   b. Test. For binary phenotypes, "score" is mandatory - The type of statistical test to use. Value can either be: score, wald,or lrt.
   c. Minor allele frequency threshold for filtering markers - statistical parameters to be applied in the analysis
   d. Call rate threshold for filtering markers -  statistical parameters to be applied in the analysis

   

9. Once the required inputs are complete, click Fit to start creating your GWAS analysis.

   

10. By default, the initial status will be PROCESSING, which means that the analysis is ongoing.

    

11. You can click the refresh button to see the latest STATUS.

    

11. If the analysis is successful, the STATUS column should be SUCCESS.

    

View GWAS analysis results

1. On the GWAS page, click on the record with SUCCESS status.

   

2. On the overview page, a Manhattan Plot will be displayed you can adjust the p-value and correction method (Adjust method) for quick reporting.

   

3. If you scroll down, the GWAS analysis details are displayed (Name, Genotype file, Phenotype file, Trait)

   

4. On the same page, click Interactive.

   

5. The Interactive page lets you directly interact with the GWAS analysis result. This allows you to conduct exploratory analysis and further gain insights about your data. The following attributes can be adjusted:

   a. Chromosome
   b. P-Value significance threshold
   c. Multi-testing P-Value correction method.
   d. Number of points to plot.

   

6. Click Plot to display the Manhattan Plot