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Graft manipulation: which domain to use?

Vocabulary Users
#1

Hi all,

We are mapping to OMOP-CDM 5.4 and are trying to map a ‘Graft manipulation ex-vivo’ concept, for example ‘Graft manipulation ex-vivo: CD34+ manipulation’. It seems that we will need to create a custom concept. We are not sure which domain and parent to use. Possible options are:

  • It is a procedure linked to the patient that has received the transplant ‘CD34+ manipulation’, parent could for example be ‘specimen preparation’ (Athena). This does not feel like a good fit as the patient itself did not actually undergo the procedure, rather the graft did.
  • it is an observation linked to the patient that has received the transplant ‘CD34+ manipulation done on received graft’, unsure what a good parent is.
  • it is a device (a graft) linked to the patient that has received the transplant ‘HSCT graft with CD34+ manipulation’ with parent 'Autologous fluid containing hemopoietic stem cells’ (Athena) if autologous procedure for example

We appreciate your input,
Thank you and kind regards
Freija

#2

@freija:

Remind me: What is “CD34+ manipulation”? Isn’t the whole stem cell transplantation about CD34 cells? What else are you manipulating?

#3

Thank you. I asked the experts and here is the answer:

By Graft manipulation, we mean any procedure performed to define and optimize the volume and cellular composition of stem cell sources like apheresis products, bone marrow, or umbilical cord blood. I believe “CD34+ manipulation” refers to CD34 enrichment that yields stem cell preparations with low contaminating T and B cells. Examples of Graft manipulation are:

T-cell (CD3+) depletion - Removal of T-cells (CD3+) from the donor graft. Depletion of T-cells (CD3+) provides almost untouched grafts with potential antileukemic effectors (e.g., NK cells) enabling fast engraftment and reliable prevention of GvHD.

T-cell receptor αβ depletion - Selective depletion of T cells expressing the αβ T cell receptor. This allows for the removal of cells responsible for GvHD and PTLD but maintains hematopoietic progenitor and stem cells for engraftment (CD34+ cells), as well as cells to elicit graft-versus-tumor effect and provide anti-infective activity (such as gamma-delta T cells and natural killer cells).

B-cell depletion (CD19+) by MoAB - B-cells are depleted from the graft by using monoclonal antibodies.

NK cell depletion by MoAB - NK cells are depleted from the graft by using monoclonal antibodies.

CD34+ enrichment - Positive selection of CD34 cells. The manipulation provides a graft with a very low number of T cells and therefore allows to avoid GvHD very effectively.

Genetic manipulation - This is a procedure by which techniques of gene transfer/transduction are used to alter the structure and characteristics of genes in the graft before the cell infusion.

#4

In that case we would have to create some OMOP Extension concepts all reporting into hematopoietic stem cell transplantation, like Hemopoietic stem cell transplant. We would add the specificity about how the stem cells were manipulated.

We can’t have records about the manipulation itself, because the OMOP CDM is a patient-centric database. What happens in the lab is irrelevant. Only what happens to the patient. The ETLer might run into the some time stamping problem if only the manipulation is known, but not the date of the transplantation.

What do you guys have?

#5

Thank you. Indeed: we know the date of the transplantation but not of the manipulation itself. Could you expand on what you mean by ‘create some OMOP Extension concepts all reporting into hematopoietic stem cell transplantation’? Do you mean that we create concepts that have ‘hematopoietic stem cell transplantation’ as parent and then have the specific type of transplant. For example:

  • patient x received a graft on date_a
  • we know graft was manipulated, cd34+ manipulation

Then we record a procedure ‘hematopoietic stem cell transplantation with CD34+ manipulated graft’ for patient x on date_a, which is a child concept of ‘hematopoietic stem cell transplantation’? Did I get that right?

thanks again!
Freija

#6

In the above case, I would load 2 records into OMOP CDM:

4120445 (Hemopoietic stem cell transplant) in Procedure table

36859582 (PERIPHERAL BLOOD STEM/PROGENITOR CELLS, AUTOLOGOUS, CD34+, G-CSF MOBILIZED) in Drug table

#7

Not sure, @QI_omop. Very doubtful, that this would be considered a drug. We need to clear out the RxNorm Extension.

Head on. You can make that concept yourself by using concept_id above 2 Billion or put a Github issue to the Vocab Team.

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