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Viral Pneumonia Gold Standard Phenotype

(Matt Spotnitz) #1

Has anyone created a gold standard phenotype of viral pneumonia patients? I would be happy to help with the design and validation of this phenotype.


(Daniel Prieto-Alhambra) #2

hi @mattspotnitz ,
I think @Christian_Reich was having a go at creating a concept set. It would be great if you could help the validation bit, whatever ‘validation’ means here :slight_smile:


(Matt Spotnitz) #3

I will be happy to help. I have made some viral pneumonia phenotypes and would appreciate feedback. Thanks!

(Matt Spotnitz) #4

For those who are interested, here is a viral pneumonia phenotype that had approximately a 65% PPV on the Columbia database.


@Patrick_Ryan, @Christian_Reich, @Daniel_Prieto, @rchen, @cukarthik

(Christian Reich) #5

Curious, @mattspotnitz: Why are you excluding bacterial pneumonias? Because they inevitably jump on top of a viral if only it is severe and long enough. Or do you want those cases where that hasn’t happened yet?

(Matt Spotnitz) #6

I thought it would be best to start with a more specific phenotype, and then expand into a more sensitive one. Thanks for the feedback!

(Christian Reich) #7

Yeah. That’s not easy. I would exclude all the other reasons somebody might get a bacterial pneumonia. The rest is of viral origin. A healthy lung won’t acquire a pneumonia out of nothing.

(Nigel Hughes) #8

And in the young and old there is a lot of co-infection and other causes of pneumonia, in particular RSV, flu-A, flu-B, as well as of course bacterial causes, whether primary or secondary pneumonia.