Questions regarding pharmacogenetics data mapping

Hello, my name is Marta. I have never used LOINC before but I have peruse the Knowledge Base and watch the tutorial video. I’m interested in mapping pharmacogenetics data into LOINC and would like to know how. I would like to ask several questions:

  1. Regarding the abbreviation table, where can I find the full list of the abbreviation table? I looked through the Knowledge Base and it’s directing me to the Naming section but the table listed is only partial and does not have a lot of abbreviations listed. I can’t find the table on the downloaded LOINC file data as well.

  2. I was wondering if anyone has a data mapping examples for pharmacogenomics data such as CYP2D6 mapping?

  3. If a gene for example has phenotypes like Poor metabolizers, Normal metabolizers, etc. does it count as 1 gene having multiple different LOINC codes? I understand that things like UoM can make 1 data have different LOINC codes from one another, but would things like metabolizers of a certain gene would make that data have different LOINC codes each as well?

Thank you for considering to answer my questions :slight_smile:

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Hello Marta and welcome to the community!!

I will answer as many questions as possible; I may need more clarification on some questions.

  1. Which abbreviations are you referring to? Gene abbreviations? Attribute abbreviations?
  2. Any of the pharmacogenetics mapping exercises are customized to how the local laboratory information system is set up to record answers. There could be only one field for a narrative summation OR there could be individual LIS fields available for entering information about the study. Check out US reference labs for initial examples: CYP2D6 | ARUP Laboratories Test Directory
    512150: Cytochrome P450 2D6 Genotyping | Labcorp (scroll to very bottom)
    If you’ll provide the result field labels in your system for CYP2D6 studies, I can try to make a mapping example for you.
  3. Phenotypes will have one assigned per patient, as it’s a description of how that patient’s personal gene pool will handle medication. The patient may have multiple gene studies with possibly one gene providing a poor metabolizer phenotype and a better metabolization on a different gene study. The same LOINC code 51971-0 is included in each gene study as the resulting field for the description. The example phenotypic answers include ultrarapid, rapid, normal, intermediate or poor metabolizer.
    I hope this provides an initial start for your work. Please reply and continue the conversation!!

Hello! Sorry for the late reply, I just have time to look at the forum again. Thank you so much for your help and for answering my question. Your answer on question 2 and 3 has been really helpful and I know where to look/how to proceed based on your examples.

As for question number 1, in the LOINC excel table there’s a lot of abbreviations for multiple columns For example, column SYSTEM has things like “Bld/Tiss, etc.” and column PROPERTY has “Geno, Imp, etc.”. I was looking if there’s a comprehensive list/table in a (one?) file that would include all the abbreviations across all columns? Not just limited for abbreviations for 1 columns. I hope that expand/explain my question. Thank you so much!

Hi Marta!
While there is not one table that holds all abbreviations, there are exportable .csv tables for each attribute type of modifiers, property, timing, etc. Please start in section 2 of the Knowledge Base and scroll through to the attribute you are inquiring about. Knowledge Base – LOINC

I think you’ll find over time this was just an educational hurdle and with practice you can decipher the abbreviations without problem.

Best regards,

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Hello again! Ahh, I see I see. I will try to find things that I need there. Thank you so much for the pointer. For now, that’s all my questions. Thank you! :grinning:

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