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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When I have bandwidth in a few weeks, I would love to help figure this out
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@danieltds , I don’t have a lot of personal experience with PDPB, but in case you haven’t taken a look, would draw your attention to AMP-PD (which I haven’t worked with firsthand) but includes PDPB data harmonized with BioFIND, HBS, LBD, LCC, PPMI, STEADY-PD3 and SURE-PD3 data.
More info here: https://amp-pd.org/data and https://amp-pd.org/unified-cohorts/pdbp
That said, I’m sure @fbbriggs 's firsthand experience will be more helpful 
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I forgot to reply to you, Josh, but thanks for your suggestion! Also, I do not have much experience with AMP-PD, and I haven’t accessed it yet. I think I will have to study this dataset more. Initially, I didn’t use it because I thought the harmonization technique might have left out some common information that is also of my interest and that I know both PPMI and PDBP have (such as MRI), but I’m definitely not certain about that and I have to learn more. Nonetheless, thanks!
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The ClinTrials.gov page for PDBP has some helpful information about enrollment and exclusion/inclusion criteria, and so does the PPMI page. I find these useful when I want to get a feel for a cohort.
To answer points 1 and 2 - there’s an overview of data types on the PDBP analyte data page.
1 - There are transcriptomics, NeuroX genotyping, proteomics, and metabolomics data for the blood samples, and it looks like a small subset of CSF samples as well for some assays.
2 - There’s a-SYN, tau, beta-amyloid, DJ-1, C-Reactive Protein, IL-6, and others available from the CSF data.
3 - It’s been a bit since I’ve accessed PDBP separately outside of AMP PD, but I did make an account 2-3 years ago. You can register separately for PDBP data or access it through AMP PD as @jgottesman mentioned.
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@ehutchins, I think the clinicaltrialgov site is showing one of the studies at PDBP (possibly this: PDBP-STUDY0000255. At DMR site. there are 40+ studies are in the repository. Some are cross-sectional, some are longitudinal, some are public, some are private. some only recruited PD families, some recruited MSA, PSP…
AMP-PD did really great job harmonizing these into the other major studies so accessing through AMP-PD is most straight forward if your data of interest is available there.
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Thanks @hirotaka ! Those are good points about the different studies for PDBP and AMP PD is great way to access the data.