Information for researchers

Start by browsing the introduction to Process for material request and NFBC user policies

1. Fill in the material data request in the Material request portal (Greip). Instructions for using the portal are linked below.
2. Use the template for the research plan and attach it the request. Describe clearly the aims of the research and the relevant exposure, outcome and confounders variables to be used. Only applications with this template are accepted for further processing. The link to the template below.
3. Attach a list of variables. Use the variable catalogue.
4. Submit the request (or Save to be submitted later).
5. Requests are evaluated by the NFBC Scientific committee. Once the final decision regarding the material request has been made, contact persons indicated in the form will be notified of the decision by email. The NFBC research permit is valid for five years.
6. For granted request the researcher will receive notification when the data has been compiled.
7. If the request is granted conditionally, please inform NFBCprojectcenter (at) oulu.fi once the conditions have been met.
8. To access the data via NFBC portal, a Univ-account of University of Oulu is needed.
9. Data transfer agreement (DTA) will be asked when the material request is granted if the data will be analysed outside University of Oulu.

Data Transfer Agreement (DTA) is needed with co-operational organisations needing the access to data. DTA is done once the material request is accepted by the research program.

1. Provide the Recipient organisation information needed for DTA to NFBC project center (nfbcprojectcenter(at)oulu.fi).
2. After that, the DTA is prepared by the cohort center and electronic signature process using UniOulu Sign system is initiated.
3. For eSign system, please provide the following information for persons signing from the recipient organisation: First name, Family name, email, mobile phone number with country code (+), Organisation, Title.

• DTA is available from NFBC project center (nfbcprojectcenter(at)oulu.fi).
• DTA with Data Processing Agreement (In Finnish) or with Standard contractual clauses (outside the EU) are available from NFBC project center (nfbcprojectcenter(at)oulu.fi)
• NFBC Material Transfer Agreement (MTA) is available from the project center (nfbcprojectcenter(at)oulu.fi)

☐ I am familiar with the material request process for NFBC. Information for the check list is available from the Information for researcher web page

Check list for material requests (new project)

☐ I have use the latest version of the variable catalogue, followed the instructions how to use it, used the latest version, and attached it with the application.

☐ I have attached the project plan and used the NFBC project plan template.

· see: https://www.oulu.fi/en/university/faculties-and-units/faculty-medicine/…

☐ I have public description in English and in Finnish, and I have considered the target group being the general population.

☐ I have added a short description of the material request in English.

☐ I have checked that the application and the research plan are consistent.

☐ I have read and informed the research group about the NFBC data User policies and I have attached a signed User policies document with the Greip application.

☐ I have included all researchers as contact persons in the request form.

☐ I have carefully considered and listed those researchers who need the access to the data.

☐ I am aware of the practices for data use at the University of Oulu server.

☐ I am aware of the service prices.

If you are using national register data

☐ I am aware of practices for the national register data use.

If researchers from another organisation than University of Oulu need to access the data

☐ I am aware of practices for data use with organization other than University of Oulu

If you are having a WENDY project

☐ I have follow the instructions

Check list for request for additional variables or for an amendment of the research plan

☐ I have attached an updated project plan to indicate and rationalize the use of additional variables and/or need for the amendment.

☐ I have included core researchers and leader of the research group as contact persons.

☐ I have indicated the original project number.

☐ I have indicated whether the data is analysed on the University of Oulu server or on the secured data environment (Kapseli).

If additional variables are requested:

☐ I have use the latest version of the variable catalogue, followed the instructions how to use it, used the latest version, and attached it with the application.

If you have a new researcher joining an existing project:

☐ I have read and informed the research group about the NFBC data User policies and have attached a signed User policies document with the Greip application.

If researchers from another organisation than University of Oulu need to access the data

☐ I am aware of practices for data use with organization other than University of Oulu. See data transfer agreement.

If you are using national register data

☐ I am aware of practices for the national register data use.

Check list for request to publish with the NFBC data

☐ I am aware that before submitting the manuscript to any journal the permission to publish needs to be requested. See 'Permission to publish' and User policies.

☐ In the manuscript, I have followed the instructions for data referral.

☐ In the manuscript, I have used NFBC1966, NFBC1986, Oulu1935, or Oulu1945 instead of NFBC66, NFBC86, Oulu35, Oulu45, or other variants.

☐ In the manuscript, I have indicated the authors and their affiliations.

☐ In the manuscript, I have no track changes or other editing comments.

