Apply for data access
The SCAPIS portal opened on March 17, 2021.
Apply hereThe first public release of data was on March 17, 2021. All researchers based in Sweden, or international researchers in collaboration with a researcher based in Sweden, are welcome to apply for data. Applications are to be submitted electronically on the SCAPIS portal (accessed via this website).
The SCAPIS recruitment phase, when data, bioimages and biological samples were collected from 30 154 individuals, was completed in the end of 2018. SCAPIS aims to gradually release these data resources for use in research in a form that is comprehensive, of high quality and easy to use.
The following are required to access SCAPIS data:
Connection to a research institution in Sweden
To apply for data, you have to be connected to a research institution in Sweden such as a university or a regional health care authority.
The responsible researcher must have a PhD
The researcher responsible for the project must have a PhD, but the application itself can be
registered and filled in by someone who does not have a PhD. In the case of an
approved application, however, it is always the responsible researcher who
ultimately receives and is responsible for data provided by SCAPIS.Approval from the Swedish Ethical Review Board
An approval from the Swedish Ethical Review Board (Etikprövningsmyndigheten) for the research project is obligatory before an application for data from SCAPIS. Obtaining the
ethics approval is the responsibility of the individual researcher or research
group. Individual ethics approvals are also necessary for researchers with their “own” local data generated within the SCAPIS project (“local sub-studies”). You can find the templates on Etikprövningsmyndigheten’s website.Specific wordings for applications
There are specific wordings that are recommended for inclusion in ethical applications concerning SCAPIS data. We strongly recommend reviewing these.
When applying for ethical approval for a study on national SCAPIS data, the common
core template for informed consent can be used.For local substudies, locally adapted versions of informed consent to the specific center -
Göteborg, Malmö, Linköping, Stockholm, Umeå, Uppsala - may be more appropriate.Finally here is a link to informed consent for the pilot study.
With regard to ethical approval, the SCAPIS office will review the following:
that the population described in the ethics application matches the population in the application to SCAPIS
that the project’s Principal Investigator is involved in the ethics application
that the organization responsible for the project (”forskningshuvudman”) which applies for data from SCAPIS is specified in the ethical application
that requested data is relevant to the project based on the description in the ethics application and the description in the project application
It must be stated in the ethical application that data from SCAPIS will be used
If register data are requested, this must be adequately described
Guarantee no overlap with SCAPIS core publications
Within SCAPIS, there are specific scientific topics that are of strategic importance and provide significant value to the SCAPIS cohort. These topics are defined and prioritized as core publications, and they will be coordinated by the SCAPIS team. Applications with similar research questions will not be granted data access during a limited time period.
A list of the core publications is available here.Data access board
When an application for data access requires a more thorough discussion and a decision
from scientific experts, the application is referred to SCAPIS Data access board.
The scientific members of the board are currently the following members of the SCAPIS National Steering Committee:Professor Göran Bergström, Director, University of Gothenburg (PI Gothenburg)
Professor Carl Johan Östgren, vice Director, Linköping University (PI Linköping)
Professor Gunnar Engström, Lund University (PI Malmö/Lund)
Co-authorship
The SCAPIS study is a Swedish multicentre collaboration between six host universities and university hospitals, and considerable time and resources have been invested to enable the completion of the study including more than 30,000 participants. In order to appreciate this collaboration, all scientific publications using the full SCAPIS cohort have hitherto included authors from all six host universities. It is important to continue to acknowledge this unique national collaboration within SCAPIS as well as endorsing these universities in future studies, also after the launch of the SCAPIS database as an open research resource. Accordingly, all forthcoming scientific publications based on the SCAPIS national database should acknowledge this national collaboration and include authors from all six participating universities. The applicant is obliged to invite one co-author from each host university to take part in the study. The invited host university co-author has the right to renounce co-authorship and contact the local PI to suggest a replacement. The Vancouver guidelines for authorship must be followed.
Return of new variables to SCAPIS
Researchers will be asked to return any new variables created from SCAPIS data or other SCAPIS resources to the SCAPIS database in a predefined format.
How to apply
Written instructions on how to apply
Access fee
An administrative fee will be charged before data sharing. The fee to access data for research from SCAPIS helps cover the project's running costs. Access fees are reviewed regularly. The costs are:
5 000 SEK + VAT per application for initiation of the application process. Please note that this initiation cost is mandatory for all applications even if the application is not approved.
An additional cost of 30 000 SEK + VAT for access to data including up to 250 variables. For access to data of more than 250 variables an extra cost of 100 SEK + VAT per variable applied for will be added. For access to a total of 950 or more variables, a maximum fee of 100 000 SEK + VAT is applied.
