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OHDSI / OncologyWG

Oncology Working Group Repository
https://ohdsi.github.io/OncologyWG
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Task Group: Disease Progression #469

Open rtmill opened 1 year ago

rtmill commented 1 year ago

Problem Space

Create discrete set of standard concepts to encapsulate disease "status" observations over time. Likely the majority of these observations will come from notes and consequentially be curated or NLP derived.

One difficulty here will be when the determination of trajectory are not clear, specifically when there are contradictory observations, e.g. one tumor improved at the same time as another worsened.

Proposed Solutions

Some suggested concept sets: 1) DFCI (custom note extraction value set)

ID Value
1 Improving/Responding
2 Stable/No change
3 Mixed
4 Progressing/Worsening/Enlarging
5 Not stated/Indeterminate

2) LOINC 97509-4 "Cancer disease progression"

CONCEPT_NAME CONCEPT_CODE VOCABULARY
Improved 45883920 LOINC
No edvidence of disease 1620321 LOINC
Stable 45879403 LOINC
Undetermined 45880649 LOINC
Worsened 1620411 LOINC

3) mCode 'Condition Status Trend Value Set' http://hl7.org/fhir/us/mcode/ValueSet-mcode-condition-status-trend-vs.html

Code System Display
268910001 http://snomed.info/sct Patient's condition improved (finding)
359746009 http://snomed.info/sct Patient's condition stable (finding)
271299001 http://snomed.info/sct Patient's condition worsened (finding)
709137006 http://snomed.info/sct Patient condition undetermined (finding)
USCRS-352236 http://hl7.org/fhir/us/mcode/CodeSystem/snomed-requested-cs Cancer in complete remission(finding)
USCRS-352237 http://hl7.org/fhir/us/mcode/CodeSystem/snomed-requested-cs Cancer in partial remission (finding)

Tasks

RKWPNW commented 1 year ago

In our EMR (EPIC) we have a reason for discontinuation as a discrete data element with disease status being one of the LOVs. When converting to OMOP, we'd want to maintain that discontinuing reason (when =progression, remission, regression) and date, mapped to OMOP standards.

cgreich commented 1 year ago

Any reason we wouldn't make a set of concepts that are exact carbon copies of the Episodes? Because if we don't we are back in the world where things are not compatible.

gkennos commented 1 year ago

In the Australian context at least, the use of 'remission' (either full or partial) is typically avoided, with preference for the more precise 'no evidence of disease' or 'complete response' concepts.

With this in mind, it is our view that the LOINC terminology aligns most closely with common clinical terminology, which is based on RECIST criteria i.e 

(ETA - the exception to this may be for haematological malignancies)

cgreich commented 1 year ago

Hm. Apart from the wording I don't see a difference. We can always change the wording if the meaning stays the same. Is that it?

gkennos commented 1 year ago

Oh no the LOINC one is fine as-is - I was just demonstrating that it aligns conceptually with what we use - the preference that I was referring to is just for that set rather than the other options (DFCI / mCode)

rtmill commented 1 year ago

Response / progression concept sets that currently exist in Cancer Modifier... Lots of duplication

