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["@amppd"].
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["@accelerating"].
Mission
"Collaborating toward biomarker discovery to advance the development of Parkinson's disease therapies"
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Introduction
Overview
Mermaid diagram (expand to render)
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["@amppd"].
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["@accelerating"].
Mission
"Collaborating toward biomarker discovery to advance the development of Parkinson's disease therapies"
Data Types Available
The AMP-PD portal provides access to multiple harmonized data types:
Genomics
Whole Genome Sequencing (WGS): From whole blood using Illumina XTen, aligned to Human Genome hg38
Postmortem Sequencing Data: Brain tissue sequencing from deceased donors
Transcriptomics
RNA-Seq: From whole blood using Illumina NovaSeq, aligned to Gencode v29
Proteomics
Targeted Proteomics: Olink Explore panels from cerebrospinal fluid (CSF) and plasma
Untargeted Proteomics: Using Orbitrap Exploris platform
Clinical Data
Demographics
Medical history
MDS-UPDRS scores
MoCA (Montreal Cognitive Assessment)
UPSIT (University of Pennsylvania Smell Identification Test)
Single Nucleus Data
Single nucleus RNA sequencing from postmortem brain tissue
Cohorts
AMP-PD harmonizes data from eight major