Access Data & Specimens

 

Accessing PPMI Data & Specimens

A primary goal of PPMI is to develop a large and comprehensive set of correlated clinical data and biospecimens that will be made available to the entire scientific community to help accelerate biomarker verification research. This section of the study site serves as the central hub for academic and industry researchers to download de-identified data and request specimens collected in the study.

PPMI data and specimens have been collected in a standardized manner under strict protocols developed by the steering committee. Click here to review the PPMI Research Documents and SOPs that have been developed to guide PPMI Clinical Sites in data and specimen collection.

PPMI Data: Clinical, Biomarker, Imaging and Related MetaData

The PPMI study dataset includes clinical, biological and imaging data collected at PPMI clinical sites. The data have been aggregated into the PPMI study database, which is managed by the PPMI Bioinformatics Core, the Laboratory of NeuroImaging (LONI) at the University of Southern California.

Download PPMI Data

PPMI Data: Raw Whole Exome and Genome Sequencing Data

Whole exome and genome sequencing were performed on whole-blood extracted DNA samples (details may be found in the Exome Sequencing and Genome Sequencing Methods documents available in the Genetic Data Download section of the PPMI database). Genomic VCF (gVCF) data files generated from the exome and genome sequencing processes are currently available for download by authorized PPMI investigators from within the PPMI database. PPMI also makes available the raw data files. However, due to the size of these files, they cannot be reasonably distributed over the Internet. Investigators interested in obtaining data in BAM and/or FASTQ format may submit a request for these data to be shipped on sets of loaner external drives. Note: Whole Exome Sequencing BAM files will require approximately 15TB of disk space and FASTQ files 130 GB of disk space. Whole Genome Sequencing FASTQ files will require approximately 70 TB of disk space.

Investigators requesting FASTQ and/or BAM files must have an active PPMI database account and submit a PPMI Whole Exome Sequencing Data Agreement, and/or PPMI Whole Genome Sequencing Data Agreement to ppmi@loni.usc.edu. These forms are available in the Genetic Data Download section of the PPMI database. Data requests will be filled in the order received. LONI will contact you when the hardware becomes available to verify shipping information. The hardware must be returned within 3 weeks of receipt.

PPMI Samples: Biologic Specimens

Biologic specimens collected through PPMI include urine, plasma, serum, cerebrospinal fluid, DNA and RNA. An inventory of collected specimens available for research purposes is available in the PPMI study database. Researchers may apply for access to stored samples, which are housed in the study’s biorepositories in the US, Italy and Israel.

Access PPMI Samples

For further information about the PPMI specimens, visit the Data & Specimens FAQ.

PPMI Samples: Cell Lines

Fibroblasts and iPSCs were generated from skin biopsies from 20 PD subjects and 5 healthy controls at one US PPMI site through a pilot sub-study with the New York Stem Cell Foundation (NYSCF). In 2016, PPMI expanded to generate iPSCS from blood-based collection from a subset of US sites through the Golub Capital iPSC PPMI Sub-study with Cellular Dynamics International (CDI). The sub-study with CDI aims to collect blood for iPSC generation from PPMI subjects across all study arms. Researchers may apply for access to stored cell lines, which are housed in the study’s biorepository at Indiana University.

Access PPMI Cell Lines

Analysis of PPMI Data and Samples

The PPMI Steering Committee has already identified preliminary analyses that will be conducted on the PPMI data by the study cores. Other investigators are strongly encouraged to access the study data and specimens to conduct their own analyses. To keep the scientific community apprised of analyses being completed by all investigators who are using PPMI data and specimens. A list of Ongoing Analyses has been compiled here.

 Request Specimens
 Download Data
 Data & Specimens FAQ

Months ScBL369121824303642485460728496108120132144156
Biospecimens
CSF12958504979480636191464236379140612
DNA13071119305574162151468655458362565055853526931517630
RNA11907692118562412801160123995688079974961259129933718830
Plasma11917693118563112821160124095388479774661259030033618830
Serum11910692119062812791154123495087779374160358929933118729
Urine425466133224731373643131422519027
Whole blood11739590111656812111109118491384878173961058929733118530
Months ScBL369121824303642485460728496108120132144156
PD
CSF4064252306129322842381194758735
DNA41146421581352042572932702712382179815
RNA42538528233036336836036335634934330631226823310315
Plasma42338727833536336636236536134834230531026923210315
Serum42338528333436236835936435834833930430926822710214
Urine21471941119321115921610613
Whole blood34033525030533033833334334734433630530926522810215
Months ScBL369121824303642485460728496108120132144156
SWEDD
CSF6044473811111
DNA6972912233332
RNA64575355575856113233333
Plasma64575355575856113233333
Serum64575355565856113233333
Urine14531012332
Whole blood54504749515348113233333
Months ScBL369121824303642485460728496108120132144156
Health Control
CSF18641601531136129110810535237
DNA2082141127344610213014314119957615
RNA195189179180184175171164166165162153152191018215
Plasma198188182181183177170163164165162154152191018215
Serum197189184179184176167163160162159148152191018215
Urine2256920271467168214
Whole blood135152156158161165157147151155161153152201008015