Lab Admin Manual v11 - UK Genetic Testing Network

Lab Admin Manual v11 - UK Genetic Testing Network
UKGTN Website
Lab Admin
User Manual
Lab Admin v11 02.09.13
1. Laboratory account set-up and User management
1.1 Account set-up for lab users
1.2 Manage Users
1.3 Add new user
1.4 Log-in and navigation between Admin Interface and Front site
1.5 Manage my account details
2. Manage Test Services
2.1 Summary of Workflow system
2.2 Browsing and searching your test services
2.3 Display features of your test services
2.4 Editing your test service options
2.5 UKGTN Returns
2.6 Validation Process
2.7. View history
3. Manage Laboratory Contact Details
3.1 Edit interface for lab website addresses, service type and notes
3.2 Address Type
3.3 Adding Contacts
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UKGTN Member Laboratory Admin
A system for laboratories to manage their UKGTN test service information
The UKGTN has revised the laboratory administration interface as part of the wider website
redevelopment project. This existing database model was revised to accommodate tests for
multiple disorders/genes i.e. multi-gene and NGS panels.
The interface involves a workflow management system between the UKGTN Admin team
and the laboratory membership. This is similar to the workflow system for the previous
website with a new user-friendly format to facilitate laboratories in keeping their test service
information up to date.
The dashboard lists 3 lab administration areas for management:
Manage test services
Manage laboratory contact details
Manage users.
These are also available as tabs that can be selected by clicking the title.
If you don’t have an account set up on the system, please refer to section 1 as written below.
We encourage lab administrators to have their own account to enable change to be tracked
back to the correct person if queries arise.
All laboratories have been assigned a short display name (e.g. Cardiff RGC) as agreed by
the Lab Membership Audit working group for the purpose of simplicity on the website.
1. Laboratory account set-up and User management
1.1 Account set-up for lab users
UKGTN have devised a system to enable the head of your laboratory to set up additional
users for your lab and assign permissions:
Manage test services
Manage contact details
Manage users
Manage validations
UKGTN have responsibility for setting up accounts for the head of labs only. If you don’t
have an account set-up you will need to ask your head of lab or a colleague with manage
user permission to set you up.
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Email Invitation
You will receive an email invitation requesting you activate your account via a link where you
will be asked to enter a password of your choice twice.
To activate your account
You will have 5 days to activate your account before the link is inactivated. If the link expires
you lab head or a colleague with permission to manage users can resend the e-mail
invitation as shown in 1.2. In the initial set-up process, Lab heads will need to contact
UKGTN to request an invitation resend.
1.1.2 Activation of your account with chosen password
Enter a password of your choice in the activation window as shown below. Your user name
is your e-mail address.
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1.1.3. Confirmation of the activation of your account
Your confirmation will appear as shown below.
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1.1.4 Log-in Window
Log-in using your email address and password you have chosen as shown below
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1.2 Manage Users
UKGTN have set up an account on the system that has been assigned all admin
permissions for each head of labs. There are two methods for managing users either
individually (1.2.1) or as a group (1.2.2)
1.2.1 Actions for a single user
Alphabetic filter by first name
Invite a new user
Actions for a
single user
1.2.2 Manage users as bulk action
Bulk Action by multiple
selection of users
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1.3 Add new user
To add new users to you laboratory account, select Invite New User. Fields with red star are
mandatory. Please select the permissions you wish your new user to have. If you are
adding multiple users select Save and Add and if just one user Save and Close or Save.
The saving process initiates the invite and activation process described in 1.1.1-1.1.4.
1.4 Log-in and navigation between Admin Interface and Front site
1.4.1 Log in to your admin account
Log-in to your admin account here
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1.4.2. Lab admin Dashboard
You can navigate between the dashboard options by either selecting blue links on
dashboard page or by selecting the title in each of the tabs.
Back to front site
Manage your
account details
1.4.3 Switching between the UKGTN front site and your admin interface
Selecting Back to UKGTN shown on screen shot above reveals the 7-header banner of the
front site as shown in the screen shot below.
Selecting My UKGTN on the front site will take you to the admin interface.
Click here to go back to admin interface
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1.5 Manage my account details
You can manage your account details by selecting My Account as shown in the screen shot
of your lab admin interface site below.
Manage my account details
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2. Manage Test Services
UKGTN publishes new test services on the website on the 1st April to coincide with the new
commissioning cycle. i.e. New tests endorsed at UKGTN CSAG in Sept 13 to be published
1st April 2014. Additional providers for existing services will be published throughout the
year as they are approved.
Each test service, as defined by UKGTN, represents the combination of disorder (s) and
gene (s) offered through the network. UKGTN have assigned names to each test service.
This will correspond to the approved name of the disorder (according to OMIM database) for
simpler tests and a specified name, assigned by UKGTN, for complex tests. Each test
service has a number of options i.e. test service options represented as a matrix. Each
option is comprised of a service level, referral category, reporting time, local NHS price and
a price note.
