Query Verification: Peanut Allergy Cohort

[callahantiff]

@mgkahn - Can you please help me verify the query to select Peanut Allergy patients?

---

COHORT CRITERIA Case Criteria:
CASE TYPE 1

• all_case_inclusion_criteria_1: Presence of ANY mention of "peanut" (condition strings; drug strings; measurement strings; observation strings; procedure strings - criteria # 1)
• mx_case_inclusion_criteria_1: Presence of quantitative immunoassay testing performed (RAST) (measurement strings - criteria # 2)
• px_inclusion_criteria_1: Presence of Allergen specific IgE, quantitative (CPT codes - criteria # 3)

CASE TYPE 2

• all_case_inclusion_criteria_1: Presence of ANY mention of "peanut" (condition strings; drug strings; measurement strings; observation strings; procedure strings - criteria # 1)
• Presence of at least 1 of the various allergy testing procedures:
  • px_inclusion_criteria_2: Percutaneous (scratch, prick, or puncture test) (CPT codes - criteria # 4)
  • px_inclusion_criteria_3: Intracutaneous or intradermal test (CPT codes - criteria # 5)
  • px_inclusion_criteria_4: Food ingestion challenge (CPT codes - criteria # 6)

Control Criteria:

• No control group defined

---

Cohort Logic Table

COHORT	CHUNK	LOGICAL OPERATOR
CASE TYPE 1	all_case_inclusion_criteria_1	AND
CASE TYPE 1	mx_case_inclusion_criteria_1	OR
CASE TYPE 1	px_inclusion_criteria_1	---
CASE TYPE 2	all_case_inclusion_criteria_1	AND
CASE TYPE 2	px_inclusion_criteria_2	OR
CASE TYPE 2	px_inclusion_criteria_3	OR
CASE TYPE 2	px_inclusion_criteria_4	---

---

NOTE.

1. Replace all instances of {database} with CHCO_DeID_Oct2018
2. Comment out all instances of {code_set_group}

Query can be found here and is also included below:

WITH all_case_inclusion_criteria_1 AS (
SELECT person_id, {code_set_group} AS code_set FROM
(SELECT co.person_id
FROM 
  {database}.condition_occurrence co, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 
  co.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT co.condition_concept_id) >= 1
UNION DISTINCT
SELECT de.person_id
FROM 
  {database}.drug_exposure de, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  de.drug_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 
  de.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT de.drug_concept_id) >= 1
UNION DISTINCT
SELECT m.person_id
FROM 
  {database}.measurement m, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  m.measurement_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 
  m.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT m.measurement_concept_id) >= 1
UNION DISTINCT
SELECT o.person_id
FROM 
  {database}.observation o, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  o.observation_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 
  o.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT o.observation_concept_id) >= 1
UNION DISTINCT
SELECT pr.person_id
FROM 
  {database}.procedure_occurrence pr, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  pr.procedure_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}
GROUP BY 
  pr.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT pr.procedure_concept_id) >= 1
)),

mx_case_inclusion_criteria_1 AS (
SELECT m.person_id, cohort.standard_code_set AS code_set
FROM 
  {database}.measurement m,
  {database}.PEANUTALLERGY_COHORT_VARS cohort
WHERE 
  m.measurement_concept_id = CAST(cohort.standard_concept_id AS int64)
  AND cohort.phenotype_definition_number = 2
  AND cohort.standard_code_set = {code_set_group}
GROUP BY m.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT m.measurement_concept_id) >= 1
),

px_case_inclusion_criteria_1 AS (
SELECT pr.person_id, cohort.standard_code_set AS code_set
FROM 
  {database}.procedure_occurrence pr,
  {database}.PEANUTALLERGY_COHORT_VARS cohort
WHERE 
  pr.procedure_concept_id = CAST(cohort.standard_concept_id AS int64)
  AND cohort.phenotype_definition_number = 3
  AND cohort.standard_code_set = {code_set_group}
GROUP BY pr.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT pr.procedure_concept_id) >= 1
),

px_case_inclusion_criteria_2 AS (
SELECT pr.person_id, cohort.standard_code_set AS code_set
FROM 
  {database}.procedure_occurrence pr,
  {database}.PEANUTALLERGY_COHORT_VARS cohort
WHERE 
  pr.procedure_concept_id = CAST(cohort.standard_concept_id AS int64)
  AND cohort.phenotype_definition_number = 4
  AND cohort.standard_code_set = {code_set_group}
GROUP BY pr.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT pr.procedure_concept_id) >= 1
),

