May 2nd, 2014: CEREBROSPINAL FLUID DATA POSTED TO PPMI
Dear PPMI community,
Data from the analysis of baseline CSF samples are now available on the PPMI study database. 1,266 CSF samples from all 666 PPMI (PD, Healthy subject, SWEDD) baseline visits and 300 longitudinal visits (6 and 12 month from those subjects who have reached their 12 month visit) have been analyzed for alpha-synuclein (α-SYN), Aβ1-42, total tau (t-tau), and tau phosphorylated at threonine 181 (p-tau) and data is now available on the PPMI website. These data are listed in the database as projects 110 (CSF Aβ1-42/t-tau/p-tau) and 111 (CSF α-SYN).
Be aware that the mean concentration values for a-SYN and Aβ1-42 obtained in the 2013 full-study are significantly higher and the p-tau values lower than the mean values obtained in the pilot CSF study (“Pilot Biospecimen Analysis Results Projects 101 and 103”–examining a subset of baseline CSF samples, the results of which were published in JAMA Neurology in 2013). After extensive assessment of pre-analytical and analytical procedures the Steering Committee believes the difference between the full baseline and pilot CSF analyses results are due to assay batch variability between 2011 and 2013 in these research assays. Please refer to the slide deck on the PPMI website entitled “PPMI CSF baseline analysis_Assay variability_April 2014” for more details.
Should you have any comments or questions regarding this study, please direct them to firstname.lastname@example.org. Thank you for your interest in the PPMI study.
The PPMI Steering Committee
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.
PPMI Data: Raw Whole Exome Sequencing Data
Whole Exome sequencing was performed on whole-blood extracted DNA samples (details may be found in the Exome Sequencing Methods document available in the Genetic Data Download section of the PPMI database). Genomic VCF (gVCF) data files generated from the exome sequencing process are currently available for download by authorized PPMI investigators from within the PPMI database. PPMI also makes available the raw BAM and FASTQ 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: BAM files will require approximately 15TB 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” to email@example.com. This form is availablein the Genetic Data Download section of the PPMI database. Data requests willbe 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.
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.
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.