Solved cases (rare disease)¶
For rare disease cases, an important goal is to solve them, identifying the causal variant for the rare disease. We have two tables in LabKey that describe solved cases and the variants that have been identified: gmc_exit_questionnaire, which includes diagnoses that have been approved by the Genomic Medicine Centres (GMCs), and submitted_diagnostic_discovery, which includes diagnoses that have been submitted to Genomics England by researchers.
gmc_exit_questionnaire¶
An Exit Questionnaire is filled in by the clinicians at the NHS Genomics Medical Centres (GMC) for each closed case. The given data inform to what extent a family’s presented case can be explained by the combined variants reported to the GMC from Genomics England and the Clinical Interpretation Providers (CIPs). It also includes information on any segregation testing performed, the confidence in the identification and pathogenicity of each variant, and the clinical validity of each variant or variant pair in general and clinical utility in a specific case. One Exit Questionnaire is completed per case.
The Exit Questionnaire is divided into family-level and variant-level questions. For ‘negative’ reports containing no variants, the questionnaire will only present the family level questions.
The family-level questions ask whether the combined variants between them explain the genetic basis of the family’s presenting phenotype(s). Firstly it is asking whether the case can be considered fully or partially solved, and secondly, whether any segregation testing in the family has bene performed.
The variant-level questions ask for information on each individual reported variant.
The fields in the Exit Questionnaire are listed below:
| Field | Description | Level |
|---|---|---|
event_date |
The date when the questionnaire was submitted | Family-level |
additional_comments |
Comments regarding report | Family-level |
case_solved_family |
Have the results reported here explained the genetic basis of the family's presenting phenotype(s)? | Family-level |
segregation_question |
Have you done any segregation testing in non-participating family members? | Family-level |
actionability |
Is evidence for this variant/variant pair sufficient to use it for clinical purposes such as prenatal diagnosis or predictive testing? | Variant-level |
variant_group |
This value groups variants that together could explain the phenotype according to the mode of inheritance used. (e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in the same group (i.e.: reported together). This value is an integer unique in the whole report. These values are only relevant within the same report. | Variant-level |
clinical_utility |
Has the clinical team identified any changes to clinical care which could potentially arise as a result of this variant/variant pair? | Variant-level |
acmg_classification |
What ACMG pathogenicity score (1-5) did you assign to this variant? | Variant-level |
confirmation_decision |
Did you carry out technical confirmation of this variant via an alternative test? | Variant-level |
confirmation_outcome |
Did the test confirm that the variant is present? | Variant-level |
reporting_question |
Did you include the variant in your report to the clinician? | Variant-level |
variant_details |
Variant coordinates following format chromosome:position:reference:alternate | Variant-level |
You can also look at full details of the report models for Exit Questionnaires.
submitted_diagnostic_discovery¶
If you discover any potential diagnoses, you can report these to us using the Contact clinical team and/or report potential diagnosis form which is available in Airlock. These will be sent onto the GMCs for approval, but in the meantime, all submitted diagnoses will be added to the submitted_diagnostic_discovery table.
| Field | Description |
|---|---|
participant_id |
the participant ID of the proband |
gene_of_interest |
the gene containing the causal variant, as a gene name |
variant_of_interest |
the genomic location and allele change of the causal variant in the form chr:location:ref:alt |
genome_build |
The genome build of the variant coordinates |
reporting_date |
when the association was reported |
notes |
any further relevant information |
We do not remove any entries from the submitted_diagnostic_discovery table when these have been examined by the GMCs, whether they approve the diagnoses or not.