Frequently asked questions

General

The Genomics England Clinical Interpretation Partnership (GeCIP) is the way that funders, researchers, trainees and clinicians will collaborate – forming a community of disease-specific and function-specific domains. The aim is to analyse and constantly refine the clinical interpretation of the dataset within the National Genomic Research Library.

GeCIP is the next step for the data after the whole genome sequencing, annotation and integration of existing phenotypic data is completed. GeCIP is about making the best use of the data and getting the most benefit from it once we have it. It is about enhancing the clinical interpretation of the data and deriving new findings from the data.

As new knowledge is generated by (i) the experts who are undertaking research on the dataset (which mainly consists of data from participants of the 100,000 Genomes Project) or (ii) other researchers worldwide, we will also make sure that if it’s relevant to individuals, the information is fed back to their clinicians who can use it to make decisions about their treatment.

Genomics England has developed this partnership model to ensure that maximum benefit is derived from the dataset. Through data linkage, this dataset will develop as a rich resource of longitudinal life-course data that is continually augmented and refreshed over time. This will be a truly unique resource, both with regards to its number of subjects and its breadth of variables (such as, phenotypes, health events and outcomes). Each disease area has a complex research and clinical knowledge base. By enlisting the contribution of the relevant expert clinicians, healthcare professionals and academics over the timescale of the programme and beyond, we are likely to make greater progress in shorter timescales to bring benefit to patients sooner.

Genomics England can’t do this as well on our own. The benefits of bringing the best people together to work collaboratively are well known.

In order to be a member of GeCIP, you need to add value to the 100,000 Genomes Project. Researchers, clinicians and students can apply to join any GeCIP domain that is relevant to their intended research projects.

Researchers are part of a disease-specific or function-specific domain that has been approved via inauguration by the Genomics England Chief Scientist. In the case of a disease-specific domain, the researcher is undertaking research on the data pertaining to that disease. They will:

  • undertake ethically approved research project or equivalent work
  • commit results / findings to Genomics England’s National Genomic Research Library
  • gain access to the whole of the dataset within the National Genomic Research Library via the Genomics England Research Environment, with priority to publish on the data that falls within their disease-specific domain. No fee is levied for data access.
  • have advantage when applying for strategic initiatives and response-mode funding from GeCIP funders.

Yes, clinicians of patients who take part in the 100,000 Genomes Project are automatically eligible to be part of GeCIP through their institutions and they will be able to access the data on their patients for direct patient care or the anonymised dataset for ethically approved research.

There is no central funding in GeCIP so under all circumstances you will need to show you have the resources or clear plans for obtaining the resources to do the work you intend to carry out.

Researchers wanting to undertake research through GeCIP will either apply to a funding body through response mode or specific funding calls that are targeted at using the Genomics England dataset. This applies to researchers within or outside of domains.

See also About GeCIP funders and funding

100,000 Genomes Project dataset: this is the patient-level dataset generated via the integration of the whole genome data, the phenotypic data, other sample/patient level administrative metadata with evolving linked data to other resources such as HES, ONS and registry data.

The Genomics England National Genomic Research Library (NGRL): this is a secure national database of de-identified genomic and health data managed by Genomics England. Approved researchers can securely view and analyse the data contained within the NGRL through the Research Environment. The NGRL consists of data from participants of the 100,000 Genomes Project data, as well as data from the Genomic Medicine Service and other Genomics England projects.

The Genomics England Research Environment: this provides a secure workspace for approved researchers to carry out research on the data within the National Genomic Research Library. The Research Environment provides a range of open source tools, databases and research platforms linking genomic data to a rich set of clinical, phenotypic and longitudinal data. Researchers can also develop their own software that can then be run on Genomics England’s high performance compute facilities. To protect patient data, access to the research environment is controlled and secure, and only results of analysis can be exported. Find out more about data access, security and uses.

The Genomics England computing infrastructure: This is the system of computing hardware and software with which we store, process and enable access to the data within the National Genomic Research Library.

