Citing FinnGen
Here we describe how to cite FinnGen, if you are preparing a manuscript based on FinnGen analysis or publicly available FinnGen summary statistics.
To note, similar practices should be implemented prior to the submission of abstracts to conferences where the results of your work are from FinnGen data.
When drafting a manuscript using FinnGen data (note this does not apply publicly available FinnGen results that can be downloaded from here), please familiarize yourself with the documentation below and add the relevant parts to your manuscript. Please familiarize yourself also to FinnGen publication policy.
FinnGen manuscript handling process
When you are about to submit a manuscript containing FinnGen results, it needs to first be circulated to the FinnGen Scientific Committee for review and feedback. Provide the following information to FinnGen admin team via email (finngen-admin@helsinki.fi).
Manuscript files (all files, including supplements)
The target journal's title
The target submission date
Contact person for comments
The admin team will pass the manuscript to the FinnGen Scientific Committee. Manuscript circulation time is three weeks, which should be reserved for the Scientific Committee to give feedback. The list of Scientific Committee Members can be found here. Please see the list of Scientific committee members.
Authorship
FinnGen should be listed as one of the authors in manuscripts that are mostly based on FinnGen data and approved FinnGen Analysis and FinnGen Bespoke Analysis proposals. Please use ‘FinnGen’ as the author, not ’FinnGen Consortium’, ‘FinnGen Study’ or any other variation of this, even if you see those used in other publications.
When you add 'FinnGen' as an author you often need to provide the list of FinnGen consortium members (so called ‘FinnGen banner’) as a supplementary file. Note that the ‘FinnGen banner’ is updated periodically - so make sure to include the newest version to your submission. Usually the individuals in the banner are not PubMed indexed but this depends on the journal policy. The FinnGen banner is not needed if FinnGen data is only used for replication analyses, in that case we ask you add FinnGen in the Acknowledgements. Please refer to FinnGen's publication policy to see how FinnGen should appear in the manuscripts.
In case you need to provide email or street address for the authors, you can use these for 'FinnGen':
email: finngen-info@helsinki.fi
Street address: Biomedicum Helsinki 2U, P.O.Box 20 (Tukholmankatu 8)
General description of FinnGen
If you need to describe FinnGen study here is an overall description you can modify for the use:
“FinnGen (https://www.finngen.fi/en) launched in 2017, is a public-private research project, combining genome and digital healthcare data on about 500,000 Finns. The nation-wide research project aims to provide novel medically and therapeutically relevant insight into human diseases. FinnGen is a pre-competitive partnership of Finnish biobanks and their background organizations (universities and university hospitals) and international pharmaceutical industry partners and Finnish biobank cooperative (FINBB). All FinnGen partners are listed here: https://www.finngen.fi/en/partners.”
You can also use the general description of the project on our public website.
Please don’t copy the text above directly, on our website or in the FinnGen 'flagship' paper to avoid any copyright issues.
You can also cite so-called FinnGen 'flagship' paper. Please note that the 'flagship' paper is based on FinnGen Data Freeze 5 results and methods may have changed since.
Materials and Methods
Include to your manuscript the general ethics statement paragraph and permit numbers. Note that permit numbers are updated per each Data Freeze.
Links to Data Freeze specific FinnGen ethics statements:
Samples and genotyping
FinnGen utilizes biobank samples that consist of: 1) prospective samples (‘new samples’) and 2) legacy samples. 'New samples' are collected by request to give a voluntary biobank consent and to donate a biobank sample (typically blood). Hospital biobank and Terveystalo Biobank samples are typically collected during diagnostic sampling at hospital laboratories or at the ward. Blood Service Biobank consenting and sampling occurs in conjunction of blood donation. THL Biobank consenting and sampling typically occurs in conjunction with collection of research samples. On the other hand, legacy samples are older sample cohorts that have been collected for a specific research project before the Finnish Biobank Act came into effect (September 2013). These old research cohorts have then been transferred to a biobank according to the Finnish Biobank Act 13 §.
FinnGen samples were genotyped with ThermoFisher, Illumina and Affymetrix arrays.
The ‘new samples’ were genotyped with FinnGen ThermoFisher Axiom custom array at the ThermoFisher genotyping service in San Diego, CA, US. More information (including array content) about the FinnGen custom array can be found here.
The ‘legacy samples’ were genotyped over the years using various generations of Illumina and Affymetrix GWAS arrays. Read more about legacy samples from here.
Imputation
The genotype data were imputed with a Finnish population-specific Sisu reference panel. Genotype imputation process is described here.
From Data Freeze 8 on we have used SisuV4 imputation panel.
Genotype processing
Genotype data processing from Data Freeze 7 onward is described in detail here.
You can also check out the general documentation on the genotype processing and QC and GWAS analysis on our public website. Note that the content may need to be adjusted depending on the Data Freeze/Release used.
Core Analyses
General documentation on the genotype processing and QC and GWAS analyses (the content may need to be adjusted depending on the Data Freeze/Release used).
In case you use FinnGen core analysis results in your manuscript (GWAS, fine-mapping, co-localization etc.) the analysis details are described in the Data Freeze/Release specific analysis reports. You can also use the General documentation available here.
Risteys portal can be cited by adding the webpage link https://risteys.finregistry.fi/.
Acknowledgements
Please include in the acknowledgements all FinnGen Partners and funding organizations. The up to date acknowledgements are available here. Please note that these are updated periodically, so make sure to use the newest version available.
Data access statement
Individual level data: The Finnish biobank data can be accessed through the Fingenious® services (https://site.fingenious.fi/en/) managed by FINBB. Finnish Health register data can be applied from Findata (https://findata.fi/en/data/).
Summary statistics: Summary statistics from each data release will be made publicly available after a one year embargo period and can be accessed freely from: www.finngen.fi/en/access_results.
When reporting results utilizing publicly available results:
When reporting results using publicly available summary statistics downloaded through finngen.fi website, please familiarize yourself with the following documentation and add the relevant parts to your manuscript:
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