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How to map acute lymphoid leukemia immunophenotype (T or B) in a generic way

Vocabulary Users
#1

Hi!

We are working on modelling a data source on acute lymphoblastic leukemia. The immunophenotype is provided as T-cell ALL or B-cell ALL, as a generic classification without specifying the subtype (mature or precursor). In the attempt to map this variable in the condition domain, we have found as standard concepts 4173963 (B-cell acute lymphoblastic leukemia) and 4082462 (T-cell acute lymphoblastic leukemia). However, the synonyms associated to these concepts are more specific than the name of the concept itself. For instance, B-cell acute lymphoblastic leukemia subsumes only Burkitt cell leukemia.
Also both concepts are descendants of 134305 (Acute lymphoid leukemia), which subsumes other concepts such as 4082461 (Precursor B-cell acute lymphoblastic leukemia). We wonder if these concepts can be used in our context, since other generic non standard concepts as 42542141 (B-cell acute lymphoblastic leukemia) have 4173963 (B-cell acute lymphoblastic leukemia) as Non-standard to Standard map (OMOP), or if there is a more appropriate and generic way to map this variables. We’d really appreciate it if you could help us.

Many thanks in advance!

#2

@lturg:

You are walking into a hornet’s nest here. These hematological malignancies seem to be put into a new hierarchy every 10 years, and the genomic markers add complexity. In addition, The logic that SNOMED supports may not be identical to the one ICD10 supports, and then you will have these seeming contradictions in the mapping. I would strongly suggest you go after the ICD-O based diagnostic codes. They are more granular and hopefully more in line where the medical community right now sits.

What’s your use case?

#3

Our use case is an ALL research Project. We have the same problem with the ICD-O codes. They are more specific than the classification used by the source. For example, 36402841 (Precursor B-cell lymphoblastic leukemia of blood) has 4082461 (Precursor B-cell acute lymphoblastic leukemia), that belongs to the SNOMED vocabulary, as ancestor. So, we enter in the SNOMED classification again and there is no concept that includes all the B-cell ALL subtypes.

Thank you for your reply!

#4

@lturg:

Yeah. There is no intermediate step below ALLs for only the B-cell variety. You need to make a conceptset:

Concept ID Name
4153344 Acute lymphoblastic leukemia, transitional pre-B-cell
37109936 B lymphoblastic leukemia lymphoma with t(9:22) (q34;q11.2); BCR-ABL 1
36402830 B lymphoblastic leukemia/lymphoma with hyperdiploidy of blood
44500538 B lymphoblastic leukemia/lymphoma with hyperdiploidy of bone marrow
36402760 B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL) of blood
44501122 B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL) of bone marrow
36402805 B lymphoblastic leukemia/lymphoma with t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1) of blood
36564047 B lymphoblastic leukemia/lymphoma with t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1) of bone marrow
36402802 B lymphoblastic leukemia/lymphoma with t(5;14)(q31;q32); IL3-IGH of blood
36550021 B lymphoblastic leukemia/lymphoma with t(5;14)(q31;q32); IL3-IGH of bone marrow
36402826 B lymphoblastic leukemia/lymphoma with t(v;11q23); MLL rearranged of blood
44500044 B lymphoblastic leukemia/lymphoma with t(v;11q23); MLL rearranged of bone marrow
36402801 B lymphoblastic leukemia/lymphoma, NOS, of blood
44501999 B lymphoblastic leukemia/lymphoma, NOS, of bone marrow
4173963 B-cell acute lymphoblastic leukemia
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