☐ In the request form, I have added the manuscript as an attachment(s).

☐ In the request form, I have included authors as contact persons.

☐ In the request form, I have added short description in English.

☐ In the request form, I have indicated the project number.

If you have used national register data

☐ In the manuscript, I have cited register owners as instructed on their web pages. Some examples

Cohort data

NFBC1966 and NFBC1986: Only the variable catalogue format is accepted for further evaluation process.

Oulu1935 and Oulu1945: see descriptions for the Aging Population Cohorts for variable list or contact cohortsupport(at)oulu.fi.

Variable Catalogue for NFBC1966 and 1986 (v 20250310)

• Start with the latest catalogue version available from the web pages. Load and save the file on your computer.
• Use the left panel -/+ to select the cohort (1966 or 1986), time point, and variables of interest.
• Use Variable name level for selections. Mark the selected variables of interest with 'x' in column named Choice.
• Save the file and use as an attachment in Greip application process.
• Do not modify, copy-paste, or do other modifications or filtering. Embargo column is used to indicate restrictions in use if existing.
• Use the ”Other variables” sheet of the excel to add variables that are not listed in the Catalogue of variables
• For more information on the variables, see Cohort descriptions or contact cohortsupport(at)oulu.fi.

• Physical activity data from Oura Smart ring (NFBC1986 33y)
• Sedentary and physical activity variables extracted from Hookie AM20 hip-worn accelerometer (NFBC1966 46 y)
• Sedentary and Physical activity variable from Polar Active monitor (NFBC1966 46y)

NFBC1966:

Imputed genotype data is available for 6,547 individuals. Part of NFBC1966 samples were genotyped previously with Illumina HumanCNV370DuoBeadChip (genotypes were called with BeadChip), part were genotyped by FinnGen with ThermoFisher Axiom Custom Array (Axiom_FinnGen2.r5; genotype calls were made with AxiomGT1 algorithm for Affymetrix data). Imputation was performed by FinnGen. Genotyped samples were pre-phased with Eagle 2.3.5 and imputation was done using Beagle with SISu imputation reference panel v. 4.2.

NFBC1986:

Imputed genotype data is available for 5,771 individuals. Part of NFBC1986 samples were genotyped previously with Illumina HumanOmniExpressExome-8_v1.2 (genotypes were called with BeadChip), part were genotyped by FinnGen with ThermoFisher Axiom Custom Array (Axiom_FinnGen2.r5; genotype calls were made with AxiomGT1 algorithm for Affymetrix data). Imputation was performed by FinnGen. Genotyped samples were pre-phased with Eagle 2.3.5 and imputation was done using Beagle with SISu imputation reference panel v. 4.2.

• Psychiatric and psychological data (NFBC1966 and NFBC1986)

Brain and Mind Study (NFBC1986)

1. Brain and Mind Study I: brain MRI scan, cognitive tests, questionnaires and interviews for psychosis risk
and ADHD subsamples, and controls (n=329) (age 22-24)
2. Brain and Mind Study II (Addictor): brain MRI scan, cognitive tests, questionnaires and interviews for
subsample based on maternal smoking during pregnancy (cases and controls) (n=471) (age 24-27)

NFBC - MS lipidomics method description / Baker Heart and Diabetes Institute / May 2023

Lipids were isolated as previously described (Huynh et al, 2019). Briefly, randomised samples (10 µL) were extracted
in a single-phase extraction with 100ul of BuOH:MeOH (1:1) containing an internal standard mix of non-physiological
or stable isotope-labelled lipid standards. Lipid analysis was performed by liquid chromatography electrospray
ionisation-tandem mass spectrometry using an Agilent 1290 HPLC coupled to an Agilent 6490 triple quadrupole mass
spectrometer. Liquid chromatography was performed on a Zorbax Eclipse Plus C18, 1.8 um, 100 x 2.1mm column
(Agilent Technologies) using solvents A and B consisting of water:acetonitrile:isopropanol, 50:30:20 and 1:9:90
respectively, both containing 10mM ammonium formate with solvent A also containing 0.05uM medronic acid.
Over 750 lipid species were measured using dynamic multiple reaction monitoring (dMRM) where data was
collected for a retention time window specific to each lipid species (Agilent app note). Results from the
chromatographic data was analysed using Mass Hunter Quant B9.0 where relative lipid abundances were calculated
by relating each area under the chromatogram for each lipid species to the corresponding internal standard.
Correction factors were applied to adjust for different response factors, where these were known.

