Add a new case

This section will guide you through adding new cases to the Emedgene platform.

Please follow the steps as described below:

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.

1. Click on the Add new case button on the Top navigation panel.

2. At the Select sample type page, select the file type for your case analysis. Click Next to proceed to the Family tree panel.

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

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 (checkbox).

1. In the Add patient information panel (right) for each of the family members:

   • Add a sample;
   • Fill in a sample name (for cases starting from VCF, this must correspond to the corresponding proband or family member header within the file);

   • Fill in the required patient details;
   • Click Next to proceed to the Case info screen.

1. In the Case info screen:

   • Select case type (Array, Custom Panel, Exome, Whole Genome, or other). When running cases as Exome, variants outside exons ±50 bp are filtered out and won't appear in the results.

   • Pick whether you want Carrier Analysis to be carried out (checkbox). Carrier analysis requires you to provide us with a targeted genes list.

   • Sequencing Information (Choose from existing kit, No kit). You can indicate if there was an Enrichment Kit used if you wish to compare the breadth and depth of coverage to that expected for the kit used. RefSeq coding regions will be used as a reference if no kit is provided. This option is relevant for Custom Panel and Exome case types. In the Kit info section, fill in the Enrichment Kit and optionally Lab, Machine, Sequencing reagents, and Expected coverage.

   • Select genes list (All genes, Phenotype based genes, Existing gene list, Create a new gene list) - indicate if you want the analysis to be limited to a specified list of genes.
   • Select preset group: We can implement different combinations of Presets to be used for different case types (i.e. Presets for exome may be different from Presets for genome) as defined by your SOPs to further streamline case review.

     🆕 34.0+: If the user does not select a Preset group, the system automatically assigns the default Preset group to the case. The default Preset group is indicated by the word "default" in parentheses after its name.
   • Confirm subject consent for extended sharing (32.0+).
   • Optional: Additional case info:

     • Indication for testing. Add free-text notes.

     • Label. Add labels to your case. You can choose among the labels created beforehand by your organization's manager. Labels cannot be added after case creation.

   • Summary: confirm the selected case type and genes list before completing case creation.

   • Click Next to complete case creation.

Caution: Pressing Next at this stage will create a case, so please ensure that you've carefully checked all the information. After the case is delivered, you will only be able to edit the Proband phenotypes.

1. In the Done screen:

   • The Case ID is displayed;

   • Add participants to your case - subscribe your colleagues to notifications on Case status change.