Lymphocyte count and outcomes in CCHIC - OMOP

query4grant.sql

-- P of PICO looks like
-- Lymphocyte count less than 1.2 within 72 hours of critical care admission + mechanical ventilation.
-- O 60-day mortality…. So in hospital mortality would be great

-- 1. find lymphocyte counts

SELECT 
*
FROM dsf_omop.measurement m 
WHERE m.measurement_concept_id = 3019198
LIMIT 3;

-- 2. find mechanical ventilation
-- this is tricky! https://github.com/alan-turing-institute/DECOVID-datamgmt/blob/master/derrived-concepts/ventilation.md
SELECT 
	p.procedure_concept_id
	,COUNT(*) n
FROM dsf_omop.procedure_occurrence p
GROUP BY p.procedure_concept_id
ORDER BY n DESC
--LIMIT 100
;
--this reveals that 4013354 is the concept code of insertion of an ET tube
--so now user this to define patients who are intubated
--would expect about 20% of patients in ICU to be intubated at some time


-- 3. find critical care admission
SELECT * FROM care_site WHERE 
care_site_id IN (1,2,3) LIMIT 3;

-- 4. find 60d mortality

SELECT * FROM dsf_omop.death LIMIT 3;