The inclusion of a price note is primarily for providing information on what genes are being
testing in each option for complex tests. This is to enable service comparison between
2.1 Summary of Workflow system
A diagram summarises the process below. There are 4 status versions for test services.
Editable=version that is published on the front site and is available to be edited or validated
by anyone that has that user permission.
Pending approval=awaiting approval by UKGTN for publication. When UKGTN approves it
this version will be published and the test service will be available for editing again.
Returned=UKGTN have returned your submission to you requesting further
clarification/information before publication.
Not in service= these are test services that are to be started (UKGTN upload for 1st April) or
to be ended by a specified date.
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Work flow diagram
Lab Edit
Lab considers
notes and edits to
UKGTN enter
or edit
Pending Approval
UKGTN Approve
UKGTN Return with
notes for
Not in Service
To be started
Not in Service
Fig 2.1. Workflow diagram: There are 4 statuses for a test service. Each test service may
only exist as one status at a time.
The editable status is the live/published version. Lab edits and sends for approval.
The status is then pending approval until UKGTN approves for publication.
Any queries/clarification required UKGTN return to lab and status is now returned. The
comments box is key for relaying notes between UKGTN and lab in the return
Lab considers and resends for approval.
Lab validates test services to provide assurance that information is up-to-date.
Email notifications are between lab editor and UKGTN admin.
For test services that are not in service: all lab users receive an e-mail notification when test
service is started or ended.
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2.2 Browsing and searching your test services
On the right hand panel of your screen there are various tools for searching and filtering your
test services.
2.2.1 The alphabetical filter sorts your test services by test name.
Alphabetical filter by test name
2.2.2 Search by entering a term in the search keywords
You can search by entering a term in the search keywords by test name,
approved/alternative name of disorder/gene, approved/alternative symbol of
disorder/gene, MIM number of gene/disorder or HGNC number of gene (recommend 4
digits or above) and either pressing return key or selecting search button.
Search for records in U for actin
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2.2.3 Select All to reset record list
If you have already filtered your page alphabetically performing a search will search for
records for that letter only e.g. filter by U then search UKGTN will find your record. If you
need to perform a search of entire database select All to reset to entire database.
Select All to go back to all records
2.2.4 Status Filter
You can sort your tests (or refine your search results) by status (editable, pending
approval and returned) by using the status box. All 3 options will only be available for
selection if a test service exists in that option i.e. returned will be an available option if
any of your lab’s test service has been returned.
Filter by status, all the test services are
2.2.5 Not in service filter
The 4th option Not in service behaves differently as these tests are further filtered by To be
started and ended. This box is available under validation for tests. Please note that All
needs to be selected in the Status filter for this to work.
Filter by status Not in Service, e.g. To be
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2.2.6 Validation filter
Your test services need to be validated once a year to ensure they are up-to-date. You can
sort your tests for validation status for expiry. (more about validation in section 2.6).
Filter your test services by annual validation
status e.g. less than 1 month to expiry
2.3 Display options for your list of test services
The bottom window allows you to select information for display. Due to size limitations of
monitors only a number of options may be displayed at once. This window provides the
flexibility to display what information you need to look-up. The default display is shown
From and to
are dates that
your lab have
been offering
test through
Scroll to see
all options in
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2.4 Editing your test service options
UKGTN will only list the disorders and genes that have been evaluated by UKGTN
through the Genetic Test Evaluation/Gene Dossier Process.
2.4.1 Single actions and bulk actions for managing test service.
Search or browse your listing as described above to locate a test to edit. You can edit your
test services through the single action menu only. The other actions validate and view
history may be performed on a single test or through the bulk action feature. These options
are displayed below.
Single actions for a
single test service
Bulk Actions
for multiple
test services
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2.4.2 Select edit to update a test service
Locate the test service you want to edit and select edit in right action menu.
The editing page shows details of the test service i.e. the disorders and genes
assigned to the test and test service options.
2.4.3 Test service detail page for editing
From and to are dates that your
lab have been offering test
through UKGTN
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For complex tests services with multiple providers, UKGTN have assigned the full
gene complement offered through the network. Your laboratory may not offer all
the genes (UKGTN approved) that are listed and the price note* field has been
used to specify the gene (s) by approved symbol that your lab offers (see K). This
informs the cost comparison feature between laboratories services.
Test offering date, you don’t need to change the From date but if your are ending
a test service please add an end date then Send for approval. If you add today’s
date this will go through the regular approval system i.e. test will be removed on
UKGTN approval and editor receives email notification. If you add a future end
date, all your lab members with UKGTN accounts will receive an email
notification at 7am of the date you assign. This is dependent on UKGTN
approving your submission prior to the date you assign.
