FAQs¶
Why do the tiered summary counts shown in the Interpretation Portal not match what I see in the tiering interpreted genome?
The counts shown in the Interpretation Portal are unique variant counts based on chromosome:position:reference:alternate of each variant
If the same variant has multiple report events with different tiers e.g. Tier 1 and Tier 2 it would only be counted once as Tier 1
What is a valid participant in a pedigree?
The Interpretation Portal only displays pedigree members if there is also an associated sample (LP number) in the samples array.
Why don't I see interpretation flags for my referral?
For GMS referrals you need to specify "extra_params=show_interpretation_flags" in order to see flags
See using extra-params for further info
How can I get additional help with a API question?
Issues can be raised as described here
For GMS referrals, what is the difference between the Pedigree information in the referral_data and interpretation_request_data nodes?
The pedigree you see in the “referral data” represents the pedigree information from TOMS, which is generated when
the test is first ordered by the clinician
At this point in time, potentially no blood sample has been taken, no DNA extracted, no genomes sequenced.
Only after the test is ordered, do the samples get sequenced and the referral processed through the WGS pipeline.
The Genomics England Bioinformatics Pipeline links up the referral data we get from TOMS with genomic sample data
we get via the lab and Illumina.
The pedigree you see in interpretation_request_data is the pedigree used by the bioinformatics pipeline for the
interpretation of that referral, so it has the newer, sample information, which was not there initially when the
test was ordered.
How do I get the date a GMS referral was first successfully loaded in the Decision Support System?
See dss_arrival_date described here
How do I know what the API statuses mean?
Please refer to API statuses
Why can't I find my case in the API?
Please email Genomics England Service desk, your case may be blocked upstream in the GeL Interpretation Pipeline.
What does GitVersionControl field represent?
Changes to the GeL data models are versioned in GitHub. Details of the models and the associated versions can be found on GitHub here
I can see multiple versions of an interpretation request / interpreted genome / clinical report which should I use?
It is generally recommended to use the most recent version (the version with the highest number) unless you need to use a specific version.
How often will new versions of interpretation request / interpreted genome / clinical reports be generated?
Once a case has been approved and passed to the GMC it is unlikely that a new version of the interpretation request or interpreted genome will be generated due to cases that have not yet be processed having priority over reprocessing cases. Clinical Report versions are controlled by GMCs via their actions in the CIP systems.
Can we get Cancer results via the API?
Yes. If your workspace (LDP/GMC) have had any cancer results, they can be queried from the following URL: api/2/interpretation-request?sample_type=cancer
Why does a variant have multiple report events?
Multiple report events could arise for various reasons e.g if multiple panels are applied to the family you might get tiering report events for the same variant if there are overlapping genes in the panels applied. We also now tier using “complete” and “incomplete” penetrance modes (depending on clinical review of the pedigree) so you will get “complete" and “incomplete" tiering reportEvents (see the reportEvent penetrance field).