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ICD10PCS procedure codes from inpatient admissions and facility headers are being dropped

Implementers
,
#1

The ICD10PCS procedure codes from inpatient admissions are not added to the TEMP_INPATIENT_ADMISSIONS table because per OHDSI Truevn CCAE MDCR mapping specification, page 18:

  • For the procedure codes use the query in section 3.1.2 with the
    filters: WHERE SOURCE_VOCABULARY_ID IN (‘ICD9Proc’,‘HCPCS’,‘CPT4’)
    AND TARGET_STANDARD_CONCEPT IS NOT NULL AND TARGET_INVALID_REASON IS
    NULL AND TARGET_CONCEPT_CLASS_ID NOT IN (‘HCPCS Modifier’,‘CPT4
    Modifier’)

This should be due to the inpatient admission not having the PROCTYP field. So, the mapping spec is only getting the (‘ICD9Proc’,‘HCPCS’,‘CPT4’) procedure codes from inpatient admissions, and all the inpatient admission ICD10PCS procedure codes are being dropped. The same happens to the facility header ICD10PCS procedure codes.

Shouldn’t we include the ICD10PCS vocabulary in the WHERE clause of the “filter” references on pages 18, 29 and 31 (WHERE SOURCE_VOCABULARY_ID IN (‘ICD9Proc’,‘HCPCS’,‘CPT4’,‘ICD10PCS’))?

Thanks.

#2

@marziGolbaz:

Looks like you are talking about some ETL specs, but which one? One of these?

#3

@Christian_Reich Oh. Sorry. I’m referring to the Truven CCAE and MDCR mapping specification.

#4

Yes, ICD10PCS should definitely be added. You can either fix it (it’s Open Source co-development), or ask @ericaVoss or @clairblacketer to do it.

#5

I am Amit Kumar, a CDISC SDTM Mapping Specialist working in Cytel India. Right now I have got one OMOP CDM Project for ETL creation for an observational study.

We are generating DRUG_EXPOSURE Table in which I have some doubts ,

  1. Should we collect all Drug Exposure data captured in raw data like Prior Medication, Study Medication ??
  2. Most of Medication History data does not captures date what can we about that.?
    3.What are refill? can we keep them blank?
  3. How to generate drug_exposure_id ?

Kindly guide me as our team is doing it for first time

#6

@Christian_Reich Thank you.
@ericaVoss @clairblacketer Would you please add the ICD10PCS to the WHERE clause of the filter references on pages 18, 29 and 31 (WHERE SOURCE_VOCABULARY_ID IN (‘ICD9Proc’,‘HCPCS’,‘CPT4’,‘ICD10PCS’))? Thanks.

#7

Hi Marzi,

Thank you for catching that; our ETL spec was a little outdated as you rightly pointed out. I have uploaded new files on github for Truven CCAE/MDCR here and for Truven MDCD here to reflect not only this issue but the CDM v5.0.1 changes as well. The test cases are still out of date but as I finish those up I will put the new ones out on github as well.

Clair

Tagging @ericaVoss

#8

Hi Clair - Thank you for uploading the new files onto the GitHub. But, I’m still not seeing any changes to the filter references where the procedure code comes from TEMP_INPATIENT_ADMISSIONS or
TEMP_FACILITY_HEADER. I believe it should be updated to: WHERE SOURCE_VOCABULARY_ID IN (‘ICD9Proc’,‘ICD10PCS’,‘HCPCS’,‘CPT4’,‘ICD10PCS’). Thanks.

#9

@marziGolbaz - you are right we have to think about implementing this.

The Truven documentation seems to suggest we would only find these ICD10PCS codes in FACILITY_HEADER - PROC1-PROC6. Would you still expect to see them on INPATIENT_ADMISSIONS? I’m reaching out to Truven to double check. This might suggest when mapping from FACILITY_HEADER we should only use:
('ICD9Proc','ICD10PCS')

Truven User Guide:
Up to six procedure codes (PROC1 through PROC6) are included on each Facility Header record. Most procedure codes on the Facility Header Table use the ICD-9-CM or ICD-10-PCS procedure coding systems.

