Stream: implementers
Topic: How to model primer
Patrick Werner (Mar 14 2017 at 10:46):
in a current project in the genetic diagnostic context we are wondering how to model primer. We could use medication - but it feels wrong. Has someone already had a similar problem?
Grahame Grieve (Mar 14 2017 at 19:32):
rmind me what a primer is?
Patrick Werner (Mar 15 2017 at 09:02):
it is needed for DNA synthesis / diagnostic DNA sequencing
Patrick Werner (Mar 15 2017 at 09:03):
https://en.wikipedia.org/wiki/Primer_(molecular_biology)
Patrick Werner (Mar 15 2017 at 09:04):
you have specifc primers for different sequencing questions/ DNA synthesis starting points
Grahame Grieve (Mar 15 2017 at 19:18):
My initial reaction is, why is this in scope for FHIR? @Gil Alterovitz really a clinical genomics question
Bob Milius (Mar 15 2017 at 19:40):
Would this be used to document methodology? i.e., what primers were used for the sequencing?
Bob Milius (Mar 15 2017 at 19:49):
Right now the Sequence resource (what you use to report your DNA sequence) uses Device to describe methodology, but we really haven't tested that see how appropriate that is. One option would be to point to an external methods registry, eg NCBI's Genetic Testing Registry and a accession # pointing to a particular genetic test.
Gil Alterovitz (Mar 15 2017 at 20:08):
If you are using this for provenance, that resource can be used (see examples in provenance resource linking to sequence).
Joel Schneider (Mar 15 2017 at 20:50):
An additional layer of complexity for primers is that trade secret considerations may be involved. If that's the case, it may be necessary to describe the primer in terms of its target DNA, rather than describing the primer itself.
Patrick Werner (Mar 20 2017 at 15:45):
Thanks for all the replies. @Grahame Grieve you are right this is maybe not in the scope of FHIR. In our current use case we want to manage the order entry of DNA sequencing orders with a FHIR based system. As the students like to use FHIR because of the tooling the question came up. @ Bob Milius This would be used for documentation purposes, and also for ordering and picking the correct primer for a given Sequencing request.
Patrick Werner (Mar 20 2017 at 15:46):
we maybe end with a profiled Basic resource
John Moehrke (Mar 20 2017 at 15:57):
There is equivalent issue in Lab results, where the specific method used to come to a lab result is important to record. This is often done simply with a code, where it is understood for any specific code the method used. Thus one has a living codesystem for the various methods. Does this work? Is there a need to do more than mange a set of codes?
Last updated: Apr 12 2022 at 19:14 UTC
