Uk Cystic Fibrosis Registry

Summary

UK Cystic Fibrosis Registry
User guide
Version: 1.1
Date: 27 January 2016
Updates: Dashboard section expanded
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Contents
Introduction ........................................................................................................................... 4
FAQs ................................................................................................................................. 4
Your account ......................................................................................................................... 6
Logging in.......................................................................................................................... 6
Setting or re-setting your password ................................................................................ 6
Two-factor authentication ............................................................................................... 6
My profile........................................................................................................................... 7
User types ......................................................................................................................... 7
Site administrators ......................................................................................................... 7
Site editors ..................................................................................................................... 8
Site readers ................................................................................................................... 8
Event log (Audit log) .......................................................................................................... 8
Managing patients................................................................................................................. 9
Record management screen ............................................................................................. 9
Colour coding ................................................................................................................. 9
Search for a patient ........................................................................................................ 9
Add a new patient .......................................................................................................... 9
Patient transfers ............................................................................................................. 9
Duplicates .................................................................................................................... 10
Entering data ................................................................................................................... 10
Error messages............................................................................................................ 10
Demographics .............................................................................................................. 10
Encounter .................................................................................................................... 11
Annual review encounter.............................................................................................. 12
Custom fields................................................................................................................... 14
Comments ....................................................................................................................... 17
Print friendly .................................................................................................................... 17
Data definitions................................................................................................................ 18
Help text ...................................................................................................................... 18
Data dictionary ............................................................................................................. 18
Importing data ................................................................................................................. 18
Data entry deadlines........................................................................................................ 18
Reporting and exporting ...................................................................................................... 19
Dashboard ....................................................................................................................... 19
regis[email protected] 2
Chart overview ............................................................................................................. 19
Query builder ................................................................................................................... 20
Building a query ........................................................................................................... 20
Exporting data ................................................................................................................. 22
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Introduction
Welcome to the new UK CF Registry system, launched on 1 February 2016. Please read
this user guide, particularly the key FAQs below, before entering data onto the new system,
and refer to it frequently as you familiarise yourself with it. We will update this user guide in
line with queries we receive, and as we develop the system further

FAQs
Why doesn’t my username work?
Your username is now your NHS/Academic institution email address

Why does historic data look incomplete?
All data from PortCF that has been migrated into the new system will appear ‘incomplete’

This is because the new system has a slightly different data entry procedure and we couldn’t
‘make up’ data for historic entries to force these historic records to look complete
1. Demographic data: As you enter data for each patient please check the three tabs in
this section, and update any missing data so that all tabs are ‘green’. This should
take one minute or less per patient. All demographic sections should be ‘Green’ and
‘Complete’ by the 2016 data entry deadline
2. Annual review/Encounter data: 2015 data and earlier data are locked and cannot be
edited. The fact that these records appear ‘incomplete’ will not factor in to banding
calculations or analysis – anything that was complete on PortCF will be used in
analysis as in previous years
Where is the Annual survey form?
The PortCF Annual Survey form has been combined with the annual review encounter, so
the mandatory dataset for 2016 will be one annual review encounter, and the patient’s
demographics

Annual review encounters require the full dataset to be entered, whereas other encounters’
requests minimal data only

Where is the Care episodes form?
Care episodes were previously collected in two places, the Care episodes form, and the
Annual Survey form. These data are now collected in Encounters only

How do I record shared care?
When adding a new patient select the site they are usually seen at, and click ‘Add new’. The
system stores the CF network information, so if you add a patient under their clinic, the
system ‘knows’ which centre this clinic is attached to

In the ‘Core information’ tab in an encounter, select ‘shared care’ and then indicate where
the patient was seen. This allows for scenarios where a patient is normally seen as their
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clinic, but goes to the CF centre once a year, or is seen near their university for some
appointments

What data items have been changed?
Although the data entry forms have been changed to be more user friendly, most of the data
variables are the same in the new system as they were in PortCF. A larger dataset
enhancement is planned for 2017. There are a small number of exceptions, outlined below

A significant number of fields, such as Chronic Medications, are now automatically populated
based on previously entered data. For more information about how we’ve improved data
entry, see the ‘help’ icons next to variables in the system, and the Entering data sections
below

