Introducing the Netherlands Neurogenomics Database (NND) website, a joint effort between the Netherlands Brain Bank (NBB) and the University Medical Center Groningen (UMCG). The goal with the NND-website is to offer convenient access to meticulously processed and refined clinical-pathological summaries derived from NBB donors. This resource aims to foster collaborative research across various neurodegenerative and psychiatric diseases by facilitating cross-diagnostic investigations. Our platform encompasses a diverse array of features, including advanced filtering options and visualization tools that parallel the approaches employed in our most recent publication (Mekkes et al., 2022).



The Holtman Lab


The NND is part of the Holtman Group. Click the button below to visit the Holtman Lab website.


Disclaimer


Please be aware that the figures and statistics provided on this website are meant for exploratory purposes and should not be solely relied upon for definitive conclusions. Users are advised to independently verify and interpret any findings obtained from this website and exercise their own judgment and expertise when making decisions based on the data presented here.

Website version 1


Filter results:

Datasets

Do not forget to press apply filters before creating a dataset.

View data

This tab shows the data after filtering. It is possible to view individual donors by clicking on a donor ID.


Select the data that you would like to download:

There are no datasets made, view the sidebar for more information.
No data to plot

Please create a dataset to view basic visualisations

Observation count distribution:

This violin plot illustrates the distribution of the number of observations for a specific attribute across multiple datasets. In addition, the heat map displays the -10log(FDR(corrected(p-value))) values to represent statistical significance of the pairwise comparisons.

Temporal manifestation:

The temporal plot showcases the distribution of the age at which specific attributes were observed across multiple datasets. It provides insights into the chronological pattern of attribute observations. Additionally, the heatmap represents the -10log(FDR(corrected(p-value))) values highlighting significant differences in attribute observations across the datasets.

Survival distribution:

This violin plot represents the survival distribution in years following the first manifestation of a specific attribute across multiple datasets. It provides insights into the duration of survival after the initial occurrence of the attribute. Additionally, the heat map displays the -10log(FDR(corrected(p-value))) to indicate the significance levels between the datasets, specifically in pairwise combinations.

Donor information

Donor ID:
Age:
Sex:
Main diagnosis:

Post mortem delay (hours:minutes):
PH:
Braak NFT/NT:
Braak aB:
Braak Lewy:

Clinical History Timeline


Rules of thumb

The timeline scale represents the duration in years leading up to the event, measured from the year of an individual's death.

General

Sensory/autonomic

Motoric

Psychiatric

Cognitive

General

Sensory/autonomic

Motoric

Psychiatric

Cognitive

Click on an event to see details.




The default_value is selected.

Within the NND Ontologies

Clinical Disease Trajectories: This ontology captures the disease trajectories of the clinical data within the NND.

Main Diagnosis: This ontology focuses on the main (Neuropathologically defined) diagnosis associated with each donor.

Modified Human Disease Ontology (version 03/31/2023): The modified version of the Human Disease Ontology utilized in the NND offers a structured and standardized vocabulary for categorizing and describing diseases within the database.

These ontologies play a crucial role in organizing and structuring the meta-data within the NND, enhancing the understanding and interpretation of the information contained in the database.


Version 1.0


Version 1.0

Version: 03-31-2023

MS-database

This page contains a download link for the input and (anonymised) validation datasets used in our paper on dimensions of MS neuropathology, published in Acta Neuropathologica (i.e. Online Resource 2). In addition, there is a link to download the scores of NBB MS donors on the independent neuropathological dimensions (i.e. Online Resource 3), which could serve as a starting point for further disentanglement of MS heterogeneity.

See more
Bootstrap Sidebar

Tutorial

This page contains basic information about the tutorial.

About

In 2020, the Netherlands Neurogenomics Database (NND) project was established through a collaboration involving Dr. IR Holtman, Prof. M Swertz, Prof. A Rozenmuller, Dr. J Hamann, Prof. HWGM Boddeke, Prof. BJL Eggen, and Prof. I Huitinga. This project received funding from the 'Vrienden of het Herseninstituut'.

The primary objective of the NND project is to transform the extensive clinical and neuropathological information available from the Netherlands Brain Bank (NBB) into standardized assessments of clinical and neuropathological traits. Additionally, the project aims to augment this framework by incorporating genotype and multi-omics data types. The ultimate goal is to make these comprehensive datasets openly accessible to the scientific community to facilitate cross-diagnostic research.

