Creating a single case

This guide provides a step-by-step process for creating a new case via the user interface. Detailed instructions for each step are available in the corresponding pages of the section.

Caution: Please note that refreshing or leaving the page, exiting the Add new case tab, or power failure of your computer before you've completed adding a new case will result in loss of the case creation progress.

Step 1: Start a new case

1. Click on the Add New Case button on the top navigation panel.

2. At the Select sample type page, choose the file type for your case analysis (FASTQ, gVCF, VCF, or Array).

3. Click Next to proceed.

Step 2: Build the family tree and add patient information

The page is divided into two panels: Create family tree (left) and Add patient information (right).

Create family tree (left)

1. Use the visual tool to build the pedigree.

2. Add Clinical Notes (optional) in free text, or upload a clinical presentation file (.pdf, .xls, .txt, .doc, .jpeg, .jpg).

   1. HPO terms for phenotypes and diseases will be extracted and can be linked to the proband.

3. Select suspected Inheritance mode(s) (for record only; not used in the analysis).

4. Decide whether to include Secondary findings in the proband for the AI Shortlist (checkbox).

Add patient information (right)

For each family member:

1. Add a sample (use a unique file path unless reusing samples).

• The Add New Case flow does not validate that sample IDs are unique or that input files are uncorrupted. Please ensure sample IDs are unique and that input files are valid before creating the case.

• If a QC metrics file (metrics.tar.gz) is uploaded from BSSH, it will not be processed.

• Keep file names under 255 characters and avoid spaces or parentheses in file paths.

• Always ensure sample IDs are unique to prevent case failure.

• If using joint gVCF input, place the proband first for accurate insufficient region calculation.

• The UI does not allow reusing the same gVCF file for multiple samples.

1. Fill in a sample name (for VCF input, this must match the header in the file).

2. Complete the required patient details: for a proband and for non-proband samples.

Some diseases may not suggest phenotypes automatically if the source database does not provide them. You can add phenotypes manually in these cases.

Click Next to proceed to the Case info screen.

Step 3: Case info screen

Here you define how the analysis will run:

1. Case type: Choose Array, Custom Panel, Exome, Whole Genome, or Other.

   • For Exome cases, variants outside exons ±50 bp are automatically filtered.

2. Carrier Analysis: Optional checkbox. Requires a targeted gene list.

3. Sequencing Information:

   1. Select an enrichment kit (if applicable) or "No kit".

   2. If provided, kit details (Lab, Machine, Reagents, Expected coverage) will be used to compare coverage depth and breadth.

   3. If no kit is provided, RefSeq coding regions will be used as reference.

4. Gene list options:

   1. All genes

   2. Phenotype-based genes

   3. Existing gene list

   4. Create a new gene list

      • You may combine multiple gene lists into one, or add specific genes to an existing list during case creation. The merged list behaves like any other list in the platform.

5. Preset group: Select the Preset group appropriate for this case type.

   • If none is selected, the default Preset group is applied automatically (marked as default).

6. Consent: Confirm subject consent for extended sharing.

Note: Combining/merging gene lists from the Add New Case UI is supported only via the UI — this is not available from the API or batch upload.

Additional case info (optional):

• Indication for testing (free text).

• Labels (choose from predefined organization labels; these cannot be changed later).

At the Summary stage, confirm case type, gene list, and other selections.

Caution: Clicking Next here will finalize case creation. After delivery, only the proband’s phenotypes can be edited without reanalysis.

Step 4: Done screen

After creation:

• A Case ID is displayed.

• Add participants to the case so colleagues receive notifications on case status changes.