How to define a cohort in Atlas

Quick start

The following tutorial is a step-by-step guide to define a simple case and "all who are not cases" control cohort:

How to define a simple ICD case-control cohort in Atlas

Cohort definition process

In Atlas, the cohort definition starts by creating a Concept Set using medical codes. The Concept Set is then used to create cohorts using additional criteria defined in Cohort Definitions.

Atlas cohorts are defined in two steps:

1. Define a Concept Set using medical codes

2. Define a cohort using Cohort Definitions using the Concept Set and additional criteria

An Atlas cohort is a set of people who satisfy one or more inclusion criteria for a period of time. A person may appear more than once in a cohort if they fulfil the inclusion criteria during multiple non-overlapping periods. For example, a cohort for pregnancy will include people from the day of conception until the day of delivery or interruption. If a person has multiple pregnancies they will appear in the cohort once per pregnancy.

Select the correct Finngen data release in Atlas before you define your cohorts.

Concept Sets

• Create Concept Sets using standard code descendants

• Exclude and Remove codes from Concept Set

• Simplify Concept Sets that use standard code descendants

• Create Concept Sets using equivalent standard and non-standard codes

• View standard code hierarchy in Atlas

• Concept Set from standard codes and standard visit types (NO INSTRUCTIONS FOR THIS YET)

• Concept Set from standard codes imported from OHDSI phenotype library (NO INSTRUCTIONS FOR THIS YET)

Cohort Definitions

• Using the Death register in Atlas

• Filtering by clinical registries in Atlas

• Filtering by demographic criteria in Atlas

• Defining exit rules for a cohort in rules

• Selecting the correct box in Atlas for events and medical codes

• How to define cohort entry dates (e.g. age at the first event) (NO INSTRUCTIONS FOR THIS YET)

• How to define cohort with disease onset in a time range (NO INSTRUCTIONS FOR THIS YET)

• How to define cohort using medication intervals (NO INSTRUCTIONS FOR THIS YET)

• How to define cohort with seasonal rules (NO INSTRUCTIONS FOR THIS YET)

Further information

• How to export FinnGen IDs from Atlas

• Downstream analyses after the Atlas cohorts are created