Add a new case

The Add New Case flow guides you step by step through creating and submitting a case for analysis on the Emedgene platform. Here you can define your family structure, input patient details, select case type, apply gene lists and presets, and confirm case information before analysis begins.

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.

1. In the Create family tree panel (left):

   • Build a pedigree using the visual tool;

   • Add Clinical Notes (optional) in a free text panel. In this section, you can record additional clinical information that does not fall under the other categories or provide further details that can give context and help solve the case.

   • You have an option to upload a file that includes description of the clinical presentation (.pdf, .xls, .txt, .doc, .jpeg, .jpg formats are supported). HPO terms for Phenotypes and Diseases are extracted from the files and can be added to Proband's Phenotypes in Patient info section.

   • You may select suspected Inheritance mode(s). This is for the case record and won't be used during analysis.

   • Select whether you want Secondary findings in Proband to appear in the AI Shortlist analysis results.

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).

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

3. Complete the required patient details.

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 now 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.

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.

Step 4: Done screen

After creation:

• A Case ID is displayed.

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