USER GUIDE

Section 2: PhenoTips

USER GUIDE

This guide will help users to register with RD-Connect and explain how to submit your genomic sequencing data and associated metadata

Verify & Register

Verify and register with RD-Connect to create profiles for you and your research team

Submit phenotypic data

Create records for each participant in your study and enter their clinical information

Upload genomic data

Enter the relevant experimental metadata for your sequenced genomic data

2. PhenoTips

As part of the RD-Connect Genome-Phenome Analysis Platform, we will set up each of the associated projects with an account in the clinical database at PhenoTips.

Users will be expected to enter the phenotypic data which has been collected for each of the participants, even unaffected individuals (who just need to have a note to say they are unaffected), whose samples are being sent for sequencing as part of the project.

In order to do this you need to follow the instructions in this section.

LOG-IN

Once you have completed Step 1 in this guide to verify and register with RD-Connect, you will receive your username and password.

Navigate to https://platform.rd-connect.eu/phenotips/ and log in with these credentials.

CHANGING YOUR PASSWORD

The first time you log in, you can change your password to something more memorable. To do this, click on your name at the top right of the screen, select Preferences on the left hand menu and choose Change Password.

INFORMATION

Whenever you want to return to the starting page, click the PhenoTips logo. This takes you to the home page which acts as a dashboard for the various features of PhenoTips.

We use the Human Phenotype Ontology (HPO) to record phenotypes for participants in order to match between cases.

We have grouped some HPO terms that are relevant to particular diseases into Studies, so that if the record you are creating is relevant to one of the Study forms, you can select that and it will list the phenotypic terms appropriate for that case. This will become more obvious later in the guide when we look at entering the participant information.

The Studies are also useful for filtering data when browsing the whole database of records.

The Active Groups are listed at the bottom left of the screen where you can see the members of each group and how many cases belong to each. This is important for when you come to share your data with others.

This lists participant records you have already created.

This lists participant records created by other users who have added you, or a group of which you are a member, as a collaborator.

This lists Families that you have created using the Pedigree Editor.

This will be covered later in the guide and is done when you create new participant records.

This lists Families created by other users who have added you, or a group of which you are a member, as a collaborator.

Hover over Browse and click Browse patients or Browse families to search the whole database.

You can also click in the Search Box to enter a specific record for a Patient or Family.

INFORMATION

When you are entering the record for a participant who is part of a Family, please make sure you start with the Index Case.

When you come to create the familial relationships in the Pedigree Editor, you will create the other members of this family at this point.

{ ALWAYS START WITH THE INDEX CASE }

Step-by-step guide to completing a record

  • To enter new participant data you can either click on NEW PATIENT at the top of the MY PATIENTS window, or you can hover over the + Create... dropdown menu at the top of the screen and select New patient.
  • Select the disease (Study) form you wish to use, this will determine if the form will have sections specific to that disease, otherwise choose None, and click the Create button at the bottom of the window - a blank record will appear.
  • Confirm that consent has been taken for NGS and for clinical data sharing by checking the boxes at the top of the form - if the consent is not in place, data can still be entered but the patient should be re-consented and the boxes checked once this has been done.
  • Enter your external ID code for this patient record in the Identifier field.  This must match with the ID provided for the raw sequencing data so that the PhenoTips record can be matched with the appropriate data.  Also make a note of the PhenoTips ID in the top left of the window for your records.
  • If there are any additional identifying codes for further experiments which belong to this patient, you can add these too by clicking +NEW ENTRY.  In the Label field enter the experiment type (WGS/RNA-Seq etc.) and then the corresponding identifier in the ID field.
  • Continue through the form entering the patient information as required.  For some fields you can click the ? icon for further information.
  • You can add multiple ethnicity descriptions for each parent; as you type a list of terms will appear for you to choose from.
  • Choose Y (affected) or N (unaffected) for Clinical status.
  • Ignore Family Study as this component is deprecated.  Any family relationships will be specified in the Pedigree Editor later.
  • Now work through the Inheritance, Progression and Onset data. Indented descriptions are subcategories of those above. If you click on the little ‘info’ icon, a definition will pop-up.
  • Work through the rest of the form clicking on the headers to open out the sections of the form.
  • Where a triangle exists beside an observed phenotype, clicking on it will reveal sub-categories.  Some of the sections may or may not be visible depending on the Study you selected.

FAMILY HISTORY & PEDIGREE

  • If the participant has relations you can enter these by clicking on Draw pedigree.  A window will pop up and you should select Create a new family, unless the family already exists in the system.
  • Select the most appropriate template for the family, or click on Import to pull in existing data if it is in one of the supported data formats.
  • If you hover over one of the nodes in the pedigree, you can add more relatives by selecting the relevant branch that ends with a blue button
  • Clicking on a node will open up a window where you can enter information about that family member; click on Create new to make a new record for this person
  • Next click on the PhenoTips ID (make a note of this for your records) and you will be taken to the new, blank record.  Click Edit and fill in all the information for this record (using the rest of this guide from point 18), making sure to click Save when done.
  • You can then close this browser window as the Pedigree Editor will still be open in a separate window in your browser.  Continue to create records for all other family members in the same way.
  • Once the pedigree is complete, click Save and then Close to return to the original index case record.
  • Continue through the original record for the index case, completing the sections as required.

CLINICAL SYMPTOMS & PHYSICAL FINDINGS

  • If the person is an unaffected relation, please tick the This patient is clinically normal checkbox and move on to the next section (20).
  • You may search for phenotypic information not included in the form by typing a feature in the Quick Phenotype Search box. Suggestions from the ontology will appear and you can choose the most appropriate one.
  • You can also browse the HPO terms in the form itself, clicking on a category to open up further choices, and the green triangular symbols to expand the hierarchy of HPO terms further.
  • We ask that you submit a minimum of 7 HPO terms here, if possible, as any less renders the record less useful when using the analysis platform to compare and match cases.
  • Under Diagnosis you can type in any confirmed diagnosis and choose from the pop-up OMIM descriptions. You may also select from the suggested diagnoses which have been generated based on your entered phenotype data.
  • Click on the Save button at the top of the page to save your record.

IMPORTANT

SETTING PERMISSIONS FOR ACCESS

  • You now need to decide who can view/edit your record.  At the top right of the form it will say, This case is owned by You and is Private. It is shared with No collaborators. Click on Modify permissions, next to this statement.
  • Leave Ownership and Global Visibility as they are (default is Private) but under Collaborators, you can type the name of another user or group into the relevant fields and select the appropriate pop-up.  Please make sure to add your own group as a collaborator or they will not be able to see the record.
  • Use the drop-down menu to give permission to those with whom you shared data to either view OR view and edit the record.
  • Click Update.
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