Preparing manuscripts or conference abstracts
Here we describe how to cite FinnGen, if you are preparing a manuscript based on FinnGen data.
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), 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 and conference abstract handling process
When you are about to submit a manuscript or conference abstract 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).
Manuscripts:
Manuscript files (all files, including supplements)
The target journal's title
The target submission date
Contact person for comments
Conference abstracts:
Abstract file (all files, including supplements)
Name of the conference you are aiming to attend
The target submission date
Contact person for comments
The admin team will pass the manuscript/abstract to the FinnGen Scientific Committee. Manuscript circulation time is three weeks, which should be reserved for the Scientific Committee members to give feedback. Abstract circulation time is one week.
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 in your manuscript/abstract 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 some 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.
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 §.
Read more about FinnGen sample DNA isolation protocols here.
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 make sure to include in the acknowledgements all FinnGen Partners and funding organizations. The up to date list of parties to be acknowledged available here. Please note that these are updated periodically, so make sure to use the newest version available.
Data access/availability statement
Some journals may ask you to provide data access statement.
Please refer to the Data Availability section of the FinnGen 'flagship' paper as an example for drafting the data access/availability statement in your manuscript."
In a nutshell:
Based on National and European regulations (GDPR) access to individual-level sensitive health data must be approved by national authorities for specific research projects and for specifically listed and approved researchers.
The health data used and generated in FinnGen are provided by the National Health Register Authorities including Finnish Institute of Health and Welfare, Statistics Finland, KELA, Digital and Population Data Services Agency and approved, either by the individual authorities or by the Finnish Data Authority, Findata, for purposes of FinnGen project. Therefore the project cannot grant access to individual-level data to others.
Any researcher can apply for the health register data from the Finnish Data Authority Findata (https://findata.fi/en/permits/) and for individual-level genotype data from Finnish biobanks via the Fingenious portal (https://site.fingenious.fi/en/) hosted by the Finnish Biobank Cooperative FINBB (https://finbb.fi/en/).
Please note:
We encourage you to publish your article also on an open access publishing platform. Especially, University of Helsinki affliated researchers should see the instructions for self-archiving (green open access).
We encourage you to make your custom GWAS summary statistics available to the FinnGen community. After doing so, you can easily request that they be made publicly available once your manuscript has been accepted for publication. While many FinnGen summary statistics are available in public services such as the GWAS Catalogue, we prefer that FinnGen community researchers publish their summary statistics in our public bucket.
The genotype data for the FinnGen releases are returned to the biobanks after the 1-year exclusivity period to the FinnGen consortium members.
FinnGen core analysis 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.
Last updated