For researchers at the clinical-research interface

These FAQs aim to facilitate interactions between researchers and clinical teams, to maximise benefit for participants, advance knowledge and contribute to the wider genomics community. They focus on those areas where there is potential overlap and synergism between clinical and research activities, the clinical-research interface.

Please do let us know suggestions for further FAQs that you think would be helpful to provide an answer for. Please contact us at [email protected] or by completing a service desk ticket at: https://jiraservicedesk.extge.co.uk/plugins/servlet/desk.

If you are a participant looking for similar answers, please go to our participant FAQs focused on the clinical-research interface here.

The Clinical-Research Interface: describes those areas where there are interactions and overlap between healthcare and research. By helping to make links and combine aspects of both healthcare and research, we hope to increase diagnoses and research opportunities for our participants and expand genomic knowledge.

The National Genomic Research Library: Researchers with access to the Genomics England Research Environment, work with de-identified genomic and health data from participants who consented for research, which is held within the National Genomic Research Library (NGRL).

 

Genomics England is keen to foster collaborations between researchers and clinicians. Please use the Clinical Collaboration Request form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

Once submitted this will be reviewed by the Genomics England team. Please include information that you think would be helpful for the clinician(s) and participant(s) to assess the purpose and benefits of collaborating. Examples of this type of request include: asking for further phenotype information to write a case series; offering functional testing to confirm or refute pathogenicity of a variant of uncertain significance etc. In some cases we may ask for further information to help maximise the quality of requests to clinicians. To publish phenotypic data beyond that which can be exported via the Airlock, clinical photos etc. you will need a collaboration with the clinical team(s) and explicit consent for this.

We will review your request and send it to the appropriate NHS contact. It is the clinical team’s decision whether they follow up with the request and we ask them to contact you directly.

Requests involving greater complexity and large numbers of clinicians or participants may need wider discussion and approval, for example if there is likely to be significant use of NHS resources. We are working on our processes for larger scale requests so this advice may be updated. Please contact us if you would like to discuss:
[email protected]

Please ask your colleague to submit a Contact Researcher Form at: https://jiraservicedesk.extge.co.uk/plugins/servlet/desk/portal/3/create/358.

If after review you think there are potentially diagnostic variants please see Questions 3 and 4 for further information about returning potentially diagnostic results to the clinical team.

Only participants who have consented for research will be available in the National Genomics Research Library and available for review by researchers within the Research Environment.

Related FAQs: Questions 3 and 4

Please complete a Researcher Identified Potential Diagnosis Form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

This will be reviewed within the Diagnostic Discovery Pathway, our system for returning potentially diagnostic variants from researchers to the relevant clinician(s) within the NHS. Variants will be triaged based on relevance to the participant’s phenotype and evidence for pathogenicity before returning selected variants to the NHS. Please include information that you think will be helpful for this assessment. If you feel that there is urgency (for example there are urgent treatment issues to consider), please highlight this on the form.

It is very important that any potential results are returned via Genomics England and not directly to individual clinicians. Please also see the answer to Question 4. We will only contact clinicians whose patients have consented for re-contact; in some cases, we are therefore unable to feed-back results.

Most variants reported by researchers as potentially diagnostic will be tier 3 or un-tiered, as clinical laboratories will have reviewed all tier 1 and tier 2 variants at the time of reporting. However, if you feel that new information has come to light since the diagnostic report was issued that would change the assessment of the variant please highlight this on the form.

Thank you very much for your interest in finding additional diagnoses for our participants.

Related FAQs: Question 4

Thank you very much for providing expert review and helping to find diagnoses for our participants. The form(s) will be reviewed within the Diagnostic Discovery Pathway, our system for returning potentially diagnostic variants from researchers to the relevant clinician(s) within the NHS. This will enable appropriate clinical validation of the results and will be done in batches for ease of processing within the Genomic Laboratory Hubs.

If there is urgency (for example there are urgent treatment issues to consider), and this wasn’t highlighted on the form please contact us at [email protected].

We do not feed-back the results of clinician review directly to individual researchers, however the results of the Outcome Questionnaires will become available with subsequent data releases into the National Genomic Research Library (NGRL, the de-identified data from participants who consented for research), viewed in the Research Environment.