References:
- Huynh, Kevin et al. “High-Throughput Plasma Lipidomics: Detailed Mapping of the Associations with
Cardiometabolic Risk Factors.” Cell chemical biology vol. 26,1 (2019): 71-84.e4. doi:10.1016/j.chembiol.2018.10.008
- A Comprehensive, Curated, High-Throughput Method for the Detailed Analysis of the Plasma Lipidome

List of registers

Projects planning to use national register data as part of your NFBC study, please contact NFBCprojectcenter(at)oulu.fi beforehand.

• Process flow for the projects having national register data.

The Infrastructure for Population Studies updates permissions (new researchers) from the Finnish Social and Health Data Permit Authority (Findata) and Statistics Finland twice a year.

For updates the following actions from researchers are needed:

1. Send a signed Findata confidentiality commitment by emailing to NFBCprojectcenter(at)oulu.fi

   Include your email address*, the NFBC project number and mobilephone number (needed for the access to Findata-provided secure operating environment) and invoicing information**, Kapseli. See confidentiality commitment from Findata's web pages. Indicate if you wish to use Python in Kapseli.

   *Use your organization email address. Please note that cohort center and Findata uses this email address as a primary contact information for Kapseli related issues.

2. Submit your pledge of secrecy commitment for Statistics Finland’s using their electronic licensing service.

   Please, note that you are giving Confidentiality commitment, not remote access commitment. If you have already given electrical confidentiality commitment at the Statistics Finland’s service, for another project for example, please check if you need to do a new one. Additional information from Statistics Finland web pages. Inform NFBCprojectcenter(at)oulu.fi once you have made the Confidentiality commitment at the service.

3. **To cover the increased costs there will be a yearly fee of 200 €/user (VAT0%) for the NFBC Kapseli environment users starting from 1.1.2025. To continue as a user invoicing information needs to be provided.

In the publications the national registers that have been used must be referenced

Please check the instructions from the register owner's www pages. Here are some examples.

Finnish Social and Health Data Permit Authority Findata

• Finnish Centre for Pensions
• Finnish Institute for Health and Welfare
• Social Insurance Institution of Finland Kela
• Statistics Finland data covered by secondary laws

• The research data was obtained from Findata, the Finnish Social and Health Data Permit Authority, with data permit THL/XXXX/14.XX.00/20XX. Findata was responsible for the pseudonymization of the data and ensuring the anonymity of the final results.
• The statistics were produced by Findata, the Finnish Social and Health Data Permit Authority, with data request THL/XXXX/14.XX.00/20XX. Findata was responsible for data integration and producing the anonymized statistics.

Statistics Finland

• Statistics Finland data not covered by secondary laws
• Needs to be mentioned as a reference

See further instructions here

• Note that all users need to have a University of Oulu (UNIV/UFO) account.
• Note that project folder having national register data have been closed on the University of Oulu server. Project data are analysed in Findata's secure operating environment Kapseli. Project folders can be opened on University of Oulu servers without register data by request to cohortsupport@oulu.fi.
• If the folder needs to be removed to Kapseli environment, contact cohortsupport@oulu.fi.

Findata’s secure environment Kapseli is for projects using national register data (Finnish Institute for Health and Welfare (THL), Kela, Statistics Finland (cause of death), and Finnish Centre for Pensions) for NFBC1986 and NFBC1966 projects.

• New projects are compiled by the research group. For projects moving from University of Oulu server to Kapseli, contact cohortsupport@oulu.fi.
• Researchers need to be included Findata's research permit and in Kapseli user application. For those not included, see Variables and national registers
• Researcher need to have University of Oulu account, contact NFBCprojectcenter@oulu.fi.

Instructions how to access Findata's Kapseli are available from Findata's www-pages.

Instructions how to use NFBC Kapseli are available here:

• In English set 1
• In English set 2
• In Finnish set 1
• In Finnish set 2

Instructions how to compile data in NFBC Kapseli are available In English and in Finnish at the Kapseli (W:\POIMINTA\).

___

FAQ: If you got 'Bad request' error when loging to Kapseli: Delete or clear cookies and site data on your browser or open a new private browsing for Kapseli loging/Bad request -virheilmoitus: tyhjennä selaimen välimuisti ja evästeet. Vaihtoehtoisesti kirjautumiseen voi käyttää yksityistä välilehteä.

Genetic analyses using individual genotype data have to be performed using the nfbcgenetics server on CSC ePouta. In order to have access to ePouta the UNIV/UFO user account is needed.

