Prior experience with PDBP biological and omics data

danieltds
Mon, 03 Jul 2023 15:40:28 +0000
Accessing and Understanding Data

Hello everybody! My research team is trying to understand the PDBP dataset and the biological and “omics” data that come with it. However, as we have never had any previous experience with this dataset, I have some questions. We already have access to the dataset and are working with it. We found that the dataset has these information and downloaded it, but are having difficulties in making sense of what we are seeing.

1 - What types of “omics” data are available in this dataset? Urine? Blood samples?
2 - What types of CSF data are available in this dataset? Are there any biomarkers available?
3 - How can we find, queue, and download the aforementioned data?

Please, if you know ANY of the answers and could give us a hand, I would be delighted!

Additionally, for those who do not know what PDBP is, I will share some material I’ve prepared to teach my research team about the database. Please note if I write any inconsistencies.

What is PDBP
The Parkinson’s Disease Biomarkers Program (PDBP) is a consortium aimed at facilitating the discovery of laboratory and clinical markers in Parkinson’s disease. The project is funded by the National Institute of Neurological Disorders and Stroke (NINDS). The goal of PDBP is to build a longitudinal database of collected data and biological samples from well-characterized Parkinson’s disease patients at different stages and durations, as well as patients with parkinsonism and controls.

Differences between PPMI and PDBP
There are two main differences between PDBP and PPMI. The first is that PDBP consists of many different studies that share common elements and data collection (PPMI is a single study with a single protocol). Furthermore, the studies within PDBP are hypothesis-driven (for example, a study included in PDBP may already have a hypothesis regarding a specific biomarker it is studying and its relationship with the disease). In PPMI, there are no specific hypotheses, and the patients included were treatment-naïve, which is not necessarily the case in PDBP. At the time of the publication of the article explaining how PDBP works (I recommend reading it), 11 different studies in the United States were being funded to collaborate with PDBP, and as of June 2023, 73 studies comprised this group. Ultimately, PDBP proves to be quite useful as a replication for the data discovered in PPMI.

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