RDCRN Pedigree Drawing Tool User Guide

Owned by Karen Lapthorn
Last updated: Aug 03, 2021
5 min read

The RDCRN Pedigree Drawing Tool User Guide provides detailed instructions on the primary features and functionality of the application.

Table of Contents:

Help and Resources

If you need additional help or training using the RDCRN Pedigree Drawing Tool, need to report an error, or have a question, use the RDCRN Service Desk to contact us.

Getting Started

To create a new pedigree, visit the RDCRN Pedigree Tool homepage.

  1. Use the Select Pedigree Configuration dropdown to start with a pre-configured template specific to your consortium or protocol.

  2. Or use the Default configuration to start with a generic template. The Default configuration can be updated to be specific to your consortium or protocol and saved to appear in the Configuration dropdown going forward. You may create one or many pedigree configurations.

Creating a Pedigree Configuration from Default

You may create and save a pedigree configuration with settings specific to your needs.

With the Default value set in the Configuration dropdown, select the “Click Here to Create a Pedigree” button. This will launch a generic Pedigree configuration which can be customized and saved.

Next, select the settings (gear) icon in the upper right to begin updating the configuration. These setting will apply to all individuals within the pedigree.

Fields:

  1. Birth Date/Age: collect birth date values in the pedigree by:

    1. an individual’s age (either a specific age such as 65 or a decade such as 60s)

    2. full date

    3. birth year

  2. Death Date/Age: collect death date values in the pedigree by:

    1. an individual’s age (either a specific age such as 65 or a decade such as 60s)

    2. full date

    3. birth year

  3. Output File Format: select JSON or JSON Simple

  4. Phenotype Display: select how a node will indicate a phenotype. Options include:

    1. colors

    2. black & white patterns

  5. Phenotype Value: indicate phenotypes by:

    1. age of diagnosis (either a specific age such as 65 or a decade such as 60s)

    2. date of diagnosis

    3. present/absent status (checkboxes)

Names/IDs:

ADDED aUGUST 2021

  1. Select one or more IDs to be collected

    1. Name

    2. Local ID

    3. Participant ID

    4. GUID

  2. Of the IDs selected, indicate which will display on the pedigree

  3. Select if the ID should be displayed

    1. in the node

    2. below the node (best for lengthy values)

Phenotypes:

  1. Remove any default phenotypes that are not needed. Add one or more new phenotypes.

  2. If you wish to include a phenotype labeled ‘Other’ you can also indicate if you wish to include an input ‘Other, Specify’ which will allow for a user to indicate what the ‘Other’ value is. ADDED aUGUST 2021

  3. Adjust the color or pattern values for each phenotype as needed.

  4. Drag and drop an listed phenotypes to adjust the order.

Once complete, the configuration can be saved. If you would like to save the configuration to be used again the future, click Save. You will be prompted to name the configuration (the name will be included in the configuration dropdown on the homepage) and associated it to your consortium. Click Save Configuration.

Pre-Save Questions:

Add one or more questions that will display when a user attempts to save a pedigree. Questions can be used as prompts or reminders to display to anyone creating and saving a pedigree. To add a question:

  1. Input question text (example: Did you ask about consanguinity?)

  2. Select question type

  3. Indicate of the answer to the question is Required. Leave checkbox un-checked if question is optional.

  4. Click Add Question +.

  5. Repeat steps to add additional questions

Modifying a Pedigree Configuration

To change configuration values in an existing pedigree configuration, first select the configuration from the dropdown on the RDCRN Pedigree Tool homepage.

Next, select the settings (gear) icon in the upper right to being modifying the selected configuration. These setting will apply to all individuals added to the pedigree.

Modify the desired fields. Click OK to close the configuration window and begin working on a pedigree. Or, save your configuration.

Saving a Pedigree Configuration

Once you have configure a pedigree configuration you may want to save the configuration to use again in the future. To save a pedigree configuration first select the settings (gear) icon in the upper right. Click Save Configuration. You will then be able to

  1. Add or update a Configuration Name value.

  2. Select the associated consortium.

  3. Indicate if you want to also save the current Pedigree as part of the configuration.

    1. If you select No, you will start with a blank Pedigree each time you use this configuration to create a pedigree.

    2. If you select Yes, you will start with the current Pedigree each time you use this configuration to create a pedigree.

Click Save Configuration.

You will now see your Configuration listed the Configuration dropdown on the Pedigree tool home page indicated by the Configuration Name you entered. You may create one or many pedigree configurations.

Creating a Pedigree

There are several features available in create a pedigree for an individual.

Individuals can be added to the pedigree by placing the mouse over an individual to reveal the widgets used for editing and adding a partner (two people with at least one child), parents, a sibling, or a child. Partners can be same-sex and an individual may have more than one partner.

Select the settings (gear) icon associated with an individual to open a dialog box with the attributes associated with the individual.

Attributes include:

  1. Proband or Consultand designation

  2. Name

  3. Local ID

  4. GUID

  5. Age

  6. Sex

  7. Vital status and pregnancy options such as birth, still birth, pregnancy, miscarriage, termination, or ectopic pregnancy

  8. Checkbox to indicate if DNA was collected

  9. Adopted designation including whether the individual was adopted in or adopted out

  10. Indication of Phenotype(s)

  11. Family relationship values including

    1. Whether the mother is biological, adopted, ovum donor or surrogate

    2. Whether the father is biological, adopted, sperm donor or mitochondrial donor

    3. Partner status of Divorced/Separated

Close the dialog box to save the settings on the individual.

Consanguineous partners can be created between individuals at the same or different levels in the pedigree tree, e.g. cousins. This is done by placing the mouse over one of the partners and clicking and dragging the triple dashed line widget handle in the direction of their new partner.

There are 'undo', 'redo' and 'reset' buttons at the top and a button to enable full screen editing.

Downloading a Pedigree

A pedigree can be saved/downloaded as

  1. PNG

  2. SVG

  3. JSON format

Uploading a Pedigree

A pedigree saved in the JSON format can be uploaded using the Load option.