Nomenclature attribute of measures

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1

Hi,

What is the difference between mutation and Genetic sequences class (Public Health Environmental Surveillance Open Data Model (PHES-ODM) Documentation - Sets)? Isn’t is the same idea behind?

Thanks

2

Hi there - a great question! I haven’t worked in a wet lab myself for many years, but I believe that while the two classes are very similar (and have a fair bit of overlap) there are some distinctions. Namely, that if you are testing for a specific mutation you can use specific primers and run some PCR tests. Whereas for sequencing, you’re looking at generating and reading full sequences, always. I take your point about their similarity though. Perhaps the mutation class could be split into PCR and Sequencing. Do you think that would align more intuitively?

Thank you again!

3

Hi,
Actually you can detect mutation by sequencing too. It would maybe be better to use PCR and sequencing. There is a qPCR class. Maybe simply use PCR to encompass all types of PCR. If not you could add dPCR class as it is what we use.

Thanks for your reply.

4

Thanks for this! I’ll see about better aligning the classes based on this feedback. Appreciate it!

5

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6

The mutations class has now been depreciated in the next version (2.3.0) and all members of this class moved to the PCR class. Thee sequencing class does still exist, but is more methods focused (ex: Estimated frequency of reads, Inhibition measure, PHRED quality score, etc.) than target focused. The variant class has, however, been maintained.