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Cancer diagnosis concepts missing

vocabularies

(Tina Seto) #1

Hi,

The following histology-topography diagnosis concepts are found in our EMR but do not match to a corresponding concept in the ICDO3 vocabulary.

Tina

8000/3-C56.2
8000/3-C78.0
8000/3-C79.5
8000/3-C7A.8
8000/3-C81.9
8000/3-C82.9
8000/3-C83.3
8000/3-C85.8
8000/3-C85.9
8000/3-C90.0
8001/3-C43.7
8001/3-C79.5
8001/3-C7A.8
8001/3-D05.0
8010/2-D05.1
8010/2-D05.9
8010/2-D09.9
8010/3-C56.1
8010/3-C79.8
8010/3-C79.9
8010/3-C80.1
8010/3-D05.1
8013/3-C7A.1
8013/3-C7A.8
8013/3-D3A.0
8020/3-C79.9
8020/3-D3A.0
8022/3-D05.0
8032/3-C49.A
8041/3-C04.9
8046/3-C61.9
8050/3-C79.9
8070/2-D00.0
8070/3-C77.3
8070/3-C79.3
8070/3-C79.8
8070/3-C80.1
8070/3-D06.9
8070/3-D09.9
8071/3-C49.0
8071/3-C77.0
8071/3-C79.8
8073/3-C77.9
8076/2-C76.0
8083/3-C79.8
8083/3-C80.1
8090/3-C76.0
8098/3-C34.9
8120/3-C22.0
8120/3-C65.1
8120/3-C65.2
8120/3-C66.1
8120/3-C66.2
8130/2-C64.2
8130/2-C65.2
8130/2-C66.2
8130/3-C65.2
8130/3-C66.2
8131/3-C65.1
8140/2-C78.7
8140/2-D05.1
8140/2-D06.9
8140/3-C22.9
8140/3-C56.2
8140/3-C77.2
8140/3-C78.0
8140/3-C78.7
8140/3-C79.4
8140/3-C79.5
8140/3-C79.9
8140/3-C80.1
8140/3-D05.0
8140/3-D05.1
8140/3-D49.0
8144/3-C18.0
8144/3-C18.4
8144/3-C19.9
8144/3-C21.0
8144/3-C25.9
8144/3-C78.7
8144/3-D06.9
8145/3-C22.1
8145/3-C50.9
8158/1-D13.7
8158/1-D37.2
8160/3-C22.8
8160/3-C25.9
8160/3-C78.7
8163/3-C18.9
8163/3-C25.0
8163/3-C25.9
8163/3-C78.0
8170/3-C22.8
8170/3-C22.9
8200/3-C80.1
8200/3-D49.0
8201/2-D05.1
8230/2-D05.1
8230/2-D05.9
8240/3-C54.1
8240/3-C7A.0
8240/3-C7A.1
8240/3-C7A.8
8240/3-D3A.0
8244/3-C78.7
8244/3-C7A.0
8244/3-D3A.0
8245/3-C15.9
8245/3-C33.9
8245/3-C54.1
8245/3-C55.9
8245/3-C61.9
8246/3-C09.9
8246/3-C31.2
8246/3-C78.7
8246/3-C7A.0
8246/3-C7A.1
8246/3-C7A.8
8246/3-C7B.8
8246/3-C80.1
8246/3-D05.1
8246/3-D3A.0
8246/3-D3A.8
8246/3-D49.0
8247/3-C4A.0
8247/3-C4A.3
8247/3-C4A.6
8247/3-C4A.7
8247/3-C4A.9
8247/3-C7A.8
8249/3-C7A.0
8249/3-C7A.8
8260/3-C64.1
8260/3-C64.2
8270/3-C64.1
8270/3-C68.9
8310/3-C56.1
8310/3-C56.2
8310/3-C64.1
8310/3-C64.2
8310/3-C78.0
8310/3-C79.5
8312/3-C07.9
8312/3-C64.1
8312/3-C64.2
8312/3-C68.9
8312/3-C79.8
8317/3-C64.2
8318/3-C64.1
8319/3-C64.1
8343/3-D05.1
8380/3-C56.1
8380/3-C56.2
8384/3-D06.9
8402/3-C18.9
8430/3-C50.9
8430/3-C80.1
8430/3-D49.0
8441/3-C56.1
8441/3-C56.2
8441/3-C78.6
8441/3-C80.0
8441/3-C80.1
8442/1-D39.1
8460/3-C56.2
