The Accelerating Medicines Partnership: Parkinson's Disease and Related Disorders (AMP-PD) is a National Institutes of Health (NIH)-sponsored program designed to host and share resources related to Parkinson's disease research. The initiative aims to accelerate biomarker discovery and advance the development of disease-modifying therapies.
The program is part of the broader Accelerating Medicines Partnership (AMP), described as a US$360 million NIH-industry collaboration involving multiple pharmaceutical companies and academic institutions.
"Collaborating toward biomarker discovery to advance the development of Parkinson's disease therapies"
The AMP-PD portal provides access to multiple harmonized data types:
- Whole Genome Sequencing (WGS): From whole blood using Illumina XTen, aligned to Human Genome hg38
- Postmortem Sequencing Data: Brain tissue sequencing from deceased donors
- RNA-Seq: From whole blood using Illumina NovaSeq, aligned to Gencode v29
- Targeted Proteomics: Olink Explore panels from cerebrospinal fluid (CSF) and plasma
- Untargeted Proteomics: Using Orbitrap Exploris platform
- Demographics
- Medical history
- MDS-UPDRS scores
- MoCA (Montreal Cognitive Assessment)
- UPSIT (University of Pennsylvania Smell Identification Test)
- Single nucleus RNA sequencing from postmortem brain tissue
AMP-PD harmonizes data from eight major cohort studies:
| Cohort |
Description |
| PPMI |
Parkinson's Progression Markers Initiative - longitudinal PD study |
| PDBP |
Parkinson's Disease Biomarkers Program |
| BioFIND |
Parkinson's Disease Biomarkers Discovery Initiative |
| LBD |
Lewy Body Dementia cohort |
| HBS |
Harvard Biomarkers Study |
| STEADY-PD3 |
Study of Asenapine and Glyburide in PD |
| SURE-PD3 |
Safinamide Study |
Additionally, the portal includes Postmortem Brain Cohort data, bringing the total to approximately 10,908 participants.
- The data portal contains de-identified information from approximately 4,298 Parkinson's patients and healthy control subjects in the unified analysis dataset
- Data is harmonized across multiple cohort studies including PPMI, PDBP, BioFIND, LBD, and others
- Longitudinal Data: Many participants have multiple timepoints enabling longitudinal analysis of disease progression
AMP-PD employs rigorous data harmonization protocols to ensure cross-cohort compatibility:
- Alignment Standards: All WGS data aligned to Human Genome hg38 using BWA-MEM
- Variant Calling: GATK best practices for SNP and indel identification
- Quality Control: Strict filtering for coverage depth and variant quality scores
- Harmonized Phenotypes: Unified clinical variables using common data elements (CDEs)
- Olink Panels: Standardized protein panels across all cohorts
- Batch Effect Correction: Statistical correction for technical batch effects
- Control Normalization: Protein levels normalized to internal controls
AMP-PD has enabled numerous biomarker discovery studies:
- α-Synuclein Biomarkers: Development of α-synuclein seeding assays
- Neurofilament Light Chain (NfL): Blood-based marker for neurodegeneration
- Genetic Risk Scores: Polygenic risk scores for PD susceptibility
- Expression Biomarkers: Gene expression signatures distinguishing PD subtypes
The dataset supports therapeutic development:
- Target Expression: Validation of drug targets in relevant patient tissues
- Clinical Trial Enrichment: Identification of patient subgroups for targeted trials
- Natural History Studies: Understanding disease progression patterns
- GWAS Meta-Analysis: Large-scale genome-wide association studies
- Rare Variant Discovery: Identification of rare pathogenic variants
- Gene-Environment Interactions: Analysis of lifestyle factors and genetic risk
- Register for access through the AMP PD Knowledge Portal
- Accept the Data Use Agreement
- Terra Platform: Cloud-based research workspace (https://app.terra.bio/)
- Google Cloud Platform: BigQuery for untargeted proteomics data
- Researcher Workbench: Pre-configured Jupyter notebooks in R and Python
- Jupyter notebooks that can be cloned and edited
- Example notebooks demonstrating data retrieval methods
- SmartConverter Data Curation tool
- Visualization tools
- PPMI - Parkinson's Progression Markers Initiative
- BioFIND - Parkinson's Disease Biomarkers Discovery Initiative (page pending creation)
- Parkinson's Disease - Parkinson's Disease