Biomarker Boosting

Better biomarkers through datasharing

Image: US Air Force (CC License)

The brain can store more information than a supercomputer. It can process a flood of information about the world around us by seeing, hearing, smelling, tasting, and touching. The brain has enabled humans to achieve breathtaking milestones — walking on the moon, mapping the human genome, and composing masterpieces of art, literature, and music. But brain disorders, in particular neurodegenerative diseases and mental illnesses, are also among the most prevalent and debilitating diseases of our time.

Neuroscientists are specialized in the study of the brain. Over the years, the neuroscience field has made enormous progress. Scientists continue to strive for a deeper understanding of the workings of the brain, and the causes of specific brain diseases.

By analyzing neuroimaging data, neuroscientists can find biomarkers (measurable indicator of some biological state or condition) that predict who is at risk of developing an illness. The volume of the hippocampus, for example, has huge potential as a marker for Alzheimer’s disease. The larger the sample size, the better the predictive value of the biomarker, which can be achieved by combining data sets obtained by different medical centers. This requires an eScience infrastructure for standardized image analysis, and the exchange of imaging data, meta-data, and analysis results.

The aim of the Biomarker Boosting project is to build a reusable platform for sharing patient (subject) imaging data among hospitals to run a common analysis pipeline. This considerably increases the number of datasets available for analysis, and therefore greatly improves the statistical value of the results.

The multidisciplinary team is developing tools and services for cooperative research in finding better biomarkers and demonstrating its potential by applying it to four different cohorts collected to study dementia and mild cognitive impairment (MCI). For this purpose a common catalogue (meta-data in which definitions of database objects are stored) is designed to allow for data exchange using web services, together with a template data sharing agreement to allow access to researcher-initiated consortia. The second focus is to implement a standardized image analysis pipeline to calculate biomarker features.

The product of the analysis pipeline is a set of low-dimensional properties derived from the high-dimensional images. These properties are called biomarkers, with ‘volume of the hippocampi’ as an example. The improved statistical power is called boosting, hence the title ‘biomarker boosting’.

This project will demonstrate progress in clinical neuroscience through the use of eScience by developing technologies to:

Participating organisations

Amsterdam University Medical Centers, location VU
Netherlands eScience Center
CWI
Erasmus University Medical Center
Life Sciences
Life Sciences
Maastricht University Medical Center+
Radboud University Medical Center
Radboud University Nijmegen
SURFsara
Utrecht University

Impact

Output

  • 1.
    The Biomarker Boosting project - unifying the hippocampus across scanners and protocols
    Published in 2015
  • 2.
    Digital Atlasing Infrastructure
    Author(s): Rembrandt Bakker
    Published in 2015
  • 3.
    The Biomarker Boosting project - unifying the hippocampus across scanners and protocols
    Author(s): Rembrandt Bakker
    Published in 2015
  • 4.
    Scalable Brain Atlas: towards online registration of user MRI data
    Author(s): Rembrandt Bakker
    Published in 2015
  • 5.
    Digital Atlasing Infrastructure
    Published in 2015
  • 6.
    Scalable Brain Atlas: towards online registration of user MRI data
    Published in 2015
  • 7.
    The biomarker Boosting project- data intergration across scanners and protocols
    Published in 2014
  • 8.
    The Biomarker Boosting use case
    Published in 2014
  • 9.
    Outcome of the workshop "Share and Florish, new standards for data sharing in the neurosciences"
    Author(s): Paul Tiesinga
    Published in 2014
  • 10.
    The Biomarker Boosting use case
    Author(s): Rembrandt Bakker, Marcel Koek
    Published in 2014
  • 11.
    Better biomarkers through datasharing
    Author(s): Elena Ranguelova
    Published in 2014
  • 12.
    Automated Analysis in Population Imaging
    Author(s): Marcel Koek
    Published in 2014
  • 13.
    The biomarker Boosting project- data intergration across scanners and protocols
    Author(s): Rembrandt Bakker
    Published in 2014
  • 14.
    Social aspects of data sharing across UMCs
    Author(s): Rembrandt Bakker
    Published in 2014
  • 15.
    Scalable brain atlas wih new registration services
    Author(s): Rembrandt Bakker
    Published in 2014
  • 16.
    Automated Analysis in Population Imaging
    Published in 2014
  • 17.
    Better biomarkers through datasharing
    Published in 2014
  • 18.
    Outcome of the workshop "Share and Florish, new standards for data sharing in the neurosciences"
    Published in 2014
  • 19.
    Scalable brain atlas wih new registration services
    Published in 2014
  • 20.
    Social aspects of data sharing across UMCs
    Published in 2014
  • 21.
    Frontiers | eScience Infrastructure for sharing neuroimaging data and running validated analysis pipelines on a high performance cloud
    Author(s): Piter de Boer
    Published in 2013

Team

PT
Paul Tiesinga
Principal investigator
Radboud Universiteit Nijmegen
RB
Rembrandt Bakker
PdB
Piter de Boer
RSE
Netherlands eScience Center
Elena Ranguelova
Elena Ranguelova
Technical Lead
Netherlands eScience Center

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