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Code Set | concept_id | concept_code | concept_name | Class | standard_concept |   | Domain | Vocabulary -- | -- | -- | -- | -- | -- | -- | -- | -- CHOI | 1633884 | CHOI-CR | CHOI: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier CHOI | 1633939 | CHOI-PR | CHOI: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier CHOI | 1634959 | CHOI-PD | CHOI: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier CHOI | 1633706 | CHOI-SD | CHOI: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier iRECIST | 1633954 | iRECIST-CR | iRECIST: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier iRECIST | 1635284 | iRECIST-PR | iRECIST: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier iRECIST | 1633423 | iRECIST-PD | iRECIST: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier iRECIST | 1635887 | iRECIST-SD | iRECIST: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier irRECIST | 1635393 | irRECIST-CR | irRECIST: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier irRECIST | 1634425 | irRECIST-PR | irRECIST: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier irRECIST | 1633405 | irRECIST-PD | irRECIST: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier irRECIST | 1634976 | irRECIST-SD | irRECIST: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier PERCIST | 1633705 | PERCIST-CR | PERCIST: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier PERCIST | 1634681 | PERCIST-PR | PERCIST: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier PERCIST | 1634248 | PERCIST-PD | PERCIST: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier PERCIST | 1634497 | PERCIST-SD | PERCIST: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST-1.1 | 1634772 | 1.1_RECIST-CR | RECIST 1.1: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST-1.1 | 1633368 | 1.1_RECIST-PR | RECIST 1.1: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST-1.1 | 1633597 | 1.1_RECIST-PD | RECIST 1.1: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST-1.1 | 1634680 | 1.1_RECIST-SD | RECIST 1.1: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST | 1635108 | RECIST-CR | RECIST: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST | 1633979 | RECIST-PR | RECIST: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST | 1634326 | RECIST-PD | RECIST: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RECIST | 1635340 | RECIST-SD | RECIST: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier   |   |   |   |   |   |   |   |   Mandard TRG (tumor regression grading) system | 1635233 | Mandard-TRG-1 | Mandard Tumor Response Grade 1 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Mandard TRG (tumor regression grading) system | 1633575 | Mandard-TRG-2 | Mandard Tumor Response Grade 2 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Mandard TRG (tumor regression grading) system | 1635718 | Mandard-TRG-3 | Mandard Tumor Response Grade 3 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Mandard TRG (tumor regression grading) system | 1633587 | Mandard-TRG-4 | Mandard Tumor Response Grade 4 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Mandard TRG (tumor regression grading) system | 1635376 | Mandard-TRG-5 | Mandard Tumor Response Grade 5 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Modified TRG | 1634067 | mTRG-1 | Modified Tumor Response Grade 1 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Modified TRG | 1633802 | mTRG-2 | Modified Tumor Response Grade 2 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Modified TRG | 1635198 | mTRG-3 | Modified Tumor Response Grade 3 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Modified TRG | 1635162 | mTRG-4 | Modified Tumor Response Grade 4 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier Modified TRG | 1633514 | mTRG-5 | Modified Tumor Response Grade 5 | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RANO | 1634853 | RANO-CR | RANO: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RANO | 1634574 | RANO-PR | RANO: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RANO | 1634653 | RANO-PD | RANO: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier RANO | 1633447 | RANO-SD | RANO: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier WHO | 1634174 | WHO-CR | WHO response criteria: complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier WHO | 1633388 | WHO-PR | WHO response criteria: partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier WHO | 1635650 | WHO-PD | WHO response criteria: progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier WHO | 1633992 | WHO-SD | WHO response criteria: stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1633488 | MRD | Minimal residual disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1635161 | MR | Minimal response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1633904 | OR | Objective response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1635152 | PR | Partial response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1634884 | pCR | Pathological complete response | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1633294 | PD | Progressive disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1634643 | R0 | R0: No residual tumor | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1633801 | R1 | R1: Microscopic residual tumor | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1634484 | R2 | R2: Macroscopic residual tumor | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1635506 | SD | Stable disease | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1633501 | PsP | Tumor pseudoprogression | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier (Cancer Modifier custom) | 1634539 | Transformation | Tumor transformation | Staging/Grading | Standard | Valid | Measurement | Cancer Modifier
jam560 commented 1 year ago

Agree that the LOINC list is good. DFCI list was only contributed as a real world example, but LOINC covers all of its concepts (and the DFCI list is missing NED!).

rtmill commented 10 months ago

Proposal for disease status: the newest version of mCode

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Condition Status Trend Value Set | SNOMED CT |   | 103337004 | In partial remission (qualifier value) -- | -- | -- | -- | -- Condition Status Trend Value Set | SNOMED CT |   | 103338009 | In full remission (qualifier value) Condition Status Trend Value Set | SNOMED CT |   | 268910001 | Patient's condition improved (finding) Condition Status Trend Value Set | SNOMED CT |   | 271299001 | Patient's condition worsened (finding) Condition Status Trend Value Set | SNOMED CT |   | 359746009 | Patient's condition stable (finding) Condition Status Trend Value Set | SNOMED CT |   | 399409002 | Distant metastasis present (finding) Condition Status Trend Value Set | SNOMED CT |   | 709137006 | Patient condition undetermined (finding)