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Members of staff from NHS Genomics Medicine Centres (GMCs) that have assisted with participant recruitment to the 100,000 Genomes Project are entitled to GeCIP membership, but are still required to complete the GeCIP membership application form
so that they can be added to the membership of their chosen domain.
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There are details of how to apply to join GeCIP
on the Genomics England website. In short, after filling in the online form, the applicant's details will be sent to the domain leads of the domains they selected in their application. The domain lead(s) will consider the applicant's skills and compatibility with the domain's research interests and decide whether to accept or reject the application. GeCIP has been founded with a 'team-science' mindset and the domain leads are encouraged to bear this in mind. The applicant will be notified of the domain's decision by email.
If you would like to join another domain or subdomain, please contact the domain or subdomain lead(s) listed on our key contactsP page GeCIP domains page to discuss your interest and how you may effectively contribute to the domain. Please note that membership of domains does not govern members’ access to data – all GeCIP members can see all de-identified 100,000 Genomes Project data within the Research Environment. GeCIP members should only consider joining a new domain if their intended research activities fit within its scope.
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- contribution to the knowledge base for genome interpretation (for example via PanelApp)
- active and effective collaboration within your GeCIP domain and with other GeCIP domains
- expert assistance in genome interpretation to improve diagnostic yield for NHS GMCs
- contribution to training within your domain where needed
- contribution to the ongoing management and administration of the GeCIP domain where requested
- responsible and safe access to participant data
- submission to a Genomics England Intellectual Property policy
- other activities in line with the provisions of the GeCIP Rules.
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Prior to being considered for data access, each GeCIP domain must submit a detailed research plan to the Access Review Committee (ARC) who will consider whether the research plans of the domain are in line with the stated acceptable uses of the Genomics England dataset. The acceptable uses are outlined in the Research Ethics Committee (REC)-approved 100,000 Genomes Project Protocol and the Data Access and Acceptable Uses Policy. The ARC will decide to approve, decline or amend requests for access to data. The domain leads, or a deputy, will be asked to call in at the appropriate time to answer any questions or queries, and external expertise may be called upon to assist the decision-making process, where appropriate.
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Each institution that is represented within GeCIP is required to sign a contract, the Participation Agreement, with Genomics England. The provisions of the agreement are manifold, but in particular it outlines the various obligations of both the institution and Genomics England with regard to the data access granted to that institution's researchers. It also deals with the ownership of intellectual property (IP) resulting from research on the 100,000 Genomes Project, citing the project's IP Policy. To promote a fair, open and co-operative environment, all GeCIP members are expected to work within the agreed terms of the Participation Agreement signed by their host institution and abide by the terms outlined in the GeCIP Rules. Detailed information on these and other documentation related to GeCIP guidance and policies can be found on the GeCIP Documents and Resources page. A list of institutions and whether they have signed the Participation Agreement can be found here.
During the signing process, each institution will provide a verified list of GeCIP members from their institution to Genomics England. The complete list of users and access requirements is then processed by the Genomics England Service Desk. You must be verified by your institution in order to gain access to the project dataset.
Account issue
When it comes is time to give you access to the data, a Genomics England account will be issued to you using the institutional email address that we hold for you. You will receive two emails:
- An email with your username and a link to complete your information governance training
- An email with a link to set your password.
Included within this email will be your username and instructions on how to access your password using a secure and encrypted service provided by NHS Mail. The same username and password will be needed to log in to applications, eg LabKey, within the Research Environment individually. The safety of your password is of upmost importance:
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Try to be a little unusual when adding special characters. Replacing an s with $ and a ! on the end are very common, and is something a person will try if they think they might know your password. When was the last time you put a # into a password? Just adding one random character can make your password much more secure.
Never write it down, except in a secure password manager. If you write down your password, it defeats the purpose of having one entirely. If you need clues as to which password you have used to each system, keep a log of clues, but make sure they do not contain anything to do with the password (For example, if my password is '@range$86' – my clue could be 'Fruit' or 'Vitamin C”) - Spend time to make a good quality password and clue.
Never share it – if you need to for some reason share a password protected document or system with someone else, change the password to something specific to that task. NEVER share your own password.
Public or shared computer? Do not SAVE your password. Be mindful when letting a system remember your password. You could potentially be giving other people full access without the need to guess anything!
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- You will need to complete an Information Governance course.
- You will need to sign the GeCIP Rules agreement.
- You will need to inform the Genomics England Service Desk of the successful completion of your Information Governance trainingwait for email confirmation that your have completed IG training and can now access the Research Environment. Please note, this confirmation can take up to 5 days.
Information governance training
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You must first access the Genomics England Moodle training environment. There will be a training course entitled 'Information Governance and GeCIP Rules'. Select this course and work through the pages and final quiz.
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To access the Research Environment, you should open a browser and navigate to https://re.extge.co.uk/ovd/. You will then be provided with a login dialog box for which you should use the username and password that have been issued to you. If this does not give you access then it would be worth trying a different browser, eg either Google Chrome or Mozilla Firefox. If you're still unable to get access, please submit an issue to the Genomics England Service Desk stating your username, the operating system you are using, the different browsers you have tried and any error messages that are shown.
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Accessing clinical data in LabKey
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Unfortunately LabKey is not immediately accessible when you first enter the Research Environment. To get access the clinical data, you need to:
- log into the Research Environment
- open LabKey by double-clicking on the LabKey icon on the desktop
- sign in using the same credentials you used to access the Research Environment by clicking 'sign-in' in the top-right corner of the browser window
- at this point, you should see a folder called 'MAIN PROGRAMME', which contains each data release from the Genomics England main programme
- if you are takin no data will be visible and you will be taken to an empty LabKey page Submit and no data are visible, submit an issue to the Genomics England Service Desk entitled 'GeCIP researcher <username> requesting LabKey access' stating that you have successfully logged into LabKey within the Research Environment and are now requesting that your account be upgraded and you are given access to the LabKey projects to which you are entitledbut do not have access to any data. You should state you are a GeCIP member and need access to the main programme data. You will be notified when this has been completed, and the next time you log into LabKey you should have access to the appropriate data.
Accessing your home drive
Your home drive contains links to shared files:
- genomes - gives you access to the Genomics England datacentre and all of the sequencing data.
- re_gecip - contains the shared folders for each of the GeCIP domains. Access to the individual GeCIP domain folders is restricted to members of the domain.
Principles of data access
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However, Genomics England has in place a 9-month moratorium on the publication of results to provide a degree of preferential permission to publish on participant data. This is in recognition of those domains and individuals that have assisted in recruiting to the project. In effect, the moratorium will prevent other GeCIP researchers from publishing research on that domain’s corresponding data until the domain has had access to the data for at least 9 months. The moratorium begins when a meaningful number of whole genomes is available to researchers in a specific domain. More detail on the moratorium policy can be found in the Genomics England Publication Moratorium policy.
Given that the research will be based on work carried out in the Genomics England Research Environment, and within a GeCIP domain, all publications will be made ‘on behalf of the 100,000 Genomes Project and Genomics England’ as a banner heading. In general, issues relating to authorship (whom to include, the order of authors, etc) will follow the guidelines issued by the International Committee of Medical Journal Editors (ICMJE
). For a full description of how and when to publish your results, please refer to the Genomics England Publication Policy. It includes detailed sections on authorship, patentability and review.
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