All historic data, exactly as it appeared in PortCF, can be accessed via the Registry team if
required. Depending on demand this will be made available to all users. If you wish to
continue collecting any retired fields, you can add the question as a custom field

Retired PortCF fields
1. Biological paternal heights
2. Socio economic status of parents
3. Duplicated CFRD fields have been merged
Fields now auto-calculated
1. Hospital IV days
2. Home IV days
3. Non IV hospital admissions days
4. Best FEV₁ data (if entered in prior encounters)
New Registry system variables
1. PolyT status (where relevant)
2. Encounter setting
3. Liver test detail
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Your account
Logging in
The UK CF Registry portal can be found at https://cfregistry.org.uk. When logging in you will
be asked to confirm agreement with the Registry terms of use. Please read these carefully
before proceeding

The first time you log in you need to click the link shown below to set up your password,
using your institution’s email address as your username:
Setting or re-setting your password
To set your password for the first time, or re-set a forgotten password, you will need to have
first been set up as a User by your Site Administrator or the Registry Team. Your username
should your NHS or academic institution email address

When logging in for the first time, click the link after ‘Need to set your password or forgotten
your password?’ on the home screen

On the password request screen enter your registered email address. The system will
generate a unique code, which will be emailed to you. Click the link within the email and
enter your code to set your password

Two-factor authentication
The Registry uses two-factor authentication to protect patient data (similar to logging in to
online banking). When logging in for the first time from a new web browser, you will be asked
to retrieve and enter a verification code. A code will be sent to the email that acts as your
username. Once you’ve received the code, return to the site and enter it to login. You can
opt to remember your browser to avoid having to repeat this process next time you login. If
you don’t receive your code within 5 minutes, check your Junk and/or Clutter folders. If you
still haven’t received your code, email [email protected]

Registry users sharing a computer: For security purposes two-factor authentication is re-
set when Registry accounts are switched using the same browser on the same PC. So,
Registry users sharing a computer may have to repeat the security code process after the
other user has been logged in

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My profile
Using the ‘My profile’ menu, you can amend your email address, password, and telephone
number. You can also see which cystic fibrosis sites you have permission to access

User types
Site administrators
Site administrators are responsible for managing the Registry access for their CF site. They
can add new users with the appropriate permission level, and must disable users when
they no longer require access to the system. Site administrators are the only users
authorised to set up custom fields and access their site’s audit log

Site administrators are also responsible for responding to requests from the Registry team
for periodic User audits; confirming which users still require access to their site(s). Failure to
respond to these requests within the given time period will result in access to the Registry
being revoked for all site users until a response is received

Setting up new users
To set up a new user, it is important to establish the level of access required, always
applying the minimum required with reference to the user roles detailed in this section. You
can only assign user permission levels that are equal to or lower than your own, so some
options (such as CFT administrator) will be disabled

1. To set up a new user, go to the ‘User management’ menu, and select the ‘Add new’
button

2. Enter the email address (doubles up as a username), which must be a valid NHS or
academic institution email address
3. Enter the user’s full name (first name and surname)
4. Select the ‘CF sites’ radio button to tell the system you are setting up a new site user
5. Against the site(s) that you wish the user to be able to access (you will only see the
site(s) you have access to) select whether they should be a Site Administrator, Site
Editor, or Site Reader. You can select different permission levels for the same person
for different sites
6. Click ‘Insert’ to save your changes. The new user can now select ‘Need to set your
password’ on the login screen and use their email address to set a password and
access the site
Editing users
To edit a user’s details or permission levels, find the user in question (note: you can ‘sort’
users using the column headers), and click the pencil edit icon to the right of their details

From there you can edit all of the details entered at the time of setting up the user

Remember to click the ‘update’ button prior to moving on to save your changes

Disabling users
To disable a user, who may have moved onto a new role or left the CF site, simply click the
recycling bin icon to delete their profile

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Site editors
Site editors are able to edit unlocked data, add new encounters, annual reviews, and
patients. They can also transfer patients, view reports and the event log, query, and export
data

Site readers
Site readers are able to view all data for their site, but they cannot edit data within the
system. They can view reports, query and export data

Event log (Audit log)
Site administrators can use the Event log to access an overview of actions relating to data at
your site. This includes user activity and data edits. You can also search for specific events,
event types, and date ranges

