# 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.