If you are interested in collaborating with the clinician to potentially publish the results, for example for a case series and / or because they reflect a novel finding, please consider requesting a collaboration with the clinician(s) and please see the answer to Question 1 for information on how to do this. This would also be the best route if you are able to offer specialist functional testing that may help to confirm or refute the pathogenicity of a variant; please also see the answer to Question 6 about requesting further samples.

It is important to note that some results may fall within the remit of Incidental Findings of clinical significance, as they are unrelated to the primary reason for genetic testing and in this case will be processed within the Genomics England Additional Findings workstream. Whilst many participants will have consented to receive additional findings, others have not consented and it is of utmost importance that we follow the participant’s wishes.

Related FAQs: Questions 1 and 6

Researchers can review the participants recruited from a specific GMC within the Research Environment but are not allowed to attempt to re-identify any participants from the de-identified data within the National Genomic Research Library.

For potentially diagnostic findings relating to individual participants please complete a Researcher Identified Potential Diagnosis Form which can be found within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

This will be reviewed within the Diagnostic Discovery Pathway, our system for returning potentially diagnostic variants from researchers to the relevant clinician(s) within the NHS. For further information please see the answers to Questions 3 and 4.

We are working on our processes for enabling clinician-researcher interactions and returning researcher-identified variants to clinicians. This guidance may therefore be updated over time. If you have large numbers of variants to return and would like to discuss please contact us at [email protected].

Thank you for your interest in helping to find diagnoses.

Related FAQs: Questions 3 and 4

There are two possible routes for obtaining additional samples. The first mechanism for requesting samples, for example where this may help to confirm or refute variant pathogenicity, is to request a collaboration with the clinician(s) for the participant(s) with the relevant variant(s).  Arranging a collaboration facilitates both the use of additional samples and obtaining consent and further information that may be required if a publication is planned.

Please use the Clinical Collaboration Request form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found within the Research Environment at:

https://re-confluence.gel.zone/display/OC/Researcher-identified+potential+diagnoses+and+Contact+recruiting+clinician+forms

Please also see the answer to Question 1 for further information.

If the clinician confirms they wish to collaborate, they can discuss with their patient(s) sending you directly the required samples, either from stored samples within the Genomic Laboratory Hub or fresh samples, as appropriate. They will need to follow your research ethics and local consent and procedures for samples collected for research.

We ask that additional data collected to help with variant interpretation be made available within the Research Environment, to avoid duplication of effort. To submit data to the Research Environment please make a Service Desk ticket request here:  https://jiraservicedesk.extge.co.uk/plugins/servlet/desk

Please make clear that the information was generated through a researcher-clinician collaboration and using additional samples.

An alternative route for obtaining additional samples from participants in the 100,000 Genomes Project, is through submitting a request for access to stored samples, collected at the time of recruitment. Please complete a ticket request form at:

https://jiraservicedesk.extge.co.uk/plugins/servlet/desk

Please note that some samples will be reserved for larger scale projects run by Genomics England and where the data will be made available to the wider research community in the National Genomic Research Library (NGRL). In addition, some stored samples may not be suitable for the proposed analyses. Priority is likely to be given to larger scale projects, where there is greater diagnostic potential, those that will give results that benefit the wider research community, to help with the development of new technologies etc. There may also be some individual cases where this is an appropriate route; for example when it is not possible to obtain samples through a collaboration with a clinician because a participant is deceased and there are no stored samples in the clinical laboratory.

Requests will be considered on a case by case basis and will require internal review and approval by the Access Review Committee. We are working on these processes so this guidance may be updated over time.

Data generated from samples collected for the 100,000 Genomes Project must be submitted to the National Genomic Research Library (NGRL), which is accessed through the Research Environment. To submit data please make a Service Desk ticket request here:

https://jiraservicedesk.extge.co.uk/plugins/servlet/desk

Please make clear that the information was generated using samples collected for the 100,000 Genomes Project.

Where new diagnoses are suspected or confirmed, please complete a Researcher Identified Potential Diagnosis Form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

This will be reviewed within the Diagnostic Discovery Pathway, our system for returning potentially diagnostic variants from researchers to the relevant clinician(s) within the NHS. Please also see the answers to Questions 3 and 4.