8461/3-C80.1
8472/1-C78.6
8472/1-D39.1
8480/3-C56.2
8480/3-C77.2
8480/3-C78.0
8480/3-C79.5
8480/3-C80.1
8480/6-C78.6
8500/2-D05.0
8500/2-D05.1
8500/2-D05.8
8500/2-D05.9
8500/3-C77.2
8500/3-C77.3
8500/3-C78.7
8500/3-C79.2
8500/3-C79.5
8500/3-D05.1
8500/3-D05.9
8503/2-D05.8
8520/2-D05.0
8520/2-D05.9
8520/3-C77.3
8520/3-D05.0
8521/3-C79.5
8521/3-C80.1
8522/2-D05.1
8522/3-D05.1
8550/3-C80.1
8560/3-C80.1
8580/3-D49.8
8581/3-D49.8
8584/3-D49.8
8585/3-D49.8
8590/1-D39.1
8640/3-D29.2
8693/3-C85.8
8720/2-C43.9
8720/2-D03.3
8720/2-D03.4
8720/2-D03.6
8720/3-C43.3
8720/3-C43.4
8720/3-C43.5
8720/3-C43.6
8720/3-C43.7
8720/3-C43.9
8720/3-C77.9
8720/3-C78.7
8720/3-C79.9
8721/3-C43.3
8721/3-C43.4
8721/3-C43.6
8721/3-C43.9
8721/3-C77.9
8742/2-C43.3
8742/3-C43.5
8742/3-C43.9
8743/3-C43.2
8743/3-C43.4
8743/3-C43.5
8743/3-C43.6
8743/3-C43.7
8743/3-C43.9
8743/3-C73.9
8743/3-C79.9
8744/3-C43.6
8744/3-C43.7
8744/3-C43.9
8745/3-C43.3
8745/3-C43.4
8745/3-C43.6
8745/3-C43.9
8800/3-D49.2
8830/3-C79.8
8852/3-C79.8
8854/3-C25.9
8890/1-C49.9
8890/3-C79.8
8900/3-C64.2
8933/3-C61.9
8933/3-C77.5
8935/3-C49.9
8936/1-C49.A
8936/3-C49.A
8940/3-C34.9
8980/3-C49.9
8980/3-C56.2
9020/3-D48.6
9050/3-C45.9
9052/3-C45.0
9053/3-C45.0
9061/3-C80.1
9071/3-C56.2
9110/1-C55.9
9120/3-C22.3
9133/3-D48.9
9136/1-C79.8
9140/3-C46.0
9140/3-C46.9
9220/3-C49.9
9250/3-D48.0
9540/0-D49.2
9591/3-C82.9
9591/3-C85.1
9591/3-C91.1
9597/3-C82.6
9650/3-C81.1
9650/3-C81.7
9650/3-C81.9
9650/3-C85.9
9651/3-C81.9
9652/3-C81.2
9652/3-C81.9
9659/3-C81.0
9663/3-C81.1
9663/3-C81.4
9663/3-C81.7
9663/3-C81.9
9670/3-C82.0
9670/3-C85.8
9671/3-C83.0
9671/3-C88.0
9673/3-C83.1
9675/3-C85.9
9679/3-C85.2
9680/3-C81.9
9680/3-C83.3
9680/3-C85.1
9680/3-C85.2
9680/3-C85.8
9680/3-C85.9
9684/3-C83.3
9687/3-C83.7
9687/3-C85.1
9688/3-C83.3
9689/3-C85.9
9690/3-C82.0
9690/3-C82.8
9690/3-C85.1
9690/3-C85.8
9690/3-C85.9
9691/3-C82.0
9691/3-C82.1
9691/3-C82.8
9691/3-C82.9
9691/3-C83.0
9695/3-C82.0
9695/3-C82.5
9695/3-C82.9
9695/3-C85.9
9698/3-C82.3
9698/3-C82.4
9698/3-C82.9
9699/3-C83.0
9699/3-C85.1
9699/3-C85.8
9699/3-C85.9
9699/3-C88.4
9700/3-C84.0
9700/3-C84.1
9700/3-C84.A
9701/3-C84.0
9701/3-C84.1
9702/3-C84.4
9702/3-C85.9
9705/3-C84.9
9705/3-C85.9
9705/3-C86.5
9708/3-C84.4
9708/3-C86.3
9714/3-C85.9
9718/3-C86.6
9719/3-C86.0
9726/3-C84.A
9731/3-C90.0
9731/3-C90.2
9731/3-C90.3
9732/3-C90.0
9734/3-C90.3
9735/3-C83.3
9737/3-C84.6
9743/3-C41.9
9761/3-C85.8
