G-TACT User Guide Ensuring Accurate Classification of BRCA Variants Module: RUN 1

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G-TACT User Guide Ensuring Accurate Classification of BRCA Variants Module: RUN 1 Description The G-TACT User Guide provides assistance to users in all aspects of using the

1 G-TACT User Guide Ensuring Accurate Classification of BRCA Variants Module: RUN 1 Description The G-TACT User Guide provides assistance to users in all aspects of using the Ensuring Accurate Classification of BRCA Variants Module on the Genetics Training Assessment and Competency Tool (G-TACT) website. Authority for Issue: Farrah Khawaja Page 1 of 11

2 TABLE OF CONTENTS 1. Introduction Accessing the system Process of Participation How to participate Access to G-TACT What is required Log in to your individual G-TACT account Using G-TACT Homepage Starting a BRCA variant EQA Office reception Accessing LIMS system Beginning a patient assessment Entering results: Logging progress Returning to remaining patient results Tracking progress of the run Submiting your varient classification Tracking progress of all G-TACT scenarios Key Dates and Timelines Closing date Release of results, WebEx and Teleconference Scheme report Participation certificates Additional information Authority for Issue: Farrah Khawaja Page 2 of 11

uk G-TACT (Genetic Training Assessment Competency Tool), is a system aimed to provide individuals with an interactive knowledge-based training assessment that can evidence competency in both

The aim of this external quality assessment (EQA) scheme is to provide an online competency assessment for the classification of BRCA1 and BRCA2 gene variants related to ovarian cancer and the

3 1. Introduction UK NEQAS [Edinburgh] G-TACT (Genetic Training Assessment Competency Tool), is a system aimed to provide individuals with an interactive knowledge-based training assessment that can evidence competency in both practical applications of genomic medicine training as well as theoretical knowledge. The aim of this external quality assessment (EQA) scheme is to provide an online competency assessment for the classification of BRCA1 and BRCA2 gene variants related to ovarian cancer and the predicted response to PARP inhibitor treatment. This EQA is open to individuals who classify the pathogenicity of variants and provides evidence of their level of competency to achieve this accurately and in the most up-to-date manner. 2. Accessing the system G-TACT can be operated on several browsers including Internet Explorer, Edge, Firefox, Safari and Chrome. Please ensure that the browser is enabled to allow pop ups. 3. Process of Participation 3.1. How to participate Please complete that online form to register your interest in participating Access to G-TACT Individuals will be provided with their own secure password protected website account which gives access to a defined set of BRCA1 and BRCA2 gene variants. All information including log in details, key dates and full instructions on how to complete the EQA will be sent to you What is required Individuals are required to review the full set of variants listed within the G-TACT module, following their routine procedures and submit the classification along with their reasoning. If the BRCA1 and BRCA2 gene variants are interpreted in relation to predicted response to PARP inhibitor treatment then the individual should complete this section. If treatment interpretation is not routinely provided, then please use the N/A button. 4. Log in to your individual G-TACT account Once your account has been created, navigate to the UK NEQAS for Molecular Genetics website ( and click on the G-TACT button. G-TACT button If you are logging in for the first time, select the forgotten password option. This will prompt you to enter your address or unique username twice (please remember that the addresses and usernames are case sensitive). You should then receive an containing a link to set your password. Authority for Issue: Farrah Khawaja Page 3 of 11

Once you have logged into G-TACT, click enter as shown below 5. Using G-TACT 5.1.

Starting a BRCA variant EQA There are three options displayed at the top of the homepage.

Office reception A new pop-up window will appear as shown below to inform you that there are variants to interpret.

4 Once you have logged into G-TACT, click enter as shown below 5. Using G-TACT 5.1. Homepage The G-TACT homepage will be displayed as shown below Starting a BRCA variant EQA There are three options displayed at the top of the homepage. Click on start new scenario at the top of the home page to open the BRCA variant EQA Office reception A new pop-up window will appear as shown below to inform you that there are variants to interpret. To continue, close the box within the pop-up window. A virtual office area will be displayed as shown below. The computer screen and the office door handle will be highlighted in red when the mouse is hovered over each area. Authority for Issue: Farrah Khawaja Page 4 of 11

Click on the computer screen to start the assessment If you click on the exit door this ends open scenarios and you will receive a score based on what has been completed up to that point.

Accessing LIMS system Once the computer screen has been clicked, the next screen provides three options (shown below): Home: access to the laboratory information management system (LIMS).

