Inflammatory bowel disease (IBD) time to operation & refined disease start data

Overview

This data lists surgical operations of interest for IBD patients. For samples with operations, one row represents one operation. For samples without operations, one row represents that sample. This data also contains refined disease onset. The disease is considered to start if 1) the person starts mesalazine, 2) the person has a colonoscopy with inflammation, or 3) the person gets an IBD diagnosis or reimbursement for IBD medications.

Files

Name	Description
refined_ibd_onset_and_time_of_operations.tsv	Data file containing time to operation & redined disease onset
operation_codes.txt	List of operation codes used

Column descriptions

Column name	Column description
FINNGENID	Individual's FinnGen ID
K11_IBD_STRICT_FU_AGE	Age of individual at time of endpoint K11_IBD_STRICT
K11_IBD_STRICT_APPROX_EVENT_DAY	Date of endpoint K11_IBD_STRICT
DISEASE_ONSET_DATE	Refined disease onset date
DISEASE_ONSET_AGE	Refined disease onset age
DISEASE_ONSET_REASON	refined disease onset reason, either "Diagnosis" i.e. not refined, "Medication purchase" = due to started medication (mesalazine), or "Inflamed colonoscopy" = inflammation in colonoscopy
DISEASE_ONSET_CODE	If reason is medication, the ATC code of the mecication. If reason is "Inflamed colonoscopy", it is the topography and morphology codes of the colonoscopy from SNOMED data, joined with an underscore. Otherwise NA
OPERATION_CODE	NOMESCO code for operation if operation was done, otherwise NA
OPERATION_DATE	Date of operation, or end of followup date for individuals without operations
OPERATION_AGE	Age at time of operation or age at end of followup if no operations
OPERATION_STATUS	1 if operation(s) was performed on individuals, 0 otherwise
APPROX_BIRTH_DATE	Birth date of individual
DEATH_FU_AGE	Age at end of followup for individual
DEATH	1 if individual has died, otherwise NA

Data Specifics

Samples were restricted to those samples that are available in analysis data (=both phenotype and genotype data available), and who had gotten the K11_IBD_STRICT endpoint.

For endpoint data, data freeze 13 endpoint data version 3.0 was used.

For operation data, data freeze 13 service sector data version 1.0 was used.

For medication data, data freeze 13 service sector data version 1.0 was used.

For colonoscopy data, FinnGen IBD Snomed data version 1.0 was used.

Colonoscopy data was restricted to codes T67* and T68*, as well as to morphology codes D6255 and M4* in SNOMED classification.

Surgical codes indicative of IBD related surgery are mainly drawn from https://doi.org/10.1186/s12911-019-0948-z. Not all codes from the study are included, and additional codes have been manually added to ensure coverage of procedures relevant to IBD.