9761/3-C88.0
9809/3-C91.0
9811/3-C91.0
9811/3-C91.1
9812/3-C91.0
9823/3-C91.1
9827/3-C91.5
9833/3-C91.1
9861/3-C92.0
9861/3-C93.0
9873/3-C92.0
9875/3-C92.1
9891/3-C92.0
9895/3-C92.0
9945/3-C92.1
9989/3-D46.9
NULL-C22.8
NULL-C22.9
NULL-C43.0
NULL-C43.1
NULL-C43.2
NULL-C43.3
NULL-C43.4
NULL-C43.5
NULL-C43.6
NULL-C43.7
NULL-C43.8
NULL-C43.9
NULL-C45.0
NULL-C45.1
NULL-C45.7
NULL-C45.9
NULL-C46.0
NULL-C46.9
NULL-C49.A
NULL-C4A.0
NULL-C4A.1
NULL-C4A.2
NULL-C4A.3
NULL-C4A.4
NULL-C4A.6
NULL-C4A.7
NULL-C4A.9
NULL-C56.1
NULL-C56.2
NULL-C64.1
NULL-C64.2
NULL-C65.1
NULL-C65.2
NULL-C66.1
NULL-C66.2
NULL-C78.0
NULL-C78.1
NULL-C78.4
NULL-C78.5
NULL-C78.6
NULL-C78.7
NULL-C78.8
NULL-C79.0
NULL-C79.1
NULL-C79.2
NULL-C79.3
NULL-C79.4
NULL-C79.5
NULL-C79.6
NULL-C79.7
NULL-C79.8
NULL-C79.9
NULL-C7A.0
NULL-C7A.1
NULL-C7A.8
NULL-C7B.0
NULL-C7B.1
NULL-C7B.8
NULL-C80.0
NULL-C80.1
NULL-C81.0
NULL-C81.1
NULL-C81.2
NULL-C81.4
NULL-C81.7
NULL-C81.9
NULL-C82.0
NULL-C82.1
NULL-C82.2
NULL-C82.3
NULL-C82.4
NULL-C82.5
NULL-C82.6
NULL-C82.8
NULL-C82.9
NULL-C83.0
NULL-C83.1
NULL-C83.3
NULL-C83.5
NULL-C83.7
NULL-C83.8
NULL-C83.9
NULL-C84.0
NULL-C84.1
NULL-C84.4
NULL-C84.6
NULL-C84.7
NULL-C84.9
NULL-C84.A
NULL-C84.Z
NULL-C85.1
NULL-C85.2
NULL-C85.8
NULL-C85.9
NULL-C86.0
NULL-C86.1
NULL-C86.2
NULL-C86.3
NULL-C86.5
NULL-C86.6
NULL-C88.0
NULL-C88.4
NULL-C90.0
NULL-C90.1
NULL-C90.2
NULL-C90.3
NULL-C91.0
NULL-C91.1
NULL-C91.4
NULL-C91.5
NULL-C91.6
NULL-C91.9
NULL-C91.Z
NULL-C92.0
NULL-C92.1
NULL-C92.4
NULL-C93.1
NULL-C95.1
NULL-C96.A
NULL-D00.0
NULL-D00.1
NULL-D01.0
NULL-D01.3
NULL-D02.0
NULL-D02.2
NULL-D02.3
NULL-D03.2
NULL-D03.3
NULL-D03.4
NULL-D03.5
NULL-D03.6
NULL-D03.7
NULL-D03.9
NULL-D04.3
NULL-D04.4
NULL-D04.9
NULL-D05.0
NULL-D05.1
NULL-D05.8
NULL-D05.9
NULL-D06.0
NULL-D06.1
NULL-D06.9
NULL-D07.1
NULL-D07.2
NULL-D07.4
NULL-D09.0
NULL-D09.9
NULL-D11.0
NULL-D11.9
NULL-D13.7
NULL-D16.5
NULL-D17.5
NULL-D24.1
NULL-D24.2
NULL-D27.0
NULL-D32.0
NULL-D32.9
NULL-D35.0
NULL-D36.9
NULL-D37.0
NULL-D37.2
NULL-D37.3
NULL-D37.6
NULL-D37.9
NULL-D39.0
NULL-D39.1
NULL-D39.2
NULL-D3A.0
NULL-D3A.8
NULL-D40.1
NULL-D41.0
NULL-D41.2
NULL-D41.4
NULL-D43.2
NULL-D44.4
NULL-D44.7
NULL-D46.1
NULL-D46.2
NULL-D46.9
NULL-D46.A
NULL-D46.Z
NULL-D47.2
NULL-D47.Z
NULL-D48.0
NULL-D48.1
NULL-D48.5
NULL-D48.6
NULL-D48.9
NULL-D49.0
NULL-D49.1
NULL-D49.2
NULL-D49.3
NULL-D49.4
NULL-D49.5
NULL-D49.6
NULL-D49.7
NULL-D49.8
NULL-D49.9
NULL-D64.8
NULL-D72.8


