GeneLeaf User Manual

Getting started

GeneLeaf runs entirely in your browser. No installation needed. Visit app.geneleaf.com to start.

You can use GeneLeaf as a guest (no sign-in required) or create an account with Google or Microsoft. Guest access is limited to 24 hours; accounts persist longer. Either way, your pedigrees stay on your device—we never store them on our servers.

The editor opens with an empty canvas. Add your first person by clicking the Add person button, or paste in a family narrative to have the AI draft a pedigree for you.

Drawing a pedigree

Symbols and notation

GeneLeaf uses standard pedigree notation:

• Square: Male
• Circle: Female
• Diamond: Unknown or other sex
• Filled symbol: Affected by a condition
• Half-filled symbol: Carrier
• Horizontal line: Partnership/marriage
• Vertical line: Parent-child relationship
• Horizontal line with siblings: Sibling group

Adding people

Click Add person to create a new individual. You can then:

• Set their sex (M, F, Unknown, Other)
• Add a name (optional)
• Set birth and death dates (optional)
• Mark as proband (the index case)
• Add health conditions

All fields are optional. Start with just what you know and add detail as you learn more.

Adding relationships

After creating people, connect them:

• Parents: Click on a person and select "Add parent" or drag from a parent to a child
• Partners: Draw a line between two adults to create a partnership
• Siblings: The editor automatically detects children of the same parents and groups them

You can specify relationship types (biological, step, adoptive, foster) when adding a parent.

Editing people and relationships

Click on any symbol to open the person's details panel. You can edit:

• Name (given, middle, family, or pseudonym)
• Sex
• Birth and death dates (ISO 8601: YYYY-MM-DD, or year only)
• Proband status
• Ancestry and genetic results
• Notes and links

To delete a person, open their details and click "Delete." To change a relationship, click on the connecting line or re-assign parents.

You can drag symbols to reposition them on the canvas. The layout adjusts as you work.

Adding health conditions

Health information is stored in a condition dictionary. Each condition appears once (e.g., "Colon cancer") and can be assigned to multiple people.

To add a condition to a person:

1. Open the person's details panel
2. Under "Health," click "Add condition"
3. Enter or select a condition name
4. Optionally set:
   • Onset age: Age at diagnosis (e.g., 45 years old)
   • Status: Affected (default), unaffected (asked and denied), carrier, presymptomatic, unknown
   • Source: Reported (someone said so) or documented (medical record)
   • ICD-10 code: For interoperability (optional)

People with an assigned condition will have their symbols filled or colored in the diagram.

Tip: For research, add ICD-10 or other standard codes when possible. It makes your pedigree data reusable across systems.

Using narrative parsing

Instead of manually adding people, you can paste a family history narrative (a written description) and have GeneLeaf's AI model extract the relationships and conditions.

Example narrative:

Sarah is 48 years old. Her husband Michael is 50. They have a son David, age 22,
and a daughter Emily, age 20. Sarah's father Robert was diagnosed with colon cancer
at age 60 and died at 72. Her mother Carol is still living and is 66.

To use this feature:

1. Open the app and click "Analyze Narrative"
2. Paste or type a family history
3. Click "Generate pedigree"
4. Review the extracted relationships and conditions
5. Correct any misunderstandings by editing people or relationships

Note: Narrative parsing is a demo feature. Results depend on how clearly the narrative is written. Always review and correct the output before using it clinically. Do not paste real patient data; use fictional or de-identified examples.

Exporting and saving

Your pedigree lives in your browser while you work. When you're ready to save:

• PNG/SVG: Click "Export" and choose image format. Good for reports and presentations.
• PDF: Export as PDF to print or email.
• Pedigree JSON: Export as a structured JSON file that you can open, edit, or import into another tool. This is the format that carries all your data (conditions, dates, notes, relationships).

To open a saved pedigree, click "Open" and select a .pedigree.json file from your device.

Tip: Always keep a copy of your pedigree as a JSON file. Image formats (PNG, SVG, PDF) are great for sharing and printing, but they don't preserve the underlying data.

File format (Pedigree JSON)

When you export a pedigree as JSON, you get a Pedigree JSON file: a structured, human-readable format that any tool can read.

A simple example:

{
  "format": "pedigree-json/0.4",
  "meta": {
    "family": "doe",
    "title": "Doe Family"
  },
  "pedigree": {
    "conditions": {
      "crc": { "label": "Colon cancer", "codes": ["ICD10:C18.9"] }
    },
    "people": [
      { "id": 1, "sex": "M", "name": "Robert", "dob": "1955-02-10", "deceased": true },
      { "id": 2, "sex": "F", "name": "Carol", "dob": "1957-08-22" },
      { "id": 3, "sex": "F", "name": "Sarah", "dob": "1978-03-15", "proband": true,
        "parents": [1, 2] }
    ],
    "couples": [{ "partners": [1, 2] }]
  }
}

You can open and edit these files in any text editor, import them into spreadsheets or databases, or use them in research pipelines. The format is open and documented.

Read the full Pedigree JSON specification to learn more.

Feedback and support

GeneLeaf is in active development. If you find a bug, have a feature request, or want to suggest an improvement, please contact us. We're particularly interested in feedback from genetic counselors, geneticists, and researchers working with pedigrees every day.