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Managing patients
Record management screen
This is the patient data home screen; from this screen you can view the completeness of
individual patients’ data, search for patients, add new patients, and enter data

Colour coding
Completeness of data is represented using the following colours:
Tabs and records that are saved as complete

Saved with some but not all mandatory data complete
Saved but with errors, such as invalid dates or information in the wrong
format
Tab/encounter hasn’t been opened and saved
Search for a patient
You can search for a patient using their CFTID, first name, surname, date of birth, or NHS
number using the box at the top right of the patient management screen

Advanced search
As well as the standard search, you can use an advanced search to locate a patient, or
group of patients

Add a new patient
Before creating a new patient, always search to ensure that they do not already exist for
your centre. A patient from another UK CF centre will normally already exist on the Registry
under their centre of origin

To add a new patient, first select the name of the CF site where the patient receives care (if
they receive care at a clinic, select the clinic, not the CF centre), then click ‘Add record’. The
system will flag if this patient might be a duplicate in the system based on the details that are
entered as their demographics. Before overriding this alert, consider whether this patient
may already exist, either in your CF care network, or whether this patient may be listed
under another centre and has not yet been transferred

Patient transfers
When a patient permanently transfers out of your CF site, you should transfer the patient’s
record to the new site by clicking the button on the record management screen

If a patient is being seen at another clinic as a ‘one off’ or on a temporary basis (e.g. if at
University), record this in the ‘core information’ tab in the relevant encounter rather than
transferring them

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For data protection reasons, you cannot search for a patient who has moved to your CF site,
but has not yet been electronically transferred by their previous care team. Please contact
[email protected], who will arrange the electronic transfer. Do not include any
patient identifiable data in the email, you will be provided with instructions

Duplicates
The system will prevent duplicate records being created by validating unique information
against all other records held on the Registry. However, if you notice a duplicate patient
record has been created, please contact [email protected] and provide the
CFTID of both patient records

Entering data
Error messages
When you click save on a data entry form, a colour coded bar will appear at the bottom of
your browser window

Green No errors – saved complete
Amber Errors or incomplete fields
Red Saved with errors, for example blank mandatory fields or answers that
contradict validation rules
If an error bar displays, the questions with errors will be highlighted with explanatory text e.g

‘Required’, if the field is mandatory, or ‘Must be after birth’. You can quickly skip to relevant
fields by clicking ‘show errors’ in the coloured bar at the bottom of the screen and then
selecting the question references that appear

Demographics
Demographic data is always associated with an individual patient, even if their care moves
from one centre to another. It isn’t locked as part of the annual reporting cycle, and can
always be updated

A complete demographic record must be available for every patient in order for that patient’s
data to be included in tariff payment calculations, registry grant payments, and the annual
report

Demographic data, even if it looks complete, should be checked for each patient at least
once per year to ensure all information, like surname, and postcode, are accurate and up to
date

To read or edit demographic data, click on the button to the right of the patient’s
name on the record management screen

Patient information
Consent
When creating a new record, or accepting a patient transferred from another CF care team,
the Registry now asks you to confirm that written consent has been taken for that patient

This is designed to act as a reminder to check that written consent is available at your centre
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for this patient. This is not a field that will be analysed by the Registry team, and copies of
consent forms on-site are part of the criteria for passing a UK CF Registry validation visit

Changing a patients’ consent status to ‘No’ will make all data associated with that patient
read-only, and prevent further data being added. It will also send an alert to the Registry
team, who will be in touch to ascertain:
1. Whether the patient has withdrawn consent from the UK CF Registry
2. Whether the patient consents for historic data to be retained
3. Whether the patient wishes for no further data to be collected and all historic data to
be deleted
Genotyping
Genotyping data for at least two mutations should be present for every person on the
Registry. Although users are allowed to indicate that a patient has not yet been genotyped,
these incomplete data will appear on in-system reports as well as being chased by the
Registry team

Up to three mutations be selected, and you can search for genotypes by starting to type the
mutation name in any of the three nomenclatures. In 2016 for the first time the Registry has
begun collecting data about another part of the CFTR gene, called the poly-T tract. The poly-
T tract occurs in one of three forms; 5T, 7T or 9T. The Registry will automatically show poly-
T tract status options where its form may affect the CF outcome