(JD Liddil) #2

These are combining two type of codes. C The 4/1 codes are morphology ICD-O-3. The Codes are ICD-10


(Tina Seto) #3

Yes, the concept_code is a concatenation of the morphology and ICD-10. The vocabulary is called ICDO3 in OMOP. There are 63k+ concepts. These 500 missing are mostly infrequently used. Some have been newly added in Oct 2020 to the 2021 ICD-10-CM edition. Hopefully we can get those added to the OMOP vocabulary too.

select *
from concept
where vocabulary_id=β€˜ICDO3’ and domain_id=β€˜Condition’;


(Eduard Korchmar (Terminologist @ Odysseus Vocabulary Team)) #4

Unfortunately, most of these codes are not viable for inclusion in ICDO3 Vocabulary.

From all 567 codes in the list:

  1. Topography codes starting with letter D are in situ and benign neoplasms, while only C codes are used in ICDO regardless of tumor behavior. All viable topographies are included in source list on IACR website, provided on the first sheet of this XLS document. (143)
  2. ICD10CM specific codes - ICDO only uses international version of ICD10 codes for topography (115)
  3. True ICD10 codes that are not used for topography identification in ICDO – due to them specifying particular morphology or tumor behavior (257)
  4. Finally, there are 50 codes that are valid from ICDO3 prospective and will be included this release
Full SQL friendly list

