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Using the Research Environment for clinical diagnostic discovery, January 2024


The rich phenotypic and medical history data, coupled with whole genome sequences available in the GEL Research Environment provides a unique opportunity for diagnostic discovery. In this training session we will take you through the data available in the GEL RE, including results of our own bioinformatic diagnostic analysis, and how you can access these, as well as tools available to filter the data, carry out your own analyses and validate your results. As part of the training, we will show you how to submit your genetic diagnoses to the clinical Genomic Medicine Service or contact clinicians, leading to direct clinical application of your work.

This training is aimed at clinical geneticists and does not require any coding skills. You will have chance to ask questions of our clinical team, who assess submitted diagnoses, and see what happens to your submissions.


13.30 Welcome and introduction 13.35 GEL ingestion of rare disease participants 13.45 Identifying participants who need a diagnosis 13.55 Finding results of GEL analysis 14.05 Exploring variants in IVA 14.15 Validate your diagnosis 14.25 Find and compare other participants with the same variant 14.35 Submit your diagnosis and/or contact clinicians 14.45 Getting help and questions

Learning objectives

After this training you will know:

  • How GEL analyses new rare disease genomes and where to find the results of these analyses
  • How to filter, analyse and validate variants in a participant of interest
  • How to submit diagnoses to the GMS

Target audience

This training is aimed at researchers:

  • Are working in the Genomics England TRE
  • Are clinical geneticists trying to do diagnostic discovery
  • Do not necessarily have any coding skills


9th January 2024


You can access the redacted slides and video below. All sensitive data has been censored.



Give us feedback on this tutorial



are EHR records longitudinal, are the date of the diagnose also available, in addition, how about the prescription records?

Yes they are longitudinal and data continues to be collected with time. They include chemotherapy and immunotherapy for cancers, but does not include other prescription records.

My understanding is that the EHRs are only collected in a subset of the rare disease participants?

We should have EHR for the vast majority of participants. I am not aware of any active filtering/subsetting to only allow EHRs for a subset of participants, regardless of whether they are part of the RD or Cancer programme. Perhaps one of my colleagues can correct me on that however. Having said that, there is definitely some level of missingness in these health records as can be expected from real world data :)

if for a specific participant, HPO terms have been updated, is it possible to re-run exomiser using the updated list of HPO terms?

live answered

Are the variants presented in Tier 3 (research) analyzed, discovered, and reported by a researcher, or list all variants from WES/WGS?

live answered

does the exomiser table in Labkey contain all rare disease cases and relatives or has it been only run for some?

The Exomiser table should contain all RD cases/families that have gone through interpretation. This is unlikely to change significantly since the 100K project has essentially wrapped up in that regard.

what if I am part of the clinical team of the participant?

If you are a GeCIP member and would like to submit a request, e.g. you think you may have found a potential diagnostic finding, please select GeCIP in the user group drop-down.

Sorry if I missed this, how can you tell what tier your variant is in? Thanks! Amy

live answered

Is there a way to search foa a cohort of patients with a variant in a particular gene or region?

live answered and pointed to

For getting bams for IGV, is it easier to download the bams to your own area or click through each time? Or what would you suggest - sorry I know you went through it

live answered