Genomics Search

PIC-SURE allows users to query genomic variables in datasets you are authorized to access. Because PIC-SURE and the associated genomic data is not available to all users, the following screenshots have been altered to remove confidential data. All participant counts are fabricated.

You can filter the data based on genomic variables such as variant class, variant severity, variant frequency, and gene.

In this example, we will create a query to explore the relationship between autism and variants of the CHD8 gene. Variants of the CHD8 gene have been linked to autism.

Citation about CHD8 gene and autism

Sugathan A., Biagioli M., Golzio C., Erdin S., Blumenthal I., Manavalan P., Ragavendran A., Brand H., Lucente D., Miles J., Sheridan S.D., Stortchevoi A., Kellis M., Haggarty S.J., Katsanis N., Gusella J.F., Talkowski M.E. CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors. Proceedings of the National Academy of Sciences of the United States of America, 111(42), E4468-E4477. https://doi.org/10.1073/pnas.1405266111

First, we will filter for participants who have autism. We will search for our keyword “autism,” find the variable of interest (Autism) and restrict by value Positive.

Results from search for "autism"

Applying a filter to those participants with autism

Next, we will find the data pertaining to the gene of interest by searching “CHD8” and selecting Gene_with_variant: CHD8.

Searching for gene and selecting the Gene_with_variant variable

Finally, we will filter the variants to include only variants of high or moderate severity. We will search for “variant_severity” and select HIGH and MODERATE.

Searching "variant_severity" in the Query Builder

Selecting "High" and "Moderate" variant severity to filter

When we run our query, the resulting participants have high or moderate-severity variants in the CHD8 gene and autism.

Total participant count is updated to reflect query criteria

We can now choose to export this data for further analysis. See the Data Export section for more details.