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GAPS

The overall goal of the Genomic Aggregation Project in Sweden (GAPS) is to gather genetic data from Swedish subjects with and without complex genetic diseases in a single location to be processed and analyzed in a standardized way. Standardization enables investigations of individual data collections and cross-disease comparisons to further our understanding of biomedical conditions.

This is team-science! Multiple groups make critical contributions, and we have 40 member groups so far. Briefly stated, we can do more together than separately.

In the last decade, genome-wide association studies (GWAS) have evolved from small studies of few hundreds of subjects to global consortia with hundreds of thousands of subjects. This has dramatically improved power and has yielded large numbers of genetic associations for many human traits (e.g., type 2 diabetes, many cancers, cardiovascular disease, schizophrenia, Crohn’s disease, height, and educational attainment). While tremendous advances have been made by combining samples, genetic heterogeneity across populations continues to hinder these efforts.

Sweden has a relatively homogeneous population and comprehensive national registers of health, environmental exposures, and demography. There are Swedish GWAS for many diseases and traits: we estimate that there are now GWAS data on >200,000 Swedes. Recruiting research subjects, drawing blood samples, purifying DNA and genotyping are time and labor-intensive and demand a large portion of research budgets. This consortium allows researchers to skip these steps, offering a fast and cost-effective route to increase the numbers of subjects available for large genetic studies in Sweden. A Swedish GWAS “meta-consortium” offers many potential benefits, and GAPS aims to maximize these possibilities.

Scientific Aims

  • Use genomics directly to improve public health
  • Aggregate existing individual SNP array data from Swedish subjects
  • Use the “UNICORN” framework to estimate national SNP frequencies, to develop a synthetic, Sweden-specific control group
  • Develop a fine-grained understanding of population history of Sweden
  • Explore capacity to impute new HLA haplotypes
  • Perform new GWAS of variables common to datasets
  • Improve genetic risk scores
  • Electronic medical record research (e.g., rare adverse drug reactions)
  • Create a Sweden-specific imputation reference, return imputed dosages to participants
  • Identify human “knockouts” for key genes

Ethics

The GAPS consortium, including the proposed research aims, have ethical approval from the regional ethics board in Stockholm (approved in Dec 2016). In addition, each individual study included in GAPS has a separate ethics approval, and participants have provided informed consent. In the GAPS database, we track allowable uses for every subject, and we specifically confirm this with each GAPS Principal Investigator. The privacy and rights of participants in our studies are central to our mission. We are deeply grateful to all individuals who are willing to share information about themselves to help us further the world’s understanding of complex diseases and traits.

Conferences

Hässelby Slott 16-17 February 2017 (agenda)

Interested in joining?

  • GAPS is democratic, participatory, & modern genomics consortium
  • Principles of collaboration are codified in our memorandum of understanding (MOU)
  • Study representatives form a management group to guide all activities
  • The aims require sharing of individual genotype and phenotype data within GAPS. This occurs by secure transfer to UPPMAX. Study data will never be moved from the secure analysis server.
  • PIs retain control of their data. Study data will only be used for analyses that PIs agree upon. You can be part of some analyses and not others.
  • Study data can be withdrawn at any time. If a PI wishes, their data will be erased within 24 hours & removed from any on-going analysis
  • Processing uses an existing, high-throughput pipeline that has processed GWAS data from N~1,000,000
  • Following standardized QC, data are imputed to the best current reference (i.e., using genome sequencing results from SciLifeLab)
  • We will return cleaned and imputed genetic data to PIs for use for any purpose without restrictions
  • PIs also stand to benefit from greater power for primary analyses and the ability to propose new analyses

Please e-mail Sarah Bergen for more information or to join GAPS.

Documents for GAPS members

Allowable uses and register linkage form

Phenotype acquisition

Contact

Sarah Bergen

Senior researcher

Anna Kähler

Project manager

Our team for data processing and analysis consists of: Robert Karlsson, Johan Källberg, Amir Sariaslan, Kaarina Kowalec, Julien Bryois, Lu Yi, and Alexander Viktorin.

The GAPS Scientific Advisory Board is comprised of: Daniel McArthur (Harvard/Broad Institute, USA), Jeff Barrett (Sanger, UK), and Goncalo Abecasis (University of Michigan, USA)

GAPS publications

National-scale precision medicine for psychiatric disorders in Sweden.
Bergen SE, Sullivan PF
Am. J. Med. Genet. B Neuropsychiatr. Genet. 2018 Oct;177(7):630-634