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03_cohorts_and_clinical_coding/cluster_code_lookup.sql

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+/*
+    Clinical coding cluster lookup
+    ==============================
+
+    Purpose:
+    List SNOMED codes attached to maintained clinical coding clusters.
+
+    Use maintained clusters where possible instead of free-text matching on
+    SNOMED descriptions.
+*/
+
+SET CLUSTER_ID = 'DEPR_COD';
+
+SELECT DISTINCT
+    ccs."Cluster_ID",
+    ccs."SNOMEDCode",
+    ccs."SNOMEDDescription"
+FROM DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes" ccs
+WHERE ccs."Cluster_ID" = $CLUSTER_ID
+ORDER BY ccs."SNOMEDDescription", ccs."SNOMEDCode";

03_cohorts_and_clinical_coding/monthly_clinical_event_count_by_practice.sql

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+/*
+    Monthly clinical event count by practice
+    ========================================
+
+    Purpose:
+    Count distinct patients with a clinical code by month and practice, while
+    returning zero rows for months/practices with no events.
+
+    Good for:
+    - SMR-type activity counts.
+    - Condition or review-code monitoring.
+    - Building a complete month/practice grid for charts.
+*/
+
+SET START_MONTH = '2024-07-01';
+SET END_MONTH = CURRENT_DATE();
+SET CLUSTER_ID = 'REPLACE_WITH_CLUSTER_ID';
+
+WITH clinical_codes AS (
+    -- Maintained cluster definitions avoid fragile free-text SNOMED searches.
+    SELECT DISTINCT "SNOMEDCode"
+    FROM DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes"
+    WHERE "Cluster_ID" = $CLUSTER_ID
+),
+practices AS (
+    -- Default to active Norfolk and Suffolk parent GP practices.
+    SELECT DISTINCT
+        "OrganisationCode" AS "PracticeCode",
+        "OrganisationName" AS "PracticeName",
+        "PCNName",
+        "PlaceName",
+        "AllianceName"
+    FROM DATA_HUB.DWH."DimOrganisationAndSite"
+    WHERE "IsSiteNorfolkAndSuffolk" = 'Yes'
+      AND "OrganisationSubType" = 'GP Practice'
+      AND "IsSiteActive" = 'Yes'
+      AND "SiteCode" = "OrganisationCode"
+),
+base_population AS (
+    -- Keeps the denominator/cohort rule visible before events are counted.
+    SELECT
+        p."PracticeCode",
+        dp."PersonKey",
+        dp."PatientPseudonym"
+    FROM DATA_HUB.DWH."DimPerson" dp
+    INNER JOIN practices p
+        ON dp."CurrentGeneralPractice" = p."PracticeCode"
+    WHERE dp."RecordStatus" = 'Active'
+      AND dp."PersonStatus" = 'Known'
+      AND dp."YearMonthDeath" IS NULL
+),
+month_numbers AS (
+    -- Generates up to 120 monthly rows; extend if a longer history is needed.
+    SELECT ROW_NUMBER() OVER (ORDER BY SEQ4()) - 1 AS n
+    FROM TABLE(GENERATOR(ROWCOUNT => 120))
+),
+months AS (
+    SELECT DATE_TRUNC('MONTH', DATEADD(MONTH, n, $START_MONTH::DATE))::DATE AS "MonthStartDate"
+    FROM month_numbers
+    WHERE DATEADD(MONTH, n, $START_MONTH::DATE) <= $END_MONTH::DATE
+),
+practice_month_grid AS (
+    SELECT
+        p."PracticeCode",
+        p."PracticeName",
+        p."PCNName",
+        p."PlaceName",
+        p."AllianceName",
+        m."MonthStartDate"
+    FROM practices p
+    CROSS JOIN months m
+),
+events AS (
+    SELECT
+        bp."PracticeCode",
+        DATE_TRUNC('MONTH', cc."EventDateTime")::DATE AS "MonthStartDate",
+        COUNT(DISTINCT bp."PersonKey") AS "PatientsWithEvent"
+    FROM DATA_HUB.PHM."PrimaryCareClinicalCoding" cc
+    INNER JOIN clinical_codes c
+        ON cc."SNOMEDCode" = c."SNOMEDCode"
+    INNER JOIN base_population bp
+        ON cc."PatientPseudonym" = bp."PatientPseudonym"
+    WHERE cc."EventDateTime"::DATE BETWEEN $START_MONTH::DATE AND $END_MONTH::DATE
+    GROUP BY
+        bp."PracticeCode",
+        DATE_TRUNC('MONTH', cc."EventDateTime")::DATE
+)
+SELECT
+    pmg."PracticeCode",
+    pmg."PracticeName",
+    pmg."PCNName",
+    pmg."PlaceName",
+    pmg."AllianceName",
+    pmg."MonthStartDate",
+    COALESCE(e."PatientsWithEvent", 0) AS "PatientsWithEvent"
+FROM practice_month_grid pmg
+LEFT JOIN events e
+    ON pmg."PracticeCode" = e."PracticeCode"
+   AND pmg."MonthStartDate" = e."MonthStartDate"
+ORDER BY
+    pmg."PracticeName",
+    pmg."MonthStartDate";

