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fix(mimic-iv): update Charlson ICD-10-CM codes for C4A, C7A, and C7B #2043

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fix(mimic-iv): update Charlson ICD-10-CM codes for C4A, C7A, and C7B #2043

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42 changes: 25 additions & 17 deletions mimic-iv/concepts/comorbidity/charlson.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -285,6 +285,9 @@ WITH diag AS (

-- Any malignancy, including lymphoma and leukemia,
-- except malignant neoplasm of skin.
-- ICD-10-CM codes added after Quan et al. (2005):
-- C4A (Merkel cell carcinoma) excluded as skin malignancy per Quan.
-- C7A (malignant neuroendocrine tumors) included as primary malignancy.
, MAX(CASE WHEN
SUBSTR(icd9_code, 1, 3) BETWEEN '140' AND '172'
OR
Expand All @@ -293,22 +296,26 @@ WITH diag AS (
SUBSTR(icd9_code, 1, 3) BETWEEN '200' AND '208'
OR
SUBSTR(icd9_code, 1, 4) = '2386'
OR
SUBSTR(icd10_code, 1, 3) IN ('C43', 'C88')
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C00' AND 'C26'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C30' AND 'C34'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C81' AND 'C85'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C90' AND 'C97'
OR (
SUBSTR(icd10_code, 1, 3) IN ('C43', 'C88')
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C00' AND 'C26'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C30' AND 'C34'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C81' AND 'C85'
OR
SUBSTR(icd10_code, 1, 3) BETWEEN 'C90' AND 'C97'
OR
SUBSTR(icd10_code, 1, 3) = 'C7A'
)
AND SUBSTR(icd10_code, 1, 3) IS DISTINCT FROM 'C4A'
THEN 1
ELSE 0 END) AS malignant_cancer

Expand All @@ -326,10 +333,11 @@ WITH diag AS (
ELSE 0 END) AS severe_liver_disease

-- Metastatic solid tumor
-- ICD-10-CM C7B (secondary neuroendocrine tumors) added after Quan et al. (2005).
, MAX(CASE WHEN
SUBSTR(icd9_code, 1, 3) IN ('196', '197', '198', '199')
OR
SUBSTR(icd10_code, 1, 3) IN ('C77', 'C78', 'C79', 'C80')
SUBSTR(icd10_code, 1, 3) IN ('C77', 'C78', 'C79', 'C80', 'C7B')
THEN 1
ELSE 0 END) AS metastatic_solid_tumor