Also, it isn’t as simple as adding it to the lookup because there is cross over between some of these Vocabularies. Example of cross over in codes:
SOURCE_CODE-CONCEPT_ID-SOURCE_VOCABULARY_ID-SOURCE_DESCRIPTIONS
00160-2801517-ICD10PCS-Medical and Surgical @ Central Nervous System @ Bypass @ Cerebral Ventricle @ Open
00160-2100676-CPT4-Anesthesia for procedures on nose and accessory sinuses; not otherwise specified

I think for the other places where we can find procedures, I’m assuming we will need to check ICD10PCS for them however we’ll need to use PROCTYP to be careful which Vocab mapping we want. When I look at PROCTYP it doesn’t even look like there is a code for ICD10PCS - even if I just assume 0-ICD-10-CM is for ICD10PCS I don’t see it used either in the INPATIENT_SERVICES or OUTPATIENT_SERVICES.

Long story short - we need to talk to Truven to know the best way to do this. I did review the impact of this issue and depending on how I look at it I still think it is <1% of the records.

#10

@ericaVoss Thank you for your detailed response. I did a quick research on INPATIENT_ADMISSIONS and FACILITY_HEADER procedure codes in our Truven dataset and saw some valid ICD9Proc, ICD10PCS, HCPCS and CPT4 codes. So, I think we should use (‘ICD9Proc’,‘ICD10PCS’,‘HCPCS’,‘CPT4’,‘ICD10PCS’) when mapping from INPATIENT_ADMISSIONS and FACILITY_HEADER.

After we added the ‘ICD10PCS’ to the lookups, we faced the cross over issue. Here is the @sblyman 's comment:
That ‘00160’ code and others like that in ICD10PCS are actually not considered as real source codes, but are part of the ICD10PCS hierarchy grouping concepts. Actual ICD10PCS codes are formatted with 7 characters. I think we need to update the concept query filters to include the TARGET_CONCEPT_CLASS_ID NOT IN (‘ICD10PCS Hierarchy’). We should also filter out the CPT4 Hierarchy concepts. I would recommend updating the filters as listed on pages 18, 28, 30 and 57 of the CCAE/MDCR spec to change from:
AND TARGET_CONCEPT_CLASS_ID NOT IN (‘HCPCS Modifier’,‘CPT4 Modifier’)
to
AND TARGET_CONCEPT_CLASS_ID NOT IN (‘HCPCS Modifier’,‘CPT4 Modifier’, ‘CPT4 Hierarchy’, ‘ICD10PCS Hierarchy’)
This would also apply to the MDCD spec - wherever the filters are listed.

Thanks.

#11

I just heard back from Truven:

  • FACILITY_HEADER should only be ICD9/ICD10. It is the case they other codes could find their way in there but they do not expect much of that. We will update our mapping for FACILITY_HEADER to be ('ICD9Proc','ICD10PCS')
  • INPATIENT_SERVICES should be CPT/Revenue Codes
  • OUTPATIENT_SERVICES should be CPT/HCPCs

I am following up with Truven if INPATIENT_ADMISSIONS is only ICD9/ICD10 or can be a mix. They mentioned that INPATIENT_ADMISSIONS source some of their information from FACILITY_HEADER so this would mean definitely ICD9/ICD10 but I don’t know about CPT/HCPCs).

Thanks for your comment on the way to think about the cross over issue - we’ll apply this when we fix this in our CDM_BUILDER.

#12

Truven came back:

  • INPATIENT_ADMISSIONS - we can expect a mix a codes.

We’ll update this in a future CDM_BUILDER. I’m not expecting that this would cause a massive issue in terms of the builds we have now but it would be appropriate to put this fix in.

Thank you @marziGolbaz for highlighting this to us!

#13

Thank you @ericaVoss for the quick follow up with Truven. Looking forward to hearing more about the OHDSI’s resolution to this issue.

#14

Following up on this post. @marziGolbaz the Truven CCAE/MDCR and MDCD documents with these changes are now available on github.

#15

Thank you @clairblacketer

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