03_cohorts_and_clinical_coding/prescribing_plus_clinical_code_cohort.sql

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+/*
+    Cohort from prescribing plus clinical coding
+    ============================================
+
+    Purpose:
+    Build a patient cohort where a medicine exposure is combined with a clinical
+    coding condition, for example patients prescribed a medicine who also have
+    a relevant diagnosis code in a lookback window.
+
+    Replace:
+    - BNF_PREFIX or use a VTM/VMP product CTE.
+    - CLUSTER_ID with the maintained cluster needed for the clinical condition.
+*/
+
+SET PRESCRIBING_START_DATE = '2025-04-01';
+SET PRESCRIBING_END_DATE = '2026-03-31';
+SET CLINICAL_LOOKBACK_YEARS = -2;
+SET BNF_PREFIX = '0403';
+SET CLUSTER_ID = 'DEPR_COD';
+
+WITH practices AS (
+    -- Default reporting geography: active Norfolk and Suffolk parent GP practices.
+    SELECT DISTINCT
+        "OrganisationCode" AS "PracticeCode",
+        "OrganisationName" AS "PracticeName",
+        "PCNName",
+        "PlaceName",
+        "AllianceName"
+    FROM DATA_HUB.DWH."DimOrganisationAndSite"
+    WHERE "OrganisationSubType" = 'GP Practice'
+      AND "IsSiteActive" = 'Yes'
+      AND "IsSiteNorfolkAndSuffolk" = 'Yes'
+      AND "SiteCode" = "OrganisationCode"
+),
+base_population AS (
+    -- Active, known, living patients registered to the selected practices.
+    SELECT
+        p."PracticeCode",
+        p."PracticeName",
+        p."PCNName",
+        p."PlaceName",
+        p."AllianceName",
+        dp."PersonKey",
+        dp."PatientPseudonym",
+        dp."CurrentAge"
+    FROM DATA_HUB.DWH."DimPerson" dp
+    INNER JOIN practices p
+        ON dp."CurrentGeneralPractice" = p."PracticeCode"
+    WHERE dp."RecordStatus" = 'Active'
+      AND dp."PersonStatus" = 'Known'
+      AND dp."YearMonthDeath" IS NULL
+),
+medicine_products AS (
+    -- Replace with VTM/VMP/explicit product logic if BNF prefix is too broad.
+    SELECT DISTINCT "ProductSnomedCode"
+    FROM DATA_HUB.DWH."DimMedicineAndDevice"
+    WHERE "BNFCode" LIKE $BNF_PREFIX || '%'
+),
+clinical_codes AS (
+    -- Maintained cluster definitions avoid fragile free-text SNOMED searches.
+    SELECT DISTINCT "SNOMEDCode"
+    FROM DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes"
+    WHERE "Cluster_ID" = $CLUSTER_ID
+),
+prescribed_patients AS (
+    -- Medicine-exposed patients in the prescribing window.
+    SELECT DISTINCT
+        bp."PracticeCode",
+        bp."PracticeName",
+        bp."PCNName",
+        bp."PlaceName",
+        bp."AllianceName",
+        bp."PersonKey",
+        bp."PatientPseudonym",
+        bp."CurrentAge"
+    FROM REPORTING_DATASETS_ICB.SCRATCHPAD."MEDS__UnifiedPrescribingTable" rx
+    INNER JOIN base_population bp
+        ON rx."PersonKey" = bp."PersonKey"
+    INNER JOIN medicine_products mp
+        ON rx."SNOMEDCode" = mp."ProductSnomedCode"
+    WHERE rx."DateMedicationStart" BETWEEN $PRESCRIBING_START_DATE AND $PRESCRIBING_END_DATE
+),
+coded_patients AS (
+    -- Look back from the end of the prescribing period for matching clinical events.
+    SELECT DISTINCT
+        pp."PersonKey",
+        MIN(cc."EventDateTime"::DATE) AS "FirstMatchingClinicalEventDate",
+        MAX(cc."EventDateTime"::DATE) AS "LatestMatchingClinicalEventDate"
+    FROM prescribed_patients pp
+    INNER JOIN DATA_HUB.PHM."PrimaryCareClinicalCoding" cc
+        ON pp."PatientPseudonym" = cc."PatientPseudonym"
+    INNER JOIN clinical_codes c
+        ON cc."SNOMEDCode" = c."SNOMEDCode"
+    WHERE cc."EventDateTime"::DATE BETWEEN DATEADD('YEAR', $CLINICAL_LOOKBACK_YEARS, $PRESCRIBING_END_DATE::DATE)
+                                      AND $PRESCRIBING_END_DATE::DATE
+    GROUP BY pp."PersonKey"
+)
+SELECT
+    pp."PracticeCode",
+    pp."PracticeName",
+    pp."PCNName",
+    pp."PlaceName",
+    pp."AllianceName",
+    pp."PersonKey",
+    pp."CurrentAge",
+    CASE WHEN cp."PersonKey" IS NOT NULL THEN 1 ELSE 0 END AS "HasClinicalCodeInLookback",
+    cp."FirstMatchingClinicalEventDate",
+    cp."LatestMatchingClinicalEventDate"
+FROM prescribed_patients pp
+LEFT JOIN coded_patients cp
+    ON pp."PersonKey" = cp."PersonKey"
+ORDER BY
+    pp."PracticeName",
+    pp."PersonKey";