Kanta lab values

The Kanta lab values dataset was first released to the FinnGen Sandbox in August 2024. Publically accessible statistics are available on Risteys, and GWAS association results for Kanta lab values are available as well.

The documentation is split in three sections:

1. Data: Data location and references

2. FAQ: Explanations for common questions

3. How-to guides: step-by-step instructions for working with the data

Documentation highlights:

• Data column overview

• Which years are covered in the data?

• Why are some rows missing both the measurement value and the test outcome?

• How to load the dataset for only one OMOP Concept ID using Python pandas?

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Table of content

Data

• Location

• Data columns

• Pipeline

• Additional dataset: Values extraction analysis

• Other reference tables

FAQ

• Which years are covered in the data?
• What part of the FinnGen cohort also has data in the Kanta Lab dataset?
• Why are some rows missing both the measurement value and the test outcome?
• How do we know the reference range for each test?
• How reliable are the time measurements from APPROX_EVENT_DATETIME in the data?
• Can I differentiate between the time a test is ordered vs. the time is test is taken?
• What is the meaning of the different TEST_OUTCOME and TEST_OUTCOME_IMPUTED values?
• How do I know if a test was positive or negative, say for Covid?
• What is "vierimittaus"?
• When will the Kanta Lab dataset be updated?
• Should I use MEASUREMENT_VALUE or MEASUREMENT_VALUE_HARMONIZED for my analysis?
• Is it possible to know which test center processed the sample and made the test measurement?
• Why are some rows duplicates by FINNGENID, APPROX_EVENT_DATETIME, OMOP_CONCEPT_ID and MEASUREMENT_VALUE?
• Some of the units are unfamiliar to me, how do I know what they are?
• I have found some negative measurement values, are they a mistake?
• How was the Kanta data preprocessed before it got to FinnGen users?

How-to guides

• How to use Athena to find a test by name?
• How to load the data file using R?
• How to load the full dataset using Python pandas?
• How to load the dataset for only one OMOP Concept ID using Python pandas?
• How to access the data using BigQuery SQL?
• How to look up what data is available for a test without using the Sandbox?
• How to look up a test in the data from the Sandbox?