px_case_inclusion_criteria_3 AS (
SELECT pr.person_id, cohort.standard_code_set AS code_set
FROM 
  {database}.procedure_occurrence pr,
  {database}.PEANUTALLERGY_COHORT_VARS cohort
WHERE 
  pr.procedure_concept_id = CAST(cohort.standard_concept_id AS int64)
  AND cohort.phenotype_definition_number = 5
  AND cohort.standard_code_set = {code_set_group}
GROUP BY pr.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT pr.procedure_concept_id) >= 1
),

px_case_inclusion_criteria_4 AS (
SELECT pr.person_id, cohort.standard_code_set AS code_set
FROM 
  {database}.procedure_occurrence pr,
  {database}.PEANUTALLERGY_COHORT_VARS cohort
WHERE 
  pr.procedure_concept_id = CAST(cohort.standard_concept_id AS int64)
  AND cohort.phenotype_definition_number = 6
  AND cohort.standard_code_set = {code_set_group}
GROUP BY pr.person_id, cohort.standard_code_set
HAVING 
  COUNT(DISTINCT pr.procedure_concept_id) >= 1
)

SELECT * FROM
  (SELECT person_id, code_set, 'PEANUTALLERGY_CASE_TYPE1' AS cohort_type
    FROM (
    SELECT person_id, code_set FROM all_case_inclusion_criteria_1
      INTERSECT DISTINCT 
     (SELECT person_id, code_set FROM mx_case_inclusion_criteria_1
      UNION DISTINCT
      SELECT person_id, code_set FROM px_case_inclusion_criteria_1)
   GROUP BY person_id, code_set, cohort_type))

  UNION ALL

  (SELECT person_id, code_set, 'PEANUTALLERGY_CASE_TYPE2' AS cohort_type
    FROM (
     SELECT person_id, code_set FROM all_case_inclusion_criteria_1
      INTERSECT DISTINCT 
    (SELECT person_id, code_set FROM px_case_inclusion_criteria_2
      UNION DISTINCT
     SELECT person_id, code_set FROM px_case_inclusion_criteria_3
      UNION DISTINCT
     SELECT person_id, code_set FROM px_case_inclusion_criteria_4))
   GROUP BY person_id, code_set, cohort_type)
;

[mgkahn]

CPT codes: Just as an aside -- data from the hospitals will have spotty coverage of CPT codes, which are much more complete in CU Medicine. So the presence of the allergy testing CPT codes in UCHealth data may be very small if any. Not because it wasn't done but because it is captured in professional billing, not hospital billing

[mgkahn]

No additional comments on peanut allergy other than above.

[callahantiff]

CPT codes: Just as an aside -- data from the hospitals will have spotty coverage of CPT codes, which are much more complete in CU Medicine. So the presence of the allergy testing CPT codes in UCHealth data may be very small if any. Not because it wasn't done but because it is captured in professional billing, not hospital billing

Interesting! Would this be the same case for CHCO and MIMIC? We are not currently using UCHealth data for this project (although I'd love to)!

[mgkahn]

Same for CHCO although in the past CHCO did do some physician CPT coding. But I think that's been taken over completely by CU Medicine now. I don't know about MIMIC. You would need to rummage around in their data dictionary.

[callahantiff]

Great, it sounds like we can close this issues and wrap this up. Please re-open if you disagree or think that there is more to be done.

[mgkahn]

Can this be re-opened? I do not think the inclusion criterial logic is correct unless there is some missing English. Does CASE TYPE 1 require that a patient meet all three inclusion criteria? CASE TYPE 2 clearly has an "OR" for criteria 2, 3, & 4 but it isn't clear from the English if all three criteria for CASE TYPE 1 must be met. If so, then need to change logic.

[callahantiff]

Can this be re-opened? I do not think the inclusion criterial logic is correct unless there is some missing English. Does CASE TYPE 1 require that a patient meet all three inclusion criteria? CASE TYPE 2 clearly has an "OR" for criteria 2, 3, & 4 but it isn't clear from the English if all three criteria for CASE TYPE 1 must be met. If so, then need to change logic.

Fine to re-open, but I feel confident that we have this correct. Here is the original criteria that was provided:

Do you not agree that this is what I have represented with the logic above?