Access to register data provided directly by SCAPIS (in crude format, not derived variables) generates an additional cost of 10 000 SEK + VAT per selected register holder.
If a new linkage to an external register is requested, there is an additional cost of 12 500 SEK + VAT for one register (equivalent of 10 working hours). If linkage to more than one external register is requested, the cost will increase in proportion to the additional administrative efforts required. In addition, the other involved register holders will charge their fees.
Access to genotype data (genetics) generates an additional cost of 10 000 SEK + VAT up to 100 SNPs (single nucleotide polymorphisms). Extra SNPs, above 100, costs 100 SEK + VAT per SNP. For access to a total of 500 or more SNPs, a maximum fee of 50 000 SEK + VAT is applied.
The invoice will be sent from the SCAPIS Office after handling of the application and the case is closed.
Conditions for using SCAPIS data
SCAPIS is a collaborative project and a result of the hard work of many people and the
generous contributions of the study participants. To make best possible use of the data, the following conditions apply.Populations and data that is available
The SCAPIS study included a total of 30,154 individuals at 6 different sites (Göteborg 6,265 participants, Linköping 5,057, Malmö 6,251, Stockholm 5,039, Umeå 2,506, Uppsala 5,036). Of the 30,154 individuals, 14,646 were men and 15,508 women. In addition, a pilot study was conducted in Gothenburg the year before the main study started comprising 1,111 individuals. When applying, either the entire SCAPIS cohort can be selected or a selection based on one or more specific site/s. The pilot cohort can also be selected as a selection.
Data presently available is presented under the section "Data open for access". In the SCAPIS portal you can see the complete selection of all variables that are currently available. Available data comes mainly from the SCAPIS study's core surveys, i.e. surveys conducted on all sites. However, there is also some data from local sub-studies within SCAPIS that have been performed on some or all of the cohort participants at a particular site. Data from local sub-studies will be released gradually over time.
Please note that data applied for must not be used for prospective follow up analyses.
From application to data delivery
All information you need after having submitted your application can be found here.
In the SCAPIS portal you will see the complete selection of all variables currently available.
Available data originates mainly from the SCAPIS core examinations (all sites). There is also some data from local substudies within SCAPIS - local researchers that have performed an extra investigation on some or all of the cohort participants at a particular site. Data from local substudies will be released gradually over time.
Examination results
More than 1000 data points (variables) are open for access, covering areas such as:
Body measurements
General laboratory data: haemoglobin, triglycerides, HDL-, LDL- and, total cholesterol, glucose, HbA1cc, creatinine and high sensitivity C-reactive protein.
Extended laboratory data as biomarkers of cardiovascular disease (apolipoprotein A1, apolipoprotein B, lipoprotein A, troponin I, N-terminal pro b-type nauretic peptide, NT-proBNP), inflammation (α1-antitrypsin), liver disease (alanine aminotransferase, aspartate aminotransferase, gamma-glutamyltransferase), diabetes (insulin) and kidney function
(cystatin C).Blood pressure
Lung function measured by spirometry
Accelerometry data
Questionnaire data relating to dimensions central to the research aims
Data from structured radiologist judgement of CT images of the lung and heart.
Metabolomic and proteomic data (n=5000 from main study and n=1100 from pilot)
Register data
The register data can be accessed in two ways. Please note:
No prospective analysis is allowed using register data. When such applications can be accepted, this will be announced here at scapis.org and in the newsletter.
To access register data, specific and mandatory requirements apply regarding the ethics application.
1. Register data provided directly by SCAPIS
These register data will be shared pseudonymized.
The Swedish PrescribedDrug Register (Läkemedelsregistret)
The National Patient Register, Inpatients (Patientregistret slutenvård)
The National Patient Register, Outpatients (Patientregistret öppenvård)
The Swedish Medical Birth Register (Medicinska födelseregistret)
2. New linkages to external registers
The possibilityof implementing a requested register linkage will be considered on a case- by case basis. There may be formal or technical obstacles that result ina request being rejected.
Some register holders have long queues. We recommend that you do not submit your application to SCAPIS if the expected waiting time of the register holder is more than three months. You may then have to submit a new application and the application fee may increase.
