Clinical Research Interface FAQs¶

I want to contact one or more clinicians to get more information about a set of participants that I want to collaborate to publish a paper on

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”.

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 Service Desk if you would like to discuss.

A clinical colleague has a patient they would like me to look at more closely to see if I can find any variants that were un-tiered or tier 3 that could have caused their disorder

Please ask your colleague to submit a Contact Researcher Form.

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.

I reported a diagnosis using the Researcher Identified Potential Diagnosis form, but I have heard nothing. Has it gone back to the doctor? Did they think it was the answer?

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 Service Desk.

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). 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.

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.

I want to look at all the participants recruited from my local Genomic Medicine Service (GMS) and see if I can identify new diagnoses

Researchers can review the participants recruited from a specific GMS 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.

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.

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 Service Desk.

Thank you for your interest in helping to find diagnoses.

I have found some variants that I think are probably causal but I need DNA/RNA to confirm that they are functional

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.

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.

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 is through submitting a request for access to stored samples, collected at the time of recruitment. Please make a Service Desk ticket form.

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 an initiative 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.

Please make clear that the information was generated using samples collected for the related initiative.

Where new diagnoses are suspected or confirmed, please complete a Researcher Identified Potential Diagnosis Form within the Research Environment.

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.

I want to report a variant that was found to be causal through the NGRL Genomes Project through ClinVar, can I?

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.

I want to share a gene using GeneMatcher to see if there are other cases around the world

Yes. Please submit an Airlock GeneMatcher Request from within the Research Environment.

These will be assessed on a case by case basis to ensure confidentiality for participants. Please only include top level phenotype data (e.g. ‘disorder of the immune system’).

Please make a clinical collaboration request so we can contact the clinician, if you would like to add detailed phenotypic information.

If further evidence becomes available to support pathogenicity of the variant please submit a Researcher-identified potential diagnosis form within the Research Environment.

I am working in a consortium with others treating the same disorder, can I discuss variants and phenotypes with other clinicians to identify diagnoses?

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 Research Network researcher or group, they can complete a Contact Researcher Form.

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.

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.

I have noticed missing clinical data that would help a lot with research, can I collect and import it into the Research Environment?

Thank you for very much for helping to complete the data available for research. Please contact Service Desk 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).

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.

I am both a clinician and a researcher, can I publish information about my own patients using data from the NGRL Genomes Project?

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 on our publications page.

Please also inform the Research Management team via research-network@genomicsengland.co.uk, so that we can record outputs (direct and indirect).