Diagnosis
This tab collects information about when and how a patient was diagnosed with cystic
fibrosis. It also collects outcome data about life status and diagnosis reversal; these sections
can be left blank if they do not apply. If life status is recorded in an encounter it is
automatically updated in the diagnosis section

Encounter
An encounter applies to any event where a patient is assessed by a cystic fibrosis care
team. This could be an outpatient, inpatient, or virtual appointment

You can also record scheduled visits that did not take place because a patient did not
attend, or has been transferred to another centre

Encounters are not mandatory data for the UK CF Registry, but completing them throughout
the year will auto-populate annual review data, and enable you to get better feedback about
care at your CF centre

You can find guidance about individual questions in the Encounter forms by clicking the
icon to the right of the data entry form on the UK CF Registry website

To create an encounter, click the icon next to the left of the patient’s name and click
‘add encounter’

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Annual review encounter
An annual review encounter is a more detailed set of data than a normal encounter. It is
mandatory to enter one annual review encounter for each ‘active’ consenting cystic fibrosis
patient each calendar year. These data are used for tariff payments, centre grant payments,
and the Annual reports

If encounters have been entered throughout the year, some data within the annual review
encounter will be automatically populated in the annual review encounter. Autocompleted
data should always be carefully checked and edited / added to if necessary to accurately
reflect patient care

An annual review should be carried out when a patient is ‘well’ i.e. not having an
exacerbation

If a patient has not had a “formal” annual review in the period then a “virtual” review must be
recorded from the patient’s notes. The virtual review must be compiled from a time when the
patient was stable during the period

You can find guidance about individual questions in the Annual review forms by clicking the
icon to the right of the data entry form on the UK CF Registry website

Note: In PortCF the mandatory dataset for the year included Annual Survey, Annual
Review Encounter, and Admission and Care episodes. In the new Registry these forms
have been combined in the ‘Annual Review’. This must be completed in its entirety to
constitute the minimum data for that year

To create an annual review, click the icon next to the left of the patient’s name and
click ‘add annual review’

Core information
This is the default tab you are brought to when entering an encounter. It primarily collects
information about the encounter itself, as well as some core information about the patient

If the patient is shared care, indicate this here. You can then record where the patient was
seen for the encounter you are recording. For example a patient may generally receive care
at a clinic, but be seen occasionally at the CF centre. You can also use this function to
record when a patient is seen at a clinic near their university, for example, but hasn’t been
permanently transferred to their university centre

Admissions & IVs
If there are no admissions or IVs to report, select ‘None’ in the three dropdown menus and
move on

Admissions and IVs from encounters throughout the year auto-populate the annual review
encounter; so, entering them as you go along makes things easier at year end

If in an annual review encounter you find that one or more admission or IV episode is
missing, you can edit what’s there to make sure your records are complete

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1. To set up a new user, go to the ‘User management’ menu, and select the ‘Add new’ button. 2. Enter the email address (doubles up as a username), which must be a valid NHS or academic …

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Frequently Asked Questions

How many people have cystic fibrosis?

It is estimated that more than 70,000 people worldwide are living with CF, but the incidence of the disease varies greatly across the globe. Incidence rates for CF in Canada and the U.K. are similar to those seen in the U.S. Across the European Union, about 1 in 2,000 to 3,000 babies are diagnosed with CF at birth, slightly higher than the U.S.

What is the prognosis for cystic fibrosis?

What are the prognosis for cystic fibrosis? The genetic disease cystic fibrosis has no cure. One can only try to delay the ravages that are sown in the body of patients through early diagnosis and proper treatment and rehabilitation.

How many babies are born with cystic fibrosis?

It is one of the most common genetic conditions in this country. About 1 in 3,500 babies is born with CF. What causes CF? CF is inherited. This means it’s passed from parent to child through genes.

Can people be misdiagnosed with cystic fibrosis?

Sadly, the patient can end up being at risk of developing a more advanced case of cystic fibrosis if not diagnosed properly. The Consequences of Misdiagnosis and Your Rights Any delayed or incorrect treatment after a failure to identify cystic fibrosis can impact your life in multiple ways.