PhenoTips » User Guide » Pedigree editor

Pedigree editor

PhenoTips ver 1.3

The pedigree editor can be accessed from a Family record or from the Family history and pedigree section of the patient record.

On both pages, the pedigree is shown as a thumbnail image. For new families or patients without pedigrees, the thumbnail only appears in edit mode as an empty image.

Families with defined sensitive information, as well as families containing more than one patient record, will mask the pedigree thumbnail, so that it is only viewable from within the pedigree editor. Permissions and privacy relating to shared families are summarized here.
 
The pedigree editor can be opened either by clicking on the thumbnail or by clicking on the nearby pencil button.

NO PEDIGREEPEDIGREE(no sensitive info)PEDIGREE WITH SENSITIVE INFO
PE_EmptyTumbnail.pngPE_Tumbnail.pngPE_SensitiveInfoTumbnail.png

Pedigree tools

Handles

There are 5 types of handles designed to make process of pedigree building more efficient:

  • Parents handle: located above an individual's pedigree symbol; clicking on it automatically generates a set of two parents of the opposite sex
  • Siblings handle: located to the right of an individual's pedigree symbol (connected to the parents handle); clicking on pops out several symbols to choose from to define sibling(s)
  • Partners handle: located to the left of an individual's pedigree symbol; clicking on it generates a partner of the opposite sex
  • Relationship handle: located between 2 persons defined as a couple; clicking on it pops out several symbols to choose from to define offspring
  • Offspring handle: located below an individual's pedigree symbol; clicking on it automatically generates a new partner of the opposite sex and a menu of selectable offspring symbols
 PARENTS HANDLE SIBLINGS HANDLE PARTNERS HANDLE OFFSPRING HANDLE RELATIONSHIP HANDLE
PE_HandleParents.pngPE_HandleSiblings.pngPE_HandlePartners.pngPE_HandleOffspring.pngPE_HandleRelationship.png

Legend, drag and drop functionality

  • Once a disorder, gene, or phenotype is established in one individual, a legend should appear at the top right-hand of the screen.
  • Disorders, genes, and/or phenotypes already present in a pedigree can conveniently be dragged from the legend onto other individuals.
  • Hovering over any item in the legend will highlight all individuals who are affected by/have that item (disorder, gene, or phenotyoe).
PE_Legend.png

Building a pedigree

Click on the Draw pedigree button.

If you are building a pedigree from a family record, you will be prompted to choose a pedigree template. Please skip to the choosing templates section of this guide.

If you are attempting to build a pedigree from a patient record, the following window will appear:

PE_DrawPedigree.png
  • Choose “add to an existing family” if you have access to an existing family record for this family on PhenoTips (for instance, if another patient within the same family has been previously entered). You may search for the family by family name, family identifier, or proband name. If you choose this option, the existing pedigree will appear. You may then drag and drop the new patient (the record you have just created) onto the appropriate node to merge the patient with the family. (Permissions and privacy relating to shared families are summarized here.)
  • Choose “create a new family” if there have not been any other PhenoTips entries for this patient's family. This will automatically generate a new family ID. You may later edit details of the family chart (such as family name). A new screen will pop up and prompt you to select a pedigree template. 

Choosing a template

Please choose the template that allows for as much family history entry as possible (any pedigree can be built from a single node, but it may be easier to start from a matching template.) Currently there are 5 template options: “Proband”, “Proband with parents”, “Proband with 2 generations of ancestors”, “Proband with 3 generations of ancestors” and “Consanguineous marriage - cousins”. 

PE_Templates.png

Editing pedigree

You can move the entire pedigree around by clicking on an area that cannot be edited and dragging the pedigree. You can center the pedigree on the proband by using the person icon in the middle of the navigation circle in the upper left corner. Any action can be undone using the Undo button in the top row, and reverted back using the Redo button. The Renumber button (under More) will assign generation numbers to all individuals in the pedigree. 

Note that pedigree layout is automatically computed and at the moment it is not possible to manually position individuals. The Automatic layout button in the top bar will attempt to improve the layout but may result in a pedigree that looks different from the original. We are constantly improving the algorithm and are happy to hear any feedback. 

Pedigrees can be exported by selecting Export in the top bar, and they can be imported with the Import tool (under More.) The save and close buttons are also located in the toolbar. Save any work before closing the pedigree. There is no auto-save.

Hover your cursor over any individual in the pedigree to view the different relatives/partners that you can create. You can create new siblings, a partner, parents, and offspring. 

Adding parents

Click on the parent handle that is placed above individual symbol. A couple will be created and linked to the individual as parents.

