Search for DNA/RNA

Example: User wants to search for female participants with lung cancer who have lung tumour specimens with RNA > 5 ug AND DNA > 5 ug . For queries that have child and parent samples, you need to create subqueries. Refer to wiki page for more details. 

The example query file can be imported by downloading this file- Query File

Here are the steps how to create a query for this task:

  1. Select Queries from Dashboard and Click on '+Create.'

  2. Click on the Participant form and select 'Gender'. Add a filter with Operator 'Equals' and select 'Female' under the Condition Value.

  3. To add conditions for the anatomic site, click on Specimen and select 'Anatomic Site'. Add a filter with Operator 'Equals' and select 'Lung' as a value.

  4. To define the type of specimens, click on Specimen and select 'Type'. Add 'Frozen Tissue' under the value.

  5. To define tissue type, which is cancer in this case, click on Specimen and select 'Pathological Status'. Add a filter with Operator 'Equals' and select 'Malignant`under the condition value.

  6. Now it is time to define the sample type, RNA, for the first part of this example. You will need to create a subquery with `Type` and select `RNA` as a value having a concentration greater than 5.

  7. Specify the number of required samples, click on Specimen, select `concentration`, and select `Greater than for the `Operator` field.

  8. To add DNA, you will need to create another subquery where you select `Type` under the Specimen. Click on `Equals` for the operator and select DNA as value.

  9. Follow the same steps as 7 to specify DNA concentration.

  10. To get the results from both DNA and RNA samples, create a query combining query created in steps 6 and 8 with the 'AND' operator. 

  11. Now, use the query created in step 10 as a subquery in the main query created. Since RNA and DNA samples (child samples) are derived from the original tumour tissue (parent sample), the user needs to use the 'Hierarchical' operator between the parent and the children. Keep all the filters of the children in one set of parenthesis.