See further instructions

New researchers needing the access to data

If you want to add new researchers to an already approved project, please send an email to NFBCprojectcenter (at) oulu.fi with the following information:

• Greip material request number of the project the researcher will be joined,
• the researcher's name, institute, e-mail address (University of Oulu UFO account*), and
• signed NFBC User policies document is needed (signed by the researcher and project principal investigator). For User policy document see NFBC user policies section on this web page.
• Note, that Data transfer or data access agreement is needed for researcher outside University of Oulu (more information from NFBCprojectcenter (at) oulu.fi.

*Researcher must have an University of Oulu account (UFO account for staff and researchers) to be able to access the project folder at NFBC portal at University of Oulu servers. The UNIV account email address (@oulu.fi) is used as a primary contact information for project folder related issues.

Note, that if the project contains national register data, all researcher having access to data need to have up-to-date permissions for national register data and the access to Kapseli environment. For more information see Variables and national registers section on this web page and contact NFBC project center.

See process flow for projects on University of Oulu server

See process flow for projects on Findata's Kapseli environment

Researcher not needing the access to data any more

Project principal investigator or responsible researcher needs to inform cohort center when there are changes in the researcher needing the access to NFBC data. This includes informing cohort center on researcher having access to data but not needing it any more. Send information to cohortsupport@oulu.fi

• Project number (original Greip material request number)
• the researcher's name, University of Oulu UFO account/email

If data transfer of modified variables between projects is needed, consult NFBCprojectcenter (at) oulu.fi with the description what modified variables are being transferred and if they are in line with the recipient project's accepted research plan. If not, a material request via Greip portal is needs to be submitted.

• After consultation, use the following service (link opens to a new window) to apply for the data transfer.
• The description document to be attached is here.

The same service is used for returning project's new variables to cohort center (see user policy).

This in not a process for additional variables from the variable catalogue. Use standard material request process via Greip system to apply.

Transferring cohort data to Kapseli environment

Transferring cohort data to Kapseli happens through Cohort support (kohorttituki(at)oulu.fi). Inform Cohort support on the names and file paths of the files to be transferred. Inform also project (project number) where the variables have originated from and the project (project number) they are transferred to. Please note, that variables need to be inline with the research plan of the target project.

• The transferred data format should be one of the following: ".sav", ".sas7bdat" or ".dta". Formats ".xlsx" and ".csv" are also accepted, if the files are well structured (i.e. they are correctly read in R with open.xlsx()/fread()). Other file formats require manual handling and should be avoided.
• The data to be transferred should have a clear ID column, the name of which should contain the string "id" (case insensitive) in the very least. The ID column should be of some known NFBC id format (e.g. project_ID, nfbcid), with no extra spaces or characters. Make sure the data only has a single ID column. Best practice is to name the ID column based on it's type (e.g. "project_id" or "nfbcid", case insensitive), rather than just "id".
• Avoid nordic letters (åäöÅÄÖ) in the file names and variable names.
• If more than one file needs to be transferred, gather them all under the same directory.
• The data will be transferred to Kapseli directory D:/a89/, where it will appear in a zipped folder named after the project number.

During the transfer, the ID will be changed to "idkt" (=nfbcid) and the data will be updated based on the latest consents from the cohort members. This may change the number of the cohort members in the data.

• Fill in the material request in the Material request portal (Greip) and choose Publication.
• Add authors to the researcher(s)-list as contact persons.
• Indicate in the form the number of your original material request.
• Attach the manuscript. Do not leave track changes or comments visible.
• Check that you have included all required information such as data referral, acknowledgements, Ethics committee and data availability statements (see information below).
• See the check list for request to publish with the NFBC data
• For authorship, please follow the recommendations of the Finnish National Board on Research Integrity TENK (see TENK web pages).