Genetics data
The genotyping effort of SCAPIS has been completed at the SNP&SEQ Technology Platform in Uppsala, after DNA extraction from whole blood at Karolinska Institutet Biobank. The genotyping data holds very high quality and has been imputed using the HRC panel. If you wish to apply for genetic data, make sure to make it clear in your ethical applications that genetic analyses are planned. With this data, new avenues for research is opened up in SCAPIS, such as genome-wide association studies, genetic risk score analyses and Mendelian Randomization studies.
The available SNPs are listed in the files below. Around 700 000 SNPs for the directly genotyped data and 40 million for the imputed genotype data (around 10 to 15 million per file).
SCAPIS directly genotyped SNP list (zipped CSV, 6 MB)
SCAPIS imputed SNP list, Chromosomes 1-5 (zipped CSV, 156 MB)
SCAPIS imputed SNP list, Chromosomes 6-12 (zipped CSV, 153 MB)
SCAPIS imputed SNP list, Chromosomes 13-22 and X (zipped CSV, 121 MB)In the application form, on page 6D, you can also search for available SNPs. See the application guidance for details.
Biobank samples
At his point the following criteria must be fulfilled to access samples from SCAPIS Biobank:
Analyses need to be performed on the whole cohort of 30 000 participants
Results from the analyses must be returned to the data base to enrich SCAPIS data.
The ethical application must include text that makes it possible to share results via SCAPIS data service. Formulations are provided by the SCAPIS office.
The suggested project must be in line with the goals of SCAPIS and create a clear value.
Before approval to the ethics committee a preliminary application for access is sent to scapis@scapis.org and must contain:
Information about scientific questions to be answered
Planned analyses
Sample type(s) and volume needed
Plan for financing the project. Note that the financing needs to cover costs for withdrawal of samples at six biobanks, sample transports and costs for analyses.
The SCAPIS biobank advisory board decides whether the application will be accepted by SCAPIS.
After acceptance by the SCAPIS biobank advisory board and approval by the he ethical committee the PI can apply for access to data and access to samples. Instructions will be supplied by the SCAPIS office.
Data from local sub-studies & the pilot study
At present, it is possible to apply for access to data in the following local substudies.
All sites
AS01 - Environmental exposure (air pollution, noise, green areas&water). Yearly data for 2000-2018.Göteborg
LS01 - Submaximal aerobic fitness test
LS03 - Trail Making Test
LS02 - Uric acid
LS04 - Blood metals
Malmö
LS06 - Pulse wave analysis in the arteries
LS07 - Orthostatic blood pressure
LS08 - Advanced glycated endproducts
LS09 - Satisfaction with life scale
LS10 - Life Orientation Test – Revised
LS11 - Short Dental Questionnaire
LS22 - Blood cell count
LS23 - Uric acid
LS43 - Blood metals
Stockholm
LS27 - Survey on women´s health
Linköping
LS12 - Survey on women´s health
Uppsala
LS15 - Pets and cardiovascular risk
Umeå
LS50 - Cognitive Dysfunction
LS57 - Uric acid, UmeåThere are some restrictions on access to data in the SCAPIS database from local sub-studies. To gain access to data variables that belong to a local sub-study, approval of the sub-study responsible researcher is required. Data belonging to local sub-studies are marked in the Portal. Review of which data variables that are available and are interesting for your project is recommended already in the application planning stage. If any of the variables belong to a local sub-study, it is recommended that the responsible sub-study researcher is contacted in advance. For the SCAPIS pilot study, the same procedure applies. The responsible researcher is the PI for SCAPIS Gothenburg.
When applying for SCAPIS data
It is very important that you carefully read and follow the instructions and recommendations the SCAPIS project have presented on how to write the ethics application when applying for SCAPIS data. It can specifically be noted that to access register data, specific and mandatory requirements apply regarding the ethics application. All information you need to write the ethical application is available at scapis.org and can also be found here.
Identities and selection of population in obtained data
All data released from SCAPIS is disclosed in a pseudonymous form where each SCAPIS participant is represented by an ID unique to each data set. Population selection is possible based on study site, sex and smoking status. If you can send in a list with a predefined population (e.g. participants in a particular local sub study) it is possible to use this for selection as well. SCAPIS cannot offer selection of population based on other criteria or matching of SCAPIS participants to other populations. If we are able to offer this service, it will be announced in our newsletter and at scapis.org.
The complex task of building a management system for bioimages obtained in SCAPIS is ongoing.
Bioimages (computer tomography, ultrasound and magnetic resonance imaging) for the complete cohort will be available for sharing successively in 2023. For researchers interested in utilizing SCAPIS images in their research, SCAPIS welcomes proposals on an ongoing basis. Contact scapis@scapis.org with a brief proposal to establish a personal contact.
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