SARS-CoV-2 codes discussion

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  • #435271
    Vojtech Huser
    Participant

    If multiple countries have different test, it may be a good idea to have a methodless code for quantitative and qualitative testing for SARS-CoV-2

     

    The problem with termporary codes is that the loinc part for SARS-CoV-2 is not listed.

     

    To take analogy with quantitative test for HIV 1 RNA here https://loinc.org/21333-0/

    I know that ‘HIV 1 RNA’ has code <span style=”color: #000000; font-family: Consolas, Monaco, monospace; white-space: pre-wrap;”>LP38425-2</span>

     

    It is not clear what LP code is for ‘SARS coronavirus 2 RNA’

     

    <a href=”https://loinc.org/94309-2/”>https://loinc.org/94309-2/</a&gt;

     

     

    The LOINC code info page should have an option to display LP codes for all components.

     

     

    #435308
    Tim Briscoe
    Keymaster

    Hello Vojtech, what is your use case for the Part codes?

    #435329
    Vojtech Huser
    Participant

    The use case is to create as few as possible OMOP codes outside LOINC.

    OMOP CDM uses LOINC and embraces it.

    Recently, there are efforts to better capture LOINC parts in OMOP Vocabulary. See here https://forums.ohdsi.org/t/improve-loinc-representation-in-omop-vocabulary-athena-link-parts-to-lab-tests/7925

     

    Knowing the LPs (including temporary ones) is crucial for following correctly LOINC concept model.

    LOINC will at some point adopt some framework for postcoordination.

     

    As terminologist, I have few thoughts on how from components one could create good classification codes.

    E.g., test from sputum for SARS-CoV-2, test from sputum for SARS-CoV-2 RNA,

     

    The LOINC search supports such nice searchers (unfortunately not for temporary codes). e.g. https://search.loinc.org/searchLOINC/search.zul?query=hiv+1+RNA+Methodless%3Atrue

    search is: ‘hiv 1 RNA Methodless:true’

     

    The release of those codes was coordinated with SNOMED CT (per here http://www.snomed.org/news-and-events/articles/changes-coronavirus-descriptions ) which is great. I like that LOINC has temp codes published and can respond more flexibly. No temp code page for SNOMED CT 🙁

     

    I would also like to propose a LOINC group for SARS-CoV-2 tests. (and have concept of temp groups (inbetween releases).

    I would like to propose at least one (or several) methodless codes for SARS-CoV-2

    In fact there should be a policy for methodless codes accross all of LOINC lab content. (and it should be consistent) (or some postcoordination grammar (expression language) where my expression is deemed equivalent to an existing pre-coordinated code.)

     

    I would also like to see parent-child hierarchy between LP for ‘SARS-CoV-2 RNA’ and LP ‘SARS coronavirus 2 N gene’

    And be able to search for any component that is child of ‘SARS-CoV-2’ or ‘SARS-CoV-2 RNA’

     

    (that in fact assumes temp codes do show up in <b>the </b>LOINC search page.)

     

    p.s.

    By the way, upgrading this forum to some newer platform would be great. (allow ctr+V to insert image in my post)

     

    #435333
    Vojtech Huser
    Participant

    This wikipedia page has gene targets. Generic code that covers them all (or separate code for each line in the table) may be needed.
    <p style=”box-sizing: border-box; font-family: Arial, Helvetica, sans-serif; line-height: 24px; font-stretch: normal; color: #3c4245;”><strong style=”box-sizing: border-box;”>Summary table of available protocols</p>

    <strong style=”box-sizing: border-box;”>Country <strong style=”box-sizing: border-box;”>Institute <strong style=”box-sizing: border-box;”>Gene targets
    China China CDC ORF1ab and N
    Germany Charité RdRP, E, N
    Hong Kong SAR HKU ORF1b-nsp14, N
    Japan National Institute of Infectious Diseases, Department of Virology III Pancorona and multiple targets, Spike protein
    Thailand National Institute of Health N
    US US CDC Three targets in N gene
    France Institut Pasteur, Paris Two targets in RdRP

     

    <a href=”https://en.wikipedia.org/wiki/COVID-19_testing#Antibody”>https://en.wikipedia.org/wiki/COVID-19_testing#Antibody</a&gt;

     

    #435453
    Swapna Abhyankar
    Moderator

    We have generic codes – “SARS Coronavirus 2 RNA” as well as specific codes for different targets. If you haven’t already, please check out our special SARS-CoV-2 FAQ page: https://loinc.org/sars-coronavirus-2/

    These codes will be added to our Groups content for the June release, but at this time, we are not planning to release temporary Groups or Parts before then.

    #435559
    Vojtech Huser
    Participant

    During OHDSI COVID19 study-a-thon – we found out that LOINC codes help us only half the way. It is good that we have a code for RNA test, but the result of that test can still vary and be coded as ‘Detected’ or ‘Positive’ or ‘Not Detected’ or ‘Negative’. For qualitative tests, recommending via a nudge (not requiring) some possible result values (just like example units) may be a way to do the last mile of standardization.

     

    See the details about coded values as results here: https://forums.ohdsi.org/t/covid19-etl-help-for-converting-your-data-into-omop/10269

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