Detailed longitudinal data

This page has been last updated for R11.

Service sector data contains detailed longitudinal data with additional columns.

Sandbox directory

Detailed longitudinal data is available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/phenotype_1.0/

Note, this data also available in Atlas and OMOP common data model.

Data files

The data is available in the following file:

data/finngen_R{RELEASE]_detailed_longitudinal_1.0.txt.gz

The data file has eleven columns:

Column	Description
FINNGEN ID	Sample ID
SOURCE	Register source
EVENT_AGE	Individual's age at the event to two decimals
APPROX_EVENT_DAY	A randomized event date: +/- 1-15 days are added to the confidential exact event date
CODE1 - CODE4	Register source specific codes and other information
ICDVER	ICD-code version: ICD8/9/10, ICD-O-3
CATEGORY	Register code sets (vocabularies)
INDEX	Register index number. The same INDEX value within a register means that the codes have been given in the same hospital visit, or are, for example, from the same drug purchase event.

Detailed information about the columns is available in the following file:

finngen_R[RELEASE]_detailed_longitudinal_readme_1.0.txt

This is the main register data in FinnGen and contains health register codes from different sources. The data is called longitudinal because it contains several events/entries of codes for the same individual recorded at different times.

Detailed longitudinal data was presented in the FinnGen data users meeting on 12th January 2021 and can be explored using Atlas in the Sandbox.

The data is used as input for the Endpointter to determine which individuals are included in each of FinnGen's phenotypic endpoints:

A mock example of the detailed longitudinal data file is shown below:

Sources

The detailed longitudinal data file contains codes from the following registries:

Source	Description	Types of codes
PURCH	Kela drug purchase register	Medication codes
REIMB	Kela drug reimbursement register	Medication codes
INPAT	Inpatient Hilmo register	Diagnosis codes
OPER_IN	Inpatient Hilmo register - operations	Operation codes
OUTPAT	Specialist outpatient Hilmo register	Diagnosis codes
OPER_OUT	Specialist outpatient Hilmo - register operations	Operation codes
PRIM_OUT	Primary health care outpatient visits	Diagnosis and operation codes
CANC	Cancer register	Cancer codes
DEATH	Cause of death register	Cause of death codes

Image below demonstrates how variables in the national health registries end up to the columns in the detailed longitudinal data.

On the left: source registers, middle: variables in the source register data, on the right: column names in the detailed longitudinal data.

Codes

Information stored in the CODE1 - CODE4 column depends on the register source:

Source	Description	Codes
PURCH	Kela drug purchase register	CODE1: ATC code CODE2: Kela reimbursment code CODE3: Product number CODE4: Number of packages
REIMB	Kela drug reimbursement register	CODE1: Kela reimbursment code CODE2: ICD code
INPAT OUTPAT	Inpatient Hilmo register Specialist outpatient Hilmo register	CODE1: symptom code CODE2: cause code (e.g. CODE1 could be dementia associated with Alzheimer’s disease with CODE2 as Alzheimer's disease) CODE3: ATC code for drug's adverse effect CODE4: duration of stay
OPER_IN OPER_OUT	Inpatient Hilmo register - operations Specialist outpatient Hilmo register - operations	CODE1: operation code
PRIM_OUT	Primary health care outpatient visits	CODE1: diagnosis or operation code CODE2: symptom code CODE3: ATC code for drug's adverse effect
CANC	Cancer register	CODE1: ICD-0-3 topography CODE2: ICD-0-3 morphology CODE3: ICD-0-3 behaviour
DEATH	Cause of death register	CODE1: cause of death

Categories

The register code sets (vocabularies) are stored in the CATEGORY column:

Detailed information about register code sets is available from:

• International and Finnish Health Code Sets

• More information on health code sets

For diagnosis codes:

• 0 at the end of the CATEGORY variable means the main diagnosis code (e.g. 0 in ICD0 and NOM0)

• 1:N at the end of the CATEGORY variable refers to side diagnoses (e.g. 1:N in ICD1:N, NOM1:N)

Register data availability dates

Data is available from the register start date until the end of the register-specific follow-up date. The follow-up dates are available here and in the following file:

finngen_R[RELEASE]_detailed_longitudinal_readme_1.0.txt

The start and follow-up dates differ between registries and FInnGen data releases and you should take this into account in your analyses. Register start and follow-up dates are shown below for Data Freeze 6:

Further information

• Splitting combination codes in detailed longitudinal data

• Registers in detailed longitudinal data