Adding siblings

There are two ways to add a sibling: 

  • Click on the siblings handle (diamond that hovers to the top right of an individual) and select one of the offered symbols for the sibling(s). The new sibling(s) node will be created and you may then enter more clinical details about the sibling by clicking on it (please see editing personal details)
  • If the sibling already exists in the pedigree, click and drag the sibling handle to the individual you would like to designate as the sibling. 

Adding partners

To add a partner, choose one of the following options:

  1. Click on the partner handle (the circle that hovers to the left of an individual). The partner of the opposite sex will be created along with an offspring. You may then enter more clinical details on the partner (please see editing personal details).
  2. If the partner already exists in the pedigree:
    • click on the red dot located on the partners handle (notice that all potential partner symbols of the opposite sex in the pedigree will be highlighted
    • drag the handle to the individual you would like to designate as the partner
    • when you reach the partner symbol you will notice the large green rectangle appear around the partner symbol; release the handle
    • once the relationship is established an offspring of undetermined sex will be added automatically (the offspring symbol will be highlighted; please see images below
       
1. Click on the red dot"2. Drag the handle3. Release the handle4. The relationship is established
PE_MakingRelationship1.pngPE_MakingRelationship2.pngPE_MakingRelationship3.png  PE_MakingRelationship4.png

Relationships

Once a relationship between two individuals is created, you can specify ‘consanguinity’, make the relationship ‘separated’, define a childless couple or remove the relationship if not relevant. To make a same sex couple, simply modify the sex of the specific node (please see editing personal details).  

  1. Click on the relationship handle (red dot that appears in the middle of any relationship line)  to add ‘consanguinity’ or make the relationship ‘separated'
  2. A childless relationship can be presented by removing the couple's offspring
  3. To remove the relationship, simply click on the  located on the relationship handle
1. Adding consanguinity and/or separation’2a, Removing offspring2b. Childless couple3. Removing the relationship
PE_RelationshipStatus.pngPE_RemoveOffspring.pngPE_ChildlessCouple.pngPE_RemoveRelationship.png

Adding offspring

Offspring can be added to an existing couple by using the relationship handle or to an individual by using the offspring handle.

Via relationship handle

  1. When you hover your mouse over the red dot located on the relationship line, a blue dot will appear below on the parent-offspring relationship line. This is the relationship handle. 
  2. Click on the blue dot to add offspring and/or establish twins
  3. The added offspring symbol will be highlighted
1. Relationship handle2. Click and select an offspring symbol3. Offspring added
PE_RelationshipHandle.pngPE_RelationshipOffspringTypes.pngPE_RelationshipOffspringCreated.png

Via offspring handle

The offspring "handle" is a blue diamond located underneath an individual's node.

  1. Click on the individual's offspring handle
  2. Pick a symbol that represents the offspring (please notice that a partner of an opposite sex will be created automatically)
  3. A childless relationship can be established by removing all offspring
1. Click on the offspring “handle”2a. Add offspring2b. New partner is added3. Childless relationship
PE_IndividualOffspringHandle.pngPE_IndividualOffspringTypes.pngPE_IndividualOffspringAndNewPartner.pngPE_ChildlessCouple.png

The pedigree editor supports “multiple individuals” nodes, which are indicated as the “<n>” choice when adding offspring and siblings (e.g. one can indicate “3 daughters” this way). 

Editing personal details

Click on any individual to add personal, clinical, and cancer information, found in three separate tabs:

PE_PersonalTab.pngPersonal tab: here you can modify the following information: gender, first and last name, life status, external ID, dates of birth and death, ethnicity, heredity, and adoption status. If the individual is associated with a patient record, all edits will be applied to the patient record as well. In this tab you can link a patient record to the individual, or unlink a record from the selected node (for more information please see the Linking and unlinking patient records section below).
PE_ClinicalTab.pngClinical tab: PhenoTips will suggest OMIM disorders as you type into the box titled ‘known disorders for this individual’. As you type in the box titled ‘clinical symptoms: observed phenotypes’, PhenoTips will suggest HPO terms.  As you type in the boxes titled ‘Genotype: candidate/confirmed causal genes’, PhenoTips will suggest known genes.
PE_CancersTab.pngCancers tab: in this tab you can indicate if an individual is affected with a common cancer along with the age at diagnosis. If you cannot find the patient’s cancer type in this tab, you can go back to the ‘Clinical’ tab and enter it into the "known disorders” field.