2.4.4 Selecting EQA schemes
Select EQA Scheme options that apply. If an EQA scheme is not available, please select
No EQA scheme available and if it is and you are not participating please select Not
participating. You can select multiple options that may apply i.e. EMQN and
The large free text note box (notes) is for adding any additional short notes about the test
service. This is not mandatory and this box is empty for the majority of services. This is to
be used for specific information for your test approved by UKGTN and not for highlighting
other services. UKGTN felt it was important that a note box was available and will review
usage during the approval process.
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2.4.5 Adding and managing test service options
Test service options may be edited, added, deleted and re-ordered.
Add a new option
A. Selecting a service level.
There are currently 12 service levels and they are accessible from this link here: or embedded below
Definitions of Service
Levels 10.01.13.pdf
We have numbered and shortened them for editing purposes in the drop down
selection box as the full text is not viewable in IE6-8. If you have access to Chrome,
Firefox, Safari you will be able to view as in screenshot below.
B. Add a referral category field enter days (turnaround times). Please enter the
numerical value. These have also been shortened for editing purposes.
Post ND Routine=Postnatal Diagnosis Routine
Post ND Urgent=Postnatal Diagnosis Urgent
Pre ND=Prenatal Diagnosis
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C. Band field: please ignore as this feature is still under development.
D. Enter Price e.g. £950. Please include £ sign. For Highly Specialised Services
(formerly NCG services), HSS is noted after price in brackets. e.g. £54 (HSS).
You shouldn’t need to put a price range as the interface allows you to enter as many
options as required to define all options with an exact price.
E. Price note field: the notes in this field need to be kept to a minimum. The main
purpose of this field is to note the gene symbol (s) to highlight which gene (s) are
being tested in an option for the purpose of cost comparisons in multi-gene test
services. Please check on the front site to see how this works. An example is
displayed below..
Please note only genes that have been through the evaluation process for
diagnosing the condition indicated in the test may be specified in this field.
Examples and suggested text:
and = & e.g. BRCA1 & BRCA2
2 genes from GCK, HN4A & HNF4A
1 gene from GCK, HN4A, HNF4A & HNF4B
Front site: Price note display
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F. Send for approval by UKGTN. A pop-up comment box will appear ( see the screen shot
below). You may wish to comment on your edition but this is not mandatory.
The main purpose of this comments box is for the returns process. Select send for
The status will change to Pending approval and you will be unable to make any
further changes to this record.
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When UKGTN approves your test the status will be updated to editable (published) and you
will receive an e-mail notification. Either go back, close or click manage test services to go
back to your list.
2.5 UKGTN Returns Process
UKGTN review all lab submissions and may return to lab if there are any queries about the
updated information e.g. price seems high, or data is missing. UKGTN will make
suggestions in the comments area for you to review. A suggestion to amend your data may
be made or you may just need to confirm that data is correct
2.5.1 UKGTN returns a test and the status changes to Returned.
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2.5.2 Select edit from action and review UKGTN’s comments.
2.5.3 Read UKGTN feedback comments
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2.5.4 Lab comment to UKGTN for approval
Scroll down to option, correct and submit comment and send for approval. You can also
view history to review change you have made (see 2.7).
2.5.5 Test now pending approval again
Status returns to pending approval. UKGTN review and approve and status returns to
editable and editor receives an email notification.
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2.6 Validation Process
To ensure that your test information is kept up-to-date, UKGTN have set up a validation
process. The validation date is shown on the front site for each test service option. If you
plan to edit your test service information, we suggest you do your editing first. Once they
have been approved and published you can then validate all your test services to ensure the
validation date is displayed on front site. This provides assurance to users that your
information is up-to-date.
2.6.1 Display of validation date on front site for each test service option
Validation date is displayed in each test
service option on front site
Test services that have not been validated within a certain time period can be filtered as
described in section 2.2.6. You can either validate a test by single action or in bulk. Bulk
validation is more suitable after the edit/approval process i.e. you know that your test
services are up-to-date. See section 2.4. Validation doesn’t allow any changes and your
validations are published automatically.
Please note if you are in edit mode and have made some changes and you select
validate your test service you will be notified that your changes will not be saved see
2.6.2 below. If you make changes you must send for approval
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2.6.2 Error notification if you attempt to validate a test that you have edited
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2.7. View history
All edits may be viewed by selecting view history in the single action menu or by bulk action
as shown in 2.4.
An example is shown below using UKGTN Test A, the test service that went through the
return process in 2.5.
In View history Red =previous Green =updated.
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3. Manage Laboratory Contact Details
This interface allows several website addresses and lab addresses to be set up for each
laboratory service. This was devised to accommodate the agreement by the membership to
merge listings for Molecular Genetics and Cytogenetics services in each Regional Genetics
3.1 Edit interface for lab website addresses, service type and notes
Add a new website and define
the title of the link
Summary about your lab
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3.2 Address Type
The type of address may be defined in a drop-down selection as shown in the screen shot
below. Please enter your address information without commas at the end of each line.
3.3 Adding contacts
Several contacts may be set-up for each address. Select add new address to add another
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