Illumina Connected Software

Adding patient info for the proband

Add new case page > Family tree screen > Add patient information panel > Patient info section

1. Fill in the boxes:

Note: The fields marked with (*) are mandatory.

1. Sex (33.0+) / Gender (≤32.0) (*)

Options: Male, Female, Unknown.

2. Relationship

The default fixed value for Proband is Test Subject.

3. Date of Birth

Expected format: mm/dd/yyyy.

4. Medical Condition (*)

Options: Affected, Healthy.

The default value for Proband is Affected, but you may change it to Healthy.

5. Proband Phenotypes (*)

To add all relevant phenotypes for the Proband, use one of the following methods:

  1. One by one (Selection mode),

  2. In a batch (Batch mode),

  3. Extract HPO terms from the file uploaded in the Clinical Notes section, or

  4. Automatically infer disease-associated phenotypes (see Proband Suspected Disease Condition below).

Note: the maximum permissible number of Proband Phenotypes is 100.

Selection mode

Please follow the steps described below for each phenotype:

  1. Enter an HPO term (e.g., Hypoplasia of the ulna), an HPO ID (e.g., HP:0003022), or a descriptive phenotype name (e.g., Underdeveloped ulna) in the search box.

  2. Select a matching term from a dropdown menu and press Complete after you've added all the terms and additional patient information below.

Batch mode

Paste a list of comma-separated HPO terms or HPO IDs (🆕32.0+) in the search box and press Complete.

Notes:

  • A popup notification will appear at the bottom of the page if any input HPO term or HPO ID is unknown.

  • Only phenotypes from the 'Phenotypic abnormality' HPO branch are currently supported.

Extract HPO terms from the file uploaded in the Clinical Notes section

In the Clinical Notes section upload a description of the clinical presentation in .pdf, .xls, .txt, .doc, .jpeg, or .jpg format. Among the extracted HPO terms for Phenotypes and Diseases select the ones you want to add to Proband's Phenotypes.

6. Proband Suspected Disease Condition.

Enter the disease name in the search box, select a matching term from a dropdown menu and press Complete. All the associated phenotypes will be automatically added to the Proband Phenotypes. To remove any phenotype described for the disease but not observed in your patient, click the ☒ button next to the HPO term in the Proband Phenotypes list.

7. Suspected Disease Penetrance

Enter the suspected disease penetrance as a percentage.

8. Suspected Disease Severity

Select the appropriate category to indicate the severity of the disease symptoms observed in the patient: Mild, Moderate, Severe, Profound.

9. Consanguinity

Mark the checkbox if applicable.

Note: If consanguinity is identified in the Proband's parents, but this box is not selected in case creation, this will result in a discrepancy alert in the Lab tab.

10. Patient Ethnicities

Paternal and Maternal. Enter the ethnicity name in the search box and select a matching term from a dropdown menu.

2. ​Click on Complete once all the information is added.

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