The NND integrates clinical, neuropathological, and genetic data from over 3200 donors diagnosed with neurodegenerative and or psychiatric conditions. Utilizing machine learning techniques, the project generates clinical disease trajectories and assessments of neuropathological traits. The genotype information is obtained using the Global Screening Array, and this data is combined to calculate Polygenic Risk Scores (PRS) for various Central Nervous System (CNS) disorders and traits. The project seeks to unravel underlying patterns within subtypes of these diagnoses or identify symptoms that are comorbid across two or more disorders. By providing standardized donor and tissue characteristics, including genetic information, the project enables researchers to conduct further analysis and aids in interpreting and understanding the mechanisms by which genetic variants contribute to brain diseases.

Pseudonymization of NBB donors

To safeguard donor confidentiality, the NBB has implemented a de-identification procedure, and additional measures have been taken within the NND to further anonymize donor information. These steps include:

Implementation of new random donor identifiers

The NND utilizes new random donor identifiers that do not contain the year of death. For example, a donor identifier such as NBB-2020-111, could now be converted to NND 39-PAE (not actual donor). This change ensures that the donor identifiers do not provide any direct indication of the year of death.


Age of Death Interval

The age of death has been adjusted to a 5-year interval. For example, if someone died at the age of 78, the age of death window in the NND would be represented as 75-79. This interval-based approach ensures that the precise age of death is not explicitly disclosed.


Rare diagnoses and rare combinations of diagnoses

Neuropathological Diagnoses fewer than 10 donors were added to the parent in the ontology. Also, rare combinations of diagnoses which with fewer than 10 donors were placed in the double diagnosis category.


These measures have been implemented to enhance donor confidentiality and protect the privacy of donors of the NBB.

Acknowledgements


We gratefully acknowledge the invaluable support received from the following organizations for their contributions to the NND:

...
Vrienden van de hersenstichting

The "Vrienden van de hersenstichting": We express our deep appreciation for their support and funding, which has been instrumental in advancing the NND project.

See more

...
Rosalind Franklin Fellowship

The Rosalind Franklin Fellowship from the University Medical Center Groningen: We extend our gratitude for this fellowship, which has provided essential resources and opportunities for the development and progress of the NND.

See more

...
The ERC Starting Grant

We acknowledge with gratitude the support received from the ERC Starting Grant, which allows us to study the transcriptional landscape of neuronal cell types of psychiatric disorders.

See more

...
Netherlands Brain Bank

We are incredibly grateful for the invaluable support provided by the Netherlands Brain Bank, as they serve as the indispensable source of our research data. Their unwavering dedication and contribution to our work are genuinely appreciated.

See more
We would also like to express our profound gratitude to all the current and future donors of the NBB and their families. We recognize and appreciate the immense act of courage and generosity displayed by these donors, as their contributions have been crucial in advancing our understanding of neurological and psychiatric disorders. Their selfless commitment to scientific research has laid the foundation for improving the lives of individuals affected by these conditions.

Contributors

Development Team

Development Team

Eric Hoekstra1, Sander Bouwman1, Nienke Mekkes1,2, Minke Groot3, Inge R. Holtman1,2,3

Steering Committee:

Inge R. Holtman1,2,3, Annemieke Rozemuller3, Erik Boddeke1, Jorg Hamann3, Bart Eggen1, Inge Huitinga3

Affiliations:

  1. Section of Molecular Neurobiology, Biomedical Sciences of Cells and Systems, University Medical Center Groningen, Groningen, The Netherlands
  2. Data Science in Health (DASH), University Medical Center Groningen, Groningen, The Netherlands
  3. Netherlands Brain Bank, Institute for Neuroscience, Amsterdam, The Netherlands

References

Reference 1 Image
De Boer et al., MedArxive, 2023

Identification of neuropathology-based subgroups in multiple sclerosis using a data-driven approach

Read More
Reference 2 Image
Mekkes et al., MedArxive, 2022

Natural language processing and modeling of clinical disease trajectories across brain disorders.

Read More
Reference 3 Image
Klioueva et al., 2017

Banking brain tissue for research

Read More