β€˜8246/3-C09.9’,β€˜8046/3-C61.9’,β€˜8120/3-C22.0’,β€˜8312/3-C07.9’,β€˜8980/3-C49.9’,β€˜8144/3-C18.0’,β€˜8145/3-C50.9’,β€˜8073/3-C77.9’,β€˜8854/3-C25.9’,β€˜8520/3-C77.3’,β€˜8098/3-C34.9’,β€˜8500/3-C77.2’,β€˜8090/3-C76.0’,β€˜8246/3-C31.2’,β€˜8240/3-C54.1’,β€˜8933/3-C77.5’,β€˜8076/2-C76.0’,β€˜8935/3-C49.9’,β€˜8720/3-C77.9’,β€˜8245/3-C61.9’,β€˜8144/3-C18.4’,β€˜8160/3-C25.9’,β€˜8402/3-C18.9’,β€˜8163/3-C25.0’,β€˜8071/3-C77.0’,β€˜8071/3-C49.0’,β€˜8721/3-C77.9’,β€˜8144/3-C25.9’,β€˜9220/3-C49.9’,β€˜8940/3-C34.9’,β€˜8480/3-C77.2’,β€˜8070/3-C77.3’,β€˜8245/3-C33.9’,β€˜8245/3-C15.9’,β€˜8890/1-C49.9’,β€˜8245/3-C54.1’,β€˜8312/3-C68.9’,β€˜8144/3-C21.0’,β€˜9110/1-C55.9’,β€˜8144/3-C19.9’,β€˜8430/3-C50.9’,β€˜8270/3-C68.9’,β€˜8163/3-C18.9’,β€˜8140/3-C77.2’,β€˜8245/3-C55.9’,β€˜8500/3-C77.3’,β€˜8933/3-C61.9’,β€˜8145/3-C22.1’,β€˜8163/3-C25.9’,β€˜8041/3-C04.9’

  1. This code is technically valid, too, but it encodes β€˜Low cumulative sun damage of Thyroid gland’. I don’t think it’s addition is needed :grin:
    β€˜8743/3-C73.9’

  2. Finally, this code does not correspond to existing histology concept for ICDO. If your data has text string attached to this code anywhere, we could add it manually, since google search can confirm it’s existence but not it’s meaning.
    β€˜9743/3-C41.9’

Topography codes from list items 1-3 can still be converted to ICDO3 using tables provided by SEER. Conversion tables may be outdated, but should most likely cover most of your use-cases. Also, codes having format like β€œNULL-C4A.9” are better treated as pure ICD10 or ICD10CM codes, since they have their own standard mappings: C4A.9 Merkel cell carcinoma, unspecified.


(Tina Seto) #5

Hi Eduard,

Thanks for looking into these missing codes.

Can we consider including the D codes in the vocabulary so that every institution wouldn’t need to map the D codes to ICDO C codes?

Should we revisit whether to use ICD10(CM) codes instead of ICDO if the source data is from the EMR and not the tumor registry? I haven’t seen ICDO codes in our EMR since our billing dept typically codes in ICD10CM.

For treating C4A.9 as pure ICD10(CM), I can do that. Does this mean condition_occurrence.condition_source_value can contain the ICDO histology+site OR ICD10(CM) for the OMOP Oncology implementation? Can the Oncology WG please confirm this?


(Eduard Korchmar (Terminologist @ Odysseus Vocabulary Team)) #6

I don’t think it is the best solution. These topography codes would exist as complete duplicates of already existing concepts that also break source vocabulary convention. However, we plan on including SEER crosswalks from ICD10(CM) codes to corresponding ICDO topography attribute next release. I agree that requiring each institution do this work seems wrong.

For cases where you have only the ICD10CM code with no explicitly stated histology, using ICD10CM concepts has benefits of not needing to use SEER tables and possibly losing precision when converting. ICD10CM in OMOP is updated regularly and is mapped to the same Standard concepts ICDO Conditions are.

In most cases the field that matters is condition_concept_id which points to a standard concept your source condition was mapped to. ICD10CM and ICDO concepts would probably end up mapped to the same Standard concept and end up included in the same concept sets. However, I don’t know if there are any tools specific to oncology extension that would care about the difference.


(JD Liddil) #7

So what was the original rational for this concatenation?


(Christian Reich) #8

To create cancer Condition Concepts that are more detailed than SNOMED (or ICD10).