Thank you very much for your interest in finding additional diagnoses for our participants. Genomics England is working to facilitate clinician-researcher interactions and to help advance genomic knowledge, especially for the benefit of our participants.

Related FAQs: Questions 1, 3 and 4

No. This is best done through the NHS clinical and laboratory team and with access to the most complete information for assessing pathogenicity; this will also avoid unnecessary duplication.

Yes. Please submit an Airlock GeneMatcher Request from within the Research Environment; navigate to “Airlock”, then “Forms”.

These will be assessed on a case by case basis to ensure confidentiality for participants. We would recommend submitting only high level phenotype data.

If further evidence becomes available to support pathogenicity of the variant please submit a Researcher-identified potential diagnosis form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

Please also see the answer to Question 3 for further information about returning potentially diagnostic results to the clinical team.

Related FAQs: Questions 3 and 4

We encourage researchers to make cohorts for specific disorders that are complete as possible using the data in the National Genomic Research Library (NGRL), accessed through the Research Environment. If you would like to discuss this further please contact us: [email protected]

Thank you for helping to provide expert review and increasing the likelihood of diagnosis for our participants.

Data within the National Genomics Research Library is de-identified and researchers must not attempt to re-identify individual participants within the Research Environment. If a participant’s clinical team wish to request expert review from an individual researcher or GeCIP (Genomics England Clinical Interpretation Partnership) group, they can complete a Contact Researcher Form at:

https://jiraservicedesk.extge.co.uk/plugins/servlet/desk/portal/3/create/358

Please note, the researcher must have access to the National Genomic Research Library through the Research Environment.

We are keen to foster collaborative efforts to help find diagnoses for our participants and to advance our knowledge. If after review you think there are potentially relevant variants please complete a Researcher Identified Potential Diagnosis Form within the Research Environment; navigate to “Airlock”, then “Forms”.

Further help can be found at:
https://research-help.genomicsengland.co.uk/display/OC/Researcher-identified+potential+diagnoses+and+Clinical+collaboration+request+forms

This will be reviewed within the Diagnostic Discovery Pathway, our system for returning potentially diagnostic variants from researchers to the relevant clinician(s) within the NHS. It is very important that any potential results are returned via Genomics England and not directly to individual clinicians. For further information please see the answers to Questions 3 and 4.

Related FAQs: Questions 3 and 4

Thank you for very much for helping to complete the data available for research. Please contact us at [email protected] so that we can ensure the appropriate processes are in place and that we will be able to import the information collected. Once this has been agreed and the information collected, please submit a request to upload the information to the National Genomic Research Library (NGRL) at https://jiraservicedesk.extge.co.uk/plugins/servlet/desk.

You will need to confirm that you have approval to access this data within your organisation. Once within the NGRL this data will be available to researchers with access to the Research Environment. Thank you again for your help ensuring the data is as maximally useful as possible.

You must follow the appropriate rules depending on whether you are acting in a clinical capacity or as a researcher.

Researchers who want to publish data from the National Genomic Research Library (NGRL), accessed through the Research Environment, must submit an Airlock request to extract de-identified data, that is reviewed to ensure individual participants could not be identified. For additional data collection (beyond that which was collected for the 100,000 genomes project or for testing within the Genomic Medicine Service) you would need to seek your patient’s consent for publication, according to local processes.

If you are the participant’s clinician and writing a publication solely using data returned to clinical teams, from the clinical record, and without accessing the Research Environment, there is no need to submit an Airlock request. You will need to follow usual consent processes for the publication of patient information. Genomics England is keen to encourage publications and sharing of data; we recognise that lots of work is done under local approvals and processes, using the data returned to clinical teams, that is very beneficial for our participants.

Please use the standard Genomics England acknowledgement which can be found here https://www.genomicsengland.co.uk/about-gecip/publications/.

Please also inform the GeCIP (Genomics England Clinical Interpretation Partnership) team via gecip-[email protected], so that we can record outputs (direct and indirect) of the 100,000 Genomes Project.

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