Stream: genomics
Topic: ComplexMutations
Patrick Werner (Aug 29 2018 at 16:07):
@Gideon Giacomelli
trying to extract extra topics from the panel discussion:
You already can capture all the mutations in the DescribedVariant profile in Observation(Described Variant).component:genomic-dna-chg. (Genomica DNA change (gHGVS))
Patrick Werner (Aug 29 2018 at 16:08):
HGVS lets you express deletions, indels, copy number changes etc.
Patrick Werner (Aug 29 2018 at 16:16):
I don't see the need of a new resource like geneStudy. Yes we use Observation a lot, but with different profiles. Until now i haven't encountered a restriction which legitimates the need of a new resource.
Gideon Giacomelli (Aug 30 2018 at 09:27):
@Patrick Werner @Kevin Power thank you for the detailed reply. As far as I understand it, if I have one Observation per variant I want to represent this mutation in a sequence resource and for a complex structural mutation I would connect this observation to several sequences.
We should also take into account that Whole Genome Sequencing can result in several thousand mutations therefore I am not sure if this is feasible.
Also if a somatic mutation was found I want to link this to two samples a tumor sample and a control sample (mostl likely from blood) which is not possible right now, or is it?
I don't know if this is the best way to ask all these questions here of if there is a better way for me to proceed.
Patrick Werner (Aug 30 2018 at 11:43):
I'm not sure if you need the sequence resource for that. Found Variants are captured as an Observation(Described Variant Profile)
Patrick Werner (Aug 30 2018 at 11:44):
Quote from the other Thread:
The lab returns all studied genes as Observations(Described Variant). I have one Observation per found variant or per gene. What was looked at is Observation(Described Variant).component:gene-studied, the overall result (was something found) would be Observation(Described Variant).valueCodeableConcept.
If a Variant was found the details are captured in the components.
Patrick Werner (Aug 30 2018 at 11:52):
To distinguish between somatic and germline mutations there is:
Patrick Werner (Aug 30 2018 at 11:53):
Observation(DescribedVariant).component:genomic-source-class
Kevin Power (Aug 30 2018 at 13:16):
I will just add that there are a couple of ways of referencing info about the specimen:
Observation.specimen
Observation.bodySite
I will also mention we have yet to really define how to appropriately structure those large changes. I don't disagree with what has been said so far, but just like to be clear that we haven't nailed it down yet.
Last updated: Apr 12 2022 at 19:14 UTC