(Georgie) #9

FYI we have been working on this for our MOSAIQ instance over the last little while, and would be keen to share / contribute as required. We did a SNOMED traversal from ICD10 conditions to get the morph/topog codes where possible. We have also incorporated an ICD10->ICDO3 topog mapping that is used in one of our official clinical registries.


(Dmytry Dymshyts) #10

@gkenno, sounds interesting,
Let me understand:

ICD10 -> SNOMED ->ICDO morph/topog
Right?

That’s nice. Please share. Have you used / compared your results with this table?
https://seer.cancer.gov/tools/conversion/ICD03toICD9CM-ICD10-ICD10CM.xls
it can be obtained from this resource:

In our projects we usually use this table to convert ICD10 to ICDO topography.


(shilpa) #11

@Dymshyts, @Eduard_Korchmar mentions in this chain above that β€œHowever, we plan on including SEER crosswalks from ICD10(CM) codes to corresponding ICDO topography attribute next release”. So I’m assuming you’ll make the mapping between ICD10(CM) and IDCO available in the Vocabulary. Can the same be done for ICD10(AM)? In this case Georgina is referring to ICD10(AM) where AM is Australian standard for medical coding.


(Dmytry Dymshyts) #12

Probably we need to start from the ingestion of ICD10-AM to OMOP first, and then we can make the crosswalks needed.

Yeah, that’s a good plan. More and more use cases where this is needed arise.
And once we have this you can walk from ICD10AM to ICD10CM (even if we don’t have the ICD10AM in OMOP) by code similarity and then to ICDO.


(Eduard Korchmar (Terminologist @ Odysseus Vocabulary Team)) #13

SEER tables have not been updated since 2014 and ICDO received significant updates since then. If ICD10(AM) conversion table is frequently updated, maybe we should consider includong this as base instead?


(Dmytry Dymshyts) #14

Well, the ICDO topography wasn’t updated for a while as well, so 2014 year file will work here. But the histology part (much lesser) should be reviewed as the ICDO hisology is updated frequently
And of course let’s see what @gkenno has


(shilpa) #15

@Dymshyts and @Eduard_Korchmar Are you waiting on @gkenno to provide their
ICD10 ->ICDO3 topography mapping before you can include it in the official Vocabulary release? What are the next steps to resolve the initial issues that @tseto raised and also for @gkenno?


(Eduard Korchmar (Terminologist @ Odysseus Vocabulary Team)) #16

We are expecting an answer from @gkenno to decide the best way to proceed. I would be very reluctant to use outdated SEER tables if ICD10AM crosswalks are maintained and available, given that we would have to do our own updates and our ICDO3 instance has much manual work in updating manual mappings.


(Georgie) #17

Apologies somehow I missed this notification.

ICD10 -> SNOMED ->ICDO morph/topog

Yes - that’s right. Here is an example (most of our D codes are haematology-related)

Original ICD10 code: D45 (Polycythaemia vera)

  • Maps To SNOMED: Polycythemia vera (clinical)
    • Has finding site: Bone marrow structure
      • Maps to ICDO3 topog: C42.1 (bone marrow)
    • Has associated morphology: Polycythemia vera
      • Maps to ICDO3 hist: 9950/1Polycythemia vera,uncertain behaviour
      • Maps to ICDO3 hist: 9950/3 Polycythemia vera

9950/3-C42.1 is valid and 9950/1-C42.1 is not, so propose 9950/3-C42.1 as the mapping

That’s nice. Please share. Have you used / compared your results with this table?

I will make that comparison now and report back. I should also check that this file is approved for sharing.


(Georgie) #18

It was easier to find an answer to this than I expected, due to the winding up of some local clinical registry programs - this conversion was based on a function that is now defunct and therefore will not be maintained.

Our clinical coding team are currently validating the subset of cross-walked codes, which we should be able to contribute upon completion, although they only represent the subset of codes that appear in our source data.

(updating with answer)


t