Pulmonary diseases Task Force Refined phenotypes

The files contains curated phenotypes for asthma severity and asthma/COPD overlap (ACO). Asthma severity has been estimated based on the drug purchases (specific drugs and doses are shown in the end of the document) for each month of the follow-up period (ERS/ATS 2014 criteria):

• gina_classification_max: dDtermine each patient’s highest GINA class and the duration they have continuously remained in that class.

• gina_classification_max_GINA5_GINA4_CONT_TRANS: Identify each patient’s highest GINA class in which they have remained continuously for at least one year.

• gina_classification_longitudinal_eras: GINA eras

• gina_classification_longitudinal_monthly: Raw data’, GINA class for each month of the follow-up

ACO phenotype contains individuals with the overlap of asthma and chronic obstructive pulmonary disease.

The data is available in the following Sandbox directory:

/finngen/library-red/task_force_data/Pulmonary/Refined_phenotypes/

File structure

Severe asthma

Data is in four files:

Pulmonary_task_force_gina_classification_max.txt.gz

41200 rows and 41200 unique FINNGENIDs

Group_name: Highest Global Initiative for Asthma (GINA) classification (GINA0-5) attained by the patient during follow-up.

Time_type:

1. GINA class kept continuously period of > 4 years

2. GINA class kept continuously period of 1-4 years

3. GINA class kept continuously period <1 year

Pulmonary_task_force_gina_classification_longitudinal_eras.txt.gz

379096 rows and unique 44480 FINNGENIDs

gina_step: Gina step/class from 0 to 5

start_month: start month of the GINA era

end_month: end month of the GINA era

Pulmonary_task_force_gina_classification_longitudinal_monthly.txt.gz

8060435 rows and unique 44480 FINNGENIDs

month: number of the follow-up month

gina_step: Gina step/class 0-5 of the month

Pulmonary_task_force_gina_classification_max_GINA5_GINA4_CONT_TRANS.txt 18403 rows and unique 18403 FINNGENIDs

Maximum GINA Class kept continuously a period of >1 year

Data specifics

Asthma severity (based on medication):

• Severe asthma: ERS/ATS 2014 criteria (dispensing of ICS ≥ 1600 ug budesonide daily) and at least one dispensed second controller (LTRA, LABA, LAMA, theophylline) during the same year

• GINA step 4/5 asthma (accoding to newest/most relevant GINA guideline) and at least one dispensed second controller (LTRA, LABA, LAMA, theophylline) during the same year

• Control groups for severe asthma groups: non-severe asthma GINA groups 0-3 and healthy controls (no obstructive lung disease)

ACO Data

File	Description
PULMONARY_TASK_FORCE_ACO_CASES.tsv.gz	Cases with Asthma-COPD overlap (ACO)

Phenotype definitions

Phenotype	Criteria
Asthma	Any of: ICD10: J45-J46, J82; ICD9: 493; ICD8: 493
COPD	Any of: ICD10: J41-J44; ICD9: 491, 492, 496; ICD8: 49104, 492
ACO (Cases)	Individuals given both diagnoses by a physician at least once during follow-up.
CONTROL	No diagnosis of Asthma, COPD, or Alpha-1 antitrypsin deficiency.

Exclusions (Cases and Controls)

Individuals with the following conditions were excluded from both case and control groups:

• Alpha-1 antitrypsin deficiency

  • ICD-10: E88.0, E88.01, E88.9

  • ICD-9: 273.4

Diagnosis Date

For ACO cases, the "Diagnosis Date" indicates the specific date when the person has satisfied the criteria for both asthma and COPD (i.e., the date of the second occurring diagnosis type).