Add pregnancy codelist and pregnancy rules to denominators

Author: viv3ckj

analysis/codelists.py

@@ -13,3 +13,10 @@
     column="snomedcode",
     category_column="Grouping_6",
 )
+
+# Import pregnancy codelist
+pregnancy_codelist = codelist_from_csv(
+    "codelists/nhsd-primary-care-domain-refsets-preg_cod.csv",
+    column="code",
+    category_column="term",
+)

analysis/measures_definition_pf_codes_conditions.py

@@ -6,7 +6,7 @@
     addresses,
     ethnicity_from_sus,
 )
-from codelists import pharmacy_first_conditions_codelist, ethnicity_codelist
+from codelists import pharmacy_first_conditions_codelist, ethnicity_codelist, pregnancy_codelist
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -101,6 +101,15 @@
     otherwise="Missing",
 )
 
+# Create variable which when not null, indicates patient is pregnant
+pregnancy_status = (
+    clinical_events.where(clinical_events.snomedct_code.is_in(pregnancy_codelist))
+    .where(clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))
+    .sort_by(clinical_events.date)
+    .last_for_patient()
+    .date
+)
+
 # Select clinical events in interval date range
 selected_events = clinical_events.where(
     clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
@@ -145,15 +154,15 @@
             intervals=months(monthly_intervals).starting_on(start_date),
         )
 
-# Create denominator variables for each clinical condition based on NHS England rules using sex and age
+# Create denominator variables for each clinical condition based on NHS England rules using sex, age and pregnancy status
 # Exclusions have not been added to these rules yet
-denominator_uncomplicated_uti = (age>=16) & (age<=64) & (patients.sex.is_in(["female"]))
-denominator_shingles = age>=18
-denominator_impetigo = age>=1
-denominator_infected_insect_bites = age>=1
-denominator_acute_sore_throat = age>=5
-denominator_acute_sinusitis = age>=12
-denominator_acute_otitis_media = (age>=1) & (age<=17)
+denominator_uncomplicated_uti = (age>=16) & (age<=64) & patients.sex.is_in(["female"]) & pregnancy_status.is_null() 
+denominator_shingles = (age>=18) & pregnancy_status.is_null()
+denominator_impetigo = (age>=1) | (pregnancy_status.is_not_null() & (age>=16))
+denominator_infected_insect_bites = (age>=1) | (pregnancy_status.is_not_null() & (age>=16))
+denominator_acute_sore_throat = (age>=5) | (pregnancy_status.is_not_null() & (age>=16))
+denominator_acute_sinusitis = ((age>=12) | (pregnancy_status.is_not_null() & (age>=16)))
+denominator_acute_otitis_media = (age>=1) & (age<=17) | (pregnancy_status.is_not_null() & (age>=16))
 
 # Create dictionary for clinical condition denominators
 pf_condition_denominators = {

codelists/codelists.json

@@ -11,6 +11,12 @@
       "url": "https://www.opencodelists.org/codelist/opensafely/ethnicity-snomed-0removed/2e641f61/",
       "downloaded_at": "2024-10-03 11:34:59.878387Z",
       "sha": "8b849b5b785d80306e488d0109640c8c1d2da01b"
+    },
+    "nhsd-primary-care-domain-refsets-preg_cod.csv": {
+      "id": "nhsd-primary-care-domain-refsets/preg_cod/20200812",
+      "url": "https://www.opencodelists.org/codelist/nhsd-primary-care-domain-refsets/preg_cod/20200812/",
+      "downloaded_at": "2024-10-10 13:27:57.825804Z",
+      "sha": "4a1cbc5c12ce8589030b376905ac47f5a68b2503"
     }
   }
 }

codelists/codelists.txt

@@ -1,2 +1,3 @@
 user/chriswood/pharmacy-first-clinical-pathway-conditions/7ec97762
-opensafely/ethnicity-snomed-0removed/2e641f61
+opensafely/ethnicity-snomed-0removed/2e641f61
+nhsd-primary-care-domain-refsets/preg_cod/20200812

codelists/nhsd-primary-care-domain-refsets-preg_cod.csv

@@ -0,0 +1,41 @@
+code,term
+10231000132102,In-vitro fertilization pregnancy
+1109951000000101,Pregnancy insufficiently advanced for reliable antenatal screening
+1109971000000105,Pregnancy too advanced for reliable antenatal screening
+1148801000000108,Monochorionic monoamniotic triplet pregnancy
+1148811000000105,Trichorionic triamniotic triplet pregnancy
+1148821000000104,Dichorionic triamniotic triplet pregnancy
+1148841000000106,Dichorionic diamniotic triplet pregnancy
+1149411000000103,Monochorionic diamniotic triplet pregnancy
+1149421000000109,Monochorionic triamniotic triplet pregnancy
+134781000119106,High risk pregnancy due to recurrent miscarriage
+16356006,Multiple pregnancy
+169488004,Contraceptive intrauterine device failure - pregnant
+169501005,"Pregnant, diaphragm failure"
+169508004,"Pregnant, sheath failure"
+169560008,Pregnant - urine test confirms
+169561007,Pregnant - blood test confirms
+169562000,Pregnant - vaginal examination confirms
+169563005,Pregnant - on history
+169564004,Pregnant - on abdominal palpation
+169565003,Pregnant - planned
+169566002,Pregnancy unplanned but wanted
+237238006,Pregnancy with uncertain dates
+237239003,Low risk pregnancy
+276367008,Wanted pregnancy
+314204000,Early stage of pregnancy
+439311009,Intends to continue pregnancy
+444661007,High risk pregnancy due to history of preterm labor
+459166009,Dichorionic diamniotic twin pregnancy
+459167000,Monochorionic twin pregnancy
+459168005,Monochorionic diamniotic twin pregnancy
+459171002,Monochorionic monoamniotic twin pregnancy
+47200007,High risk pregnancy
+60810003,Quadruplet pregnancy
+64254006,Triplet pregnancy
+65147003,Twin pregnancy
+713575004,Dizygotic twin pregnancy
+713576003,Monozygotic twin pregnancy
+72957006,Diamniotic-monochorionic twins
+77386006,Pregnant
+80997009,Quintuplet pregnancy