Information on NFBC1966 and NFBC1986 data collections (conducted so far) have been added to Fairdata.fi/Etsin. The following citations should be used in publications when using NFBC data (taking into account journal’s guidelines):

Cohort NFBC1966 Etsin-service

References to be used when referring to the NFBC1966 data collection in general (describing cohort in the material and methods section):

1. Use the NFBC1966 data reference

• In text: (University of Oulu, 1966)
• In the list of references: University of Oulu: Northern Finland Birth Cohort 1966. University of Oulu. http://urn.fi/urn:nbn:fi:att:bc1e5408-980e-4a62-b899-43bec3755243 (in the given format, information on date accessed is not needed for permanent urn reference)

and

2. Cohort profile article describing the data collection until the age of 46 years

• Nordström T, Miettunen J, Auvinen J, Ala-Mursula L, Keinänen-Kiukaanniemi S, Veijola J, Järvelin MR, Sebert S, Männikkö M. Cohort Profile: 46 years of follow-up of the Northern Finland Birth Cohort 1966 (NFBC1966). Int J Epidemiol. 2022 Jan 6;50(6):1786-1787j. https://doi.org/10.1093/ije/dyab109. Epub 2021 Aug 29. PMID: 34999878; PMCID: PMC8743124.

and when applicable,

3. NFBC1966 GWAS from the 31y follow-up samples has been described first time in

• Sabatti C, Service S:K, Hartikainen A-L, Pouta A, Ripatti S, Brodsky, Jones C.G, Zaitlen N.A, Varilo T, Kaakinen M, Sovio U, Ruokonen A, Laitinen ., Jakkula E, Coin L, Hoggart C, Collins A, Turunen H, Gabriel S, Elliot P, McCarthy M, Daly M.J, Järvelin M.R, Freimer N.B, Peltonen L. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet. 2009 Jan;41(1):35-46. Epub 2008 Dec 7. doi: 10.1038/ng.271

Cohort NFBC1986 Etsin-service

References to be used when referring to the NFBC1986 data collection in general (describing cohort in the material and methods section):

1. Use the NFBC1986 data reference

• In text: (University of Oulu, 1986)
• In the list of references: University of Oulu: Northern Finland Birth Cohort 1986. University of Oulu. http://urn.fi/urn:nbn:fi:att:f5c10eef-3d25-4bd0-beb8-f2d59df95b8e (in the given format, information on date accessed is not needed for permanent urn reference)

and one or two from

2. The study design and population of the NFBC1986 have been described in

• Järvelin MR, Elliott P, Kleinschmidt I, Martuzzi M, Grundy C, Hartikainen AL, Rantakallio P. Ecological and individual predictors of birthweight in a northern Finland birth cohort 1986. Paediatr Perinat Epidemiol. 1997 Jul;11(3):298-312. doi: 10.1111/j.1365-3016.1997.tb00007.x. PMID: 9246691.
• Järvelin MR, Hartikainen-Sorri AL, Rantakallio P. Labour induction policy in hospitals of different levels of specialisation. BJOG: An International Journal of Obstetrics & Gynaecology, 1993 100: 310-315. https://doi.org/10.1111/j.1471-0528.1993.tb12971.x

Publications with the national register data

In publications where the national register data have been used, the relevant register must be referenced. See instructions from the register owners www pages.

Acknowledgements

We wish to thank all cohort members, researchers and NFBC project center personnel who participated in the NFBC data collections.

Funding

NFBC data collections have received funding from different funding organizations at different follow-up timepoints. Below are listed the main funding received for the latest follow-up study of both cohorts. Please, indicate these in your publication when appropriate, and include your own research funding. Funding information regarding earlier follow-up studies can be found as part of the data collection description.

NFBC1966 46y follow-up study received financial support from University of Oulu Grant no. 24000692, Oulu University Hospital Grant no. 24301140, ERDF European Regional Development Fund Grant no. 539/2010 A31592.

NFBC1986 33-35y follow-up study received financial support from University of Oulu (Strategic funding from donations) and Oulu University Hospital (K65760). The oral health study was supported in part by the Research Council of Finland (former Academy of Finland, Grant no. 326189).

Ethics Committee Statement

Cohort 1966: Northern Ostrobothnia Hospital District Ethical Committee 94/2011 (12.12.2011)

Cohort 1986: Northern Ostrobothnia Hospital District Ethical Committee 108/2017 (15.1.2018)

(The current name of the committee: The regional medical research ethics committee of the Wellbeing services county of North Ostrobothnia)

Data Availability Statement

NFBC data are available from the University of Oulu, Infrastructure for Population Studies. Permission to use the data can be applied for research purposes via an electronic material request portal. In the use of data, we follow the EU general data protection regulation (679/2016) and the Finnish Data Protection Act.

The use of personal data is based on a cohort participant’s written informed consent in their latest follow-up study, which may cause limitations to its use.

Please, contact the NFBC project center (NFBCprojectcenter(at)oulu.fi) and visit the cohort website (www.oulu.fi/nfbc) for more information.