Linking and unlinking patient records

PE_SampleFamily.png

In the sample pedigree above, some individuals have links displayed under their node ( e.g. P0000001 for proband Sharon Barr ). This link indicates that the person is linked to a patient record. If you click on this link, the Patient record form will open with this patient's information in it. 

If you click on the Sharon Barr in the pedigree, the Barr's pedigree form will open:

PE_UnlinkPatient.png

On the Personal tab the patient record link will be shown under the Linked to patient record label. Beside the patient link there is an Unlink button. By clicking on this button, you can remove the association between this individual and their patient record. If you do so, the dialog shown below will pop up asking if you want to clear data from this person's node as well:

PE_RemoveConnection.png

If you choose to remove the link, the association between the patient record and pedigree individual will be removed.
Also, the following will take place:

Patient Sharon Barr now appears in the "Unlinked patients" menu on the upper left corner of the pedigree editor. Any unlinked patient record can be dragged and dropped over any pedigree individual (node).PE_UnlinkedPatient.png
The Link to an existing patient record label appears in the Personal tab, along with a field below it into which you can type the name of the patient you want to link to. As you type, matching patient names will show up as suggestions.PE_TypePatientName.png
The Create new button appears in the Personal tab, allowing you to create a new patient record that will contain all of the information associated with this individual.PE_LinkToPatientRecord.png

Pedigree Print Guide

PE_PrintPreview.png
  • Navigate to the family history section and draw your pedigree. If you have already completed this step, you will need to select “Edit Pedigree”.
  • Select “Print” at the top of the page.
  • A print preview will appear within PhenoTips. From here you can customize many things.
    • Zoom in and out to print the pedigree across multiple pages. 
    • Nudge the pedigree left and right to centre it on your page. 
    • Add or remove names, MRNs and DOBs.
  • Select “Print”. A separate print preview will appear. Here you can send it to print from your local printer, or you can select 'Save to PDF'/'Print to PDF'.

Exporting and Importing Pedigree

Exporting a pedigree

Once you have completed a pedigree in the PhenoTips pedigree editor, you are able to export the file so that it can be uploaded into a different system. The Export button is located on the top menu between the Save and Close buttons. 

When you click on Export, you will be presented with the option to export in the following formats:

PED format

PED - Select this option if you wish to import the pedigree into other pedigree systems that accept PED files. A PED file will store information about the structure of the family, sex of the individuals, the ID number of the proband and the parents, and basic information on whether individuals are affected or not (but not what they are affected with). Keep in mind that PED files are simple, and so what is displayed in the PhenoTips pedigree editor may not match what you import into your system of choice from the PED file. 

PE_ExportPED.png

Select PED as format, and chose one of the options:

  • Use patient identifier (if available)
  • Replace personal identifier with numeric labels
  • Use patient names (if available)

Lastly select any phenotypes, genotypes and/or disorders (out of all those present in the family) that need to be marked in the affected (last) column of the PED file. They will all appear the same (as affected) in the output (the pedigree will not differentiate between afflictions). 

BOADICEA format

BOADICEA - Select this option if you wish to import the pedigree into BOADICEA only.

PE_ExportBOADICEA.png

Simple JSON

Simple JSON - Select this option if you wish to export all of the information stored in the PhenoTips pedigree editor, without any data loss. You will be given the option to remove personal identifying information such as name and age and free text comments. You can also use this file to import into another PhenoTips instance. 

PE_ExportSimpleJSON.png

Image

Image - select this option if you wish to save the image of the pedigree to your computer, either in PNG or SVG formats.

PE_ExportImage.png

Importing a pedigree

The PhenoTips pedigree editor allows you to import a pedigree that has been built in a different software system. If you would like to import an existing pedigree, do not build a pedigree in the pedigree editor. There are two ways to import a pedigree:

  1. When you select the “draw pedigree” option, you will be presented with the option to select a template. In this popup menu, instead of selecting a template, switch into the shaded tab labelled Import.
  2. If you are already in the pedigree editor, click on the More button on the top menu of the pedigree editor, and then click on the Import button. 

You will be presented with the following menu:

PE_Import.png 
  • You can import data in either one of two ways:
    1. Next to the Import Data label, copy and paste the data into the blank text field
    2. Next to the Import File label, click “Select File” and find the file on your computer that you wish to import
  • Select the appropriate Data Format that you are importing your pedigree from. Our pedigree editor is currently able to import PED/LINKAGE, GEDCOM, BOADICEA, and Simple JSON files. 
  • Select from the list of import Options that are available to you. Please note that not all options are available for all format types. 
  • Click Import to generate a pedigree in the PhenoTips pedigree editor.