Using the Variant Search Feature within the Cohort Builder

To include participants with genomic data in your cohort, you can use the variant search feature in the point-and-click tool, the Cohort Builder.

The variant search feature allows you to filter by gene, consequence, ClinVar significance filter, allele count, allele number, and allele frequency. You can also sort by participant count and add all participants with structural variants (SVs) to your inclusion criteria.

Note: The variant search feature sets the query parameters to identify person IDs based on the inclusion and exclusion criteria you select in the Cohort Builder. The feature does not extract the genomic data. To extract genomic data, you must follow the extraction process directly in your analysis tool or use the Genomic Extraction tool.

To select all participants with SV data as your cohort

1. Click “” to the right of “Cohorts.”
   
   
   
   
2. Select “Add Criteria.”
   
   
   
   
3. Under “Genomics,” select “Structural Variant Data.”
   
   
   
   
4. Click “Create Cohort.”
   
   

To select participants with SNP/Indel variants

1. Click “” to the right of “Cohorts.”
   
   
   
   
2. Select “Add Criteria.”
   
   
   
   
3. Under “Genomics,” select “SNP/Indel Variants.”
   
   
   
   
4. Search for your variant of interest by typing the gene, variant, RS number, or genomic region in the search bar.
   • You can also filter your search by selecting "Filter & Sort" and choosing your filter and sort criteria based on gene, consequence, ClinVar significance filter, allele count, allele number, and allele frequency.
     
     
     
     
5. Select your variant of interest.
   
   
   
   
6. Click “Finish & Review.”
   
   
   
   
7. Follow steps 1-6 for as many inclusion criteria as needed for your research project. You can also add exclusion criteria to your cohort.
   • For additional steps on adding inclusion and exclusion criteria in the Cohort Builder, read “Selecting participants using the Cohort Builder.”
     
     
8. Click “Create Cohort.”
   The cohort you created can now be used to create a dataset using the Dataset Builder. For using short-read whole genome sequencing (srWGS) data, use the Genomic Extraction tool in the Dataset Builder.
   
   

To select all variants

With the variant search feature, you can select all variants if the result count is less than 10,000.

1. Click “” to the right of “Cohorts.”
   
   
   
   
2. Select “Add Criteria.”
   
   
   
   
3. Under “Genomics,” select “SNP/Indel Variants.”
   
   
   
   
4. Search for your variant of interest by typing the gene, variant, RS number, or genomic region in the search bar.
   
   
   
   
   
   
5. Click “Select All Results” to the right of “Filter & Sort.”
   Note: The variant count should be less than 10,000. To bring the count below 10,000, use the filter function to narrow the results.
   
   
   
   
6. Click “Finish & Review.”
   
   
   
   
7. Click “Save Criteria.”
   
   

To exclude variants from select all

You can also exclude variants with the variant search feature.

1. Follow steps 1-6 for selecting all variants.
2. Click “.”
   
   
   
   
3. Exclude specific variations by clicking “” next to the variant name.
   
   
   
   
4. Click "Save Select All Exclusions."
   
   
   
   
5. Click “Save Criteria.”
   
   
   
   
6. Click “Create Cohort.”
   • The cohort you created can now be used to create a dataset using the Dataset Builder. For using short-read whole genome sequencing (srWGS) data, use the Genomic Extraction tool in the Dataset Builder.