Expand Down
22 changes: 13 additions & 9 deletions mimic-iv/concepts_duckdb/comorbidity/charlson.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -271,14 +271,18 @@ WITH diag AS (
OR SUBSTRING(icd9_code, 1, 4) BETWEEN '1740' AND '1958'
OR SUBSTRING(icd9_code, 1, 3) BETWEEN '200' AND '208'
OR SUBSTRING(icd9_code, 1, 4) = '2386'
OR SUBSTRING(icd10_code, 1, 3) IN ('C43', 'C88')
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C00' AND 'C26'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C30' AND 'C34'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C81' AND 'C85'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C90' AND 'C97'
OR (
SUBSTRING(icd10_code, 1, 3) IN ('C43', 'C88')
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C00' AND 'C26'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C30' AND 'C34'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C37' AND 'C41'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C45' AND 'C58'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C60' AND 'C76'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C81' AND 'C85'
OR SUBSTRING(icd10_code, 1, 3) BETWEEN 'C90' AND 'C97'
OR SUBSTRING(icd10_code, 1, 3) = 'C7A'
)
AND SUBSTRING(icd10_code, 1, 3) IS DISTINCT FROM 'C4A'
THEN 1
ELSE 0
END
Expand Down Expand Up @@ -307,7 +311,7 @@ WITH diag AS (
MAX(
CASE
WHEN SUBSTRING(icd9_code, 1, 3) IN ('196', '197', '198', '199')
OR SUBSTRING(icd10_code, 1, 3) IN ('C77', 'C78', 'C79', 'C80')
OR SUBSTRING(icd10_code, 1, 3) IN ('C77', 'C78', 'C79', 'C80', 'C7B')
THEN 1
ELSE 0
END
Expand Down
43 changes: 31 additions & 12 deletions mimic-iv/concepts_postgres/comorbidity/charlson.sql
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,21 @@
-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS mimiciv_derived.charlson; CREATE TABLE mimiciv_derived.charlson AS
/* ------------------------------------------------------------------ */ /* This query extracts Charlson Comorbidity Index (CCI) based on the */ /* recorded ICD-9 and ICD-10 codes. */ /* Reference for CCI: */ /* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */ /* of classifying prognostic comorbidity in longitudinal studies: */ /* development and validation.J Chronic Dis; 40(5):373-83. */ /* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */ /* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */ /* */ /* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */ /* Comorbidities: */ /* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */ /* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */ /* Med Care. 2005 Nov; 43(11): 1130-9. */ /* ------------------------------------------------------------------ */
/* ------------------------------------------------------------------ */
/* This query extracts Charlson Comorbidity Index (CCI) based on the */
/* recorded ICD-9 and ICD-10 codes. */
/* Reference for CCI: */
/* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */
/* of classifying prognostic comorbidity in longitudinal studies: */
/* development and validation.J Chronic Dis; 40(5):373-83. */
/* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */
/* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */
/* */
/* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */
/* Comorbidities: */
/* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */
/* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */
/* Med Care. 2005 Nov; 43(11): 1130-9. */
/* ------------------------------------------------------------------ */
WITH diag AS (
SELECT
hadm_id,
Expand Down Expand Up @@ -265,21 +280,25 @@ WITH diag AS (
THEN 1
ELSE 0
END
) AS renal_disease, /* Any malignancy, including lymphoma and leukemia, */ /* except malignant neoplasm of skin. */
) AS renal_disease, /* Any malignancy, including lymphoma and leukemia, */ /* except malignant neoplasm of skin. */ /* ICD-10-CM codes added after Quan et al. (2005): */ /* C4A (Merkel cell carcinoma) excluded as skin malignancy per Quan. */ /* C7A (malignant neuroendocrine tumors) included as primary malignancy. */
MAX(
CASE
WHEN SUBSTRING(icd9_code FROM 1 FOR 3) BETWEEN '140' AND '172'
OR SUBSTRING(icd9_code FROM 1 FOR 4) BETWEEN '1740' AND '1958'
OR SUBSTRING(icd9_code FROM 1 FOR 3) BETWEEN '200' AND '208'
OR SUBSTRING(icd9_code FROM 1 FOR 4) = '2386'
OR SUBSTRING(icd10_code FROM 1 FOR 3) IN ('C43', 'C88')
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C00' AND 'C26'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C30' AND 'C34'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C37' AND 'C41'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C45' AND 'C58'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C60' AND 'C76'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C81' AND 'C85'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C90' AND 'C97'
OR (
SUBSTRING(icd10_code FROM 1 FOR 3) IN ('C43', 'C88')
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C00' AND 'C26'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C30' AND 'C34'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C37' AND 'C41'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C45' AND 'C58'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C60' AND 'C76'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C81' AND 'C85'
OR SUBSTRING(icd10_code FROM 1 FOR 3) BETWEEN 'C90' AND 'C97'
OR SUBSTRING(icd10_code FROM 1 FOR 3) = 'C7A'
)
AND SUBSTRING(icd10_code FROM 1 FOR 3) IS DISTINCT FROM 'C4A'
THEN 1
ELSE 0
END
Expand All @@ -304,11 +323,11 @@ WITH diag AS (
THEN 1
ELSE 0
END
) AS severe_liver_disease, /* Metastatic solid tumor */
) AS severe_liver_disease, /* Metastatic solid tumor */ /* ICD-10-CM C7B (secondary neuroendocrine tumors) added after Quan et al. (2005). */
MAX(
CASE
WHEN SUBSTRING(icd9_code FROM 1 FOR 3) IN ('196', '197', '198', '199')
OR SUBSTRING(icd10_code FROM 1 FOR 3) IN ('C77', 'C78', 'C79', 'C80')
OR SUBSTRING(icd10_code FROM 1 FOR 3) IN ('C77', 'C78', 'C79', 'C80', 'C7B')
THEN 1
ELSE 0
END
Expand Down