[mgkahn]

I’d rewrite the criteria to use indented bullets for the OR to make it clear like it is for Definition 2. Else you have been using ANDs between inclusion criteria bullets in your other definitions.

---

From: Tiffany J. Callahan notifications@github.com Sent: Sunday, August 11, 2019 12:19:58 PM To: callahantiff/PheKnowVec PheKnowVec@noreply.github.com Cc: Kahn, Michael MICHAEL.KAHN@CUANSCHUTZ.EDU; State change state_change@noreply.github.com Subject: Re: [callahantiff/PheKnowVec] Query Verification: Peanut Allergy Cohort (#104)

Can this be re-opened? I do not think the inclusion criterial logic is correct unless there is some missing English. Does CASE TYPE 1 require that a patient meet all three inclusion criteria? CASE TYPE 2 clearly has an "OR" for criteria 2, 3, & 4 but it isn't clear from the English if all three criteria for CASE TYPE 1 must be met. If so, then need to change logic.

Fine to re-open, but I feel confident that we have this correct. Here is the original criteria that was provided:

[Screen Shot 2019-08-11 at 12 17 00]https://user-images.githubusercontent.com/8030363/62837901-43007180-bc32-11e9-97ae-d0009aed86b9.png

Do you not agree that this is what I have represented with the logic above?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/callahantiff/PheKnowVec/issues/104?email_source=notifications&email_token=AA557TSDW5MONSKMSFQ4DLTQEBJ45A5CNFSM4IF3NOCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4BF7RY#issuecomment-520249287, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AA557TQ4B6X4NEEFAMJU2NLQEBJ45ANCNFSM4IF3NOCA.

[callahantiff]

I’d rewrite the criteria to use indented bullets for the OR to make it clear like it is for Definition 2. Else you have been using ANDs between inclusion criteria bullets in your other definitions.

I see, but that gets kind of confusing too (I had initially tried to apply something like this). Do you not think that the table is helpful?

Cohort Logic Table

COHORT	CHUNK	LOGICAL OPERATOR
CASE TYPE 1	all_case_inclusion_criteria_1	AND
CASE TYPE 1	mx_case_inclusion_criteria_1	OR
CASE TYPE 1	px_inclusion_criteria_1	---
CASE TYPE 2	all_case_inclusion_criteria_1	AND
CASE TYPE 2	px_inclusion_criteria_2	OR
CASE TYPE 2	px_inclusion_criteria_3	OR
CASE TYPE 2	px_inclusion_criteria_4	---

---

Case Criteria:
CASE TYPE 1

• all_case_inclusion_criteria_1: Presence of ANY mention of "peanut" (condition strings; drug strings; measurement strings; observation strings; procedure strings - criteria # 1)
• mx_case_inclusion_criteria_1: Presence of quantitative immunoassay testing performed (RAST) (measurement strings - criteria # 2)
• px_inclusion_criteria_1: Presence of Allergen specific IgE, quantitative (CPT codes - criteria # 3)

CASE TYPE 2

• all_case_inclusion_criteria_1: Presence of ANY mention of "peanut" (condition strings; drug strings; measurement strings; observation strings; procedure strings - criteria # 1)
• Presence of at least 1 of the various allergy testing procedures:
  • px_inclusion_criteria_2: Percutaneous (scratch, prick, or puncture test) (CPT codes - criteria # 4)
  • px_inclusion_criteria_3: Intracutaneous or intradermal test (CPT codes - criteria # 5)
  • px_inclusion_criteria_4: Food ingestion challenge (CPT codes - criteria # 6)

---

I could also add mathematical notation:

CASE_TYPE1 = all_case_inclusion_criteria_1 ∩ (mx_case_inclusion_criteria_1 ∪ px_inclusion_criteria_1)

CASE_TYPE2 = all_case_inclusion_criteria_1 ∩ (px_inclusion_criteria_2 ∪ px_inclusion_criteria_3 ∪ px_inclusion_criteria_4)

[callahantiff]

TODO FOR ME:

• [ ] Note to update the logic table here to make it clear where you are using OR with exclusion criteria! No need to re-check all of the other phenotypes.
  • Here the query is right, but the truth table needs to be fixed!
• [ ] Update criteria language for CASE TYPE 1 to match the style used for CASE TYPE 2 so that it is clear what is AND and what is OR.
• [x] Update the query on the wiki and in the GIST