ASAP launches data-sharing tool with unique dataset of human postmortem-derived brain samples
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ASAP launches data-sharing tool with unique dataset of human postmortem-derived brain samples

This blog was written by Sonya Dumanis, PhD, deputy director of ASAP, and the following Michael J. Fox Foundation for Parkinson’s Research staff: Bradford Casey, PhD, Kate Trimble, MSc, Dave Alonso, and David Kumbroch. 

Postmortem human brains are critical for the study of neurodegenerative diseases like Parkinson’s disease (PD). Donated patient brain samples are a precious resource, and their rarity is matched by a desire to ensure that each brain can be thoroughly studied. Aligning Science Across Parkinson’s (ASAP) recognizes that the ability for researchers to thoroughly study the brains by building upon the initial findings is only as strong as their ability to analyze the original data.

To address this challenge, ASAP worked with The Michael J. Fox Foundation for Parkinson’s Research, Verily, DNAstack, and DataTecnica to develop a data-sharing tool, called the ASAP CRN Cloud, which is now available to the entire research community – complete with a new, high-value dataset of human postmortem-derived brain samples to analyze.

This cooperation is empowered by the ASAP Collaborative Research Network (ASAP CRN), an international, multidisciplinary, and multi-institutional network of scientists working to address high-priority basic science questions at the heart of PD. Across the CRN, our teams are processing data that collectively leverages over 600 donated human brains.

Unique Data

The ASAP CRN Cloud launched in June 2024 with data from a human postmortem-derived brain sequencing collection, including samples from four CRN teams around the world. In the first release, there will be over 156 donors contributing to the datasets. There will be a consistent cadence of new data releases, with 629 donors contributing to the final harmonized dataset.

The ASAP CRN Cloud platform gives researchers the tools to explore data all the way down to the individual cell level. The collection contains single-cell transcriptomic data that allow each cell to be independently characterized and scrutinized for which genes are active or “expressed” in each cell type to better understand what goes wrong in neurodegeneration. This approach has already provided critical insight in many diseases, including cancer, where the ability to study adjacent cancerous and healthy cells has provided new insights into how cells go awry, and how they can be detected or targeted. Nowhere has this approach been more eagerly awaited than in the analysis of the brain, where the diverse cell types, complex structures, and subtleties of pathology can only be observed after death. 

Collaborative Platform

The ASAP CRN Cloud platform uses advanced technologies from multiple partners to ensure researchers all over the world can access, analyze, and share findings on this and other unique datasets to be hosted on the platform.

Single cell transcriptomic data provides a durable resource in the form of vast amounts of information that can be analyzed and re-analyzed by different teams. This data comes at a cost, however. While scientific manuscripts are effective for sharing images, graphs, figures, and discussion, the sharing of big data sets (>10 TB) requires more than a journal article can support. In response, ASAP worked with partners to produce a data-sharing platform that could stand up to the demands of neuroscientists all over the world. 

  • DataTecnica’s technology contributes to analysis from pre-processing to annotation, ensuring datasets are harmonized and high-quality. 
  • DNAstack provided a data platform which allows for data to be stored securely within a cloud environment while still being accessible to the broader research network – a technique called data federation.
  • Verily Viewpoint Workbench creates a collaborative environment where scientists worldwide can access, analyze, and share data. Combining the data, governance, and analytic resources in a globally shared platform democratizes the data, enabling and empowering a vibrant global research community unconstrained by local resources. 

The technologies interweave to allow scientists to conduct analysis, share data, and contribute findings in a single platform.

Open Science 

Open science does not simply depend on data sharing, but on building responsible open-access data and resources to amplify the impact of every contribution across the research community. Data from a single donor may inform a team’s work, but when combined and shared broadly, it may provide a critical case to test an unrelated hypothesis, strengthen a small study, or elucidate a crucial hidden link to disease. 

The ASAP CRN Cloud platform was developed as a purpose-built solution to enable just this type of collaboration. Leveraging shared storage and analysis software already in use by research teams in their own labs, the CRN Cloud brings resources from across the network to a single platform, enabling researchers to share, access, and work directly with other leading experts to distill discoveries, offering the potential for unprecedented insights into neurodegeneration.

From the transcriptomic data of a single brain cell to the massive, federated data network, ASAP continues to bring information and partners together in service of reducing barriers to data access and advancing Parkinson’s disease research.