5 Click on the computer screen to start the assessment If you click on the exit door this ends open scenarios and you will receive a score based on what has been completed up to that point. The system continually saves your progress so if you want to pause a scenario and continue at a later date, just close the window and you can return to the scenario at a later date Accessing LIMS system Once the computer screen has been clicked, the next screen provides three options (shown below): Home: access to the laboratory information management system (LIMS). Log Samples: allows you to view referral details. Action List: lists all the variants that need to be classified for this run. Within the log sample tab the following details are avalible: Patient details, Sample details and Notes. Authority for Issue: Farrah Khawaja Page 5 of 11

classified for this EQA. Click on a patient name to begin.

6 5.5. Beginning a patient assessment. Click on action list to view all BRCA variants to be reviewed and classified for this EQA. Click on a patient name to begin. Click on the test to reveal the test results for the patient chosen in the previous step. Authority for Issue: Farrah Khawaja Page 6 of 11

your evidence for classification under the heading Evidence for Classification.

7 Review the variant displayed. Variant 5.6. Entering results: Once you have reviewed the variant, you need to: 1) List your evidence for classification under the heading Evidence for Classification. 2) Enter your classification from the dropdown list (Class 1 to 5). Authority for Issue: Farrah Khawaja Page 7 of 11

Once a classification has been entered, click on the PARP inhibitor treatment tab and select Yes on No depending on whether treatment is recommended or not for this patient.

8 Once a classification has been entered, click on the PARP inhibitor treatment tab and select Yes on No depending on whether treatment is recommended or not for this patient. If treatment interpretation is not routinely provided, then please use the N/A button. Click SAVE in the bottom left corner to save your progress on this patient. After which it will take you back to the patient page Logging progress Log your progress with this patient as complete if finished or partially complete if you want to go back to this patient file later Returning to remaining patient results If there are more patient results to be classified, click on back button on the bottom left hand side of the screen. Repeat steps 5.5 to 5.7 for each referral. Authority for Issue: Farrah Khawaja Page 8 of 11

5.9. Tracking progress of the run Within the action list, your progress for each patient can be tracked using the coloured symbols in the progress column.

patient assessment is complete. If you wish to go back to the current run at a later date, simply close the window to exit. 5.10.

9 5.9. Tracking progress of the run Within the action list, your progress for each patient can be tracked using the coloured symbols in the progress column. A red button indicates the patient assessment has not been started, a yellow button indicates the patient assessment is partially complete and a green button indicates the patient assessment is complete. If you wish to go back to the current run at a later date, simply close the window to exit Submiting your varient classification Once you have completed the varient classification for all patients then you submit your results by submitting your scenario. First of all close the box within the window. Authority for Issue: Farrah Khawaja Page 9 of 11

The office rescption will then appear. Click on the office door handle.

Once this is done you are not able to go back to the scenario If you are unable to complete the variant classification then click on Suspend and provide your reasoning.

The homepage displays the history of any scenarios that have been completed, or are in progress, and their outcome (a green button indicates a pass and a red button indicates a fail for

10 The office rescption will then appear. Click on the office door handle. This will produce a prompt (see below), To submit, click Confirm, at which stage you may leave a comment about the scenario or simply hit continue to submit the results/scenario. Once this is done you are not able to go back to the scenario If you are unable to complete the variant classification then click on Suspend and provide your reasoning. This will allow you to return to this variant classification Tracking progress of all G-TACT scenarios After closing a scenario, the G-TACT homepage will be displayed. The homepage displays the history of any scenarios that have been completed, or are in progress, and their outcome (a green button indicates a pass and a red button indicates a fail for each scenario ). Scores will be available once the EQA has closed. If you have previously started a scenario, which is incomplete, then you can return to it at a later date by selecting the continue option. To log out of your G-TACT account, click log out in the top right-hand corner. Authority for Issue: Farrah Khawaja Page 10 of 11

11 6. Key Dates and Timelines 6.1. Closing date The assessment will be available from 1 st November 2017 to 30 th November Release of results, WebEx and Teleconference Individual results and access to WebEx videos to review classifications will be available on 8 th December Participants will be invited to submit questions for a Q&A teleconference that will be held on 25 th January 2018, 12:00BST. Questions can be submitted by ing info@ukneqas-molgen.org.uk Scheme report A scheme report summarising the results of this EQA will be available 7. Participation certificates A certificate of participation will be available once the EQA has closed. 8. Additional information This EQA is provided in ENGLISH only. The fact that you participate in the scheme and your individual data is confidential between yourself and EMQN/UK NEQAS. Further information can be found on the EMQN ( or the UK NEQAS for Molecular Genetics websites ( You can contact the Schemes at office@emqn.org or info@ukneqas-molgen.org.uk Authority for Issue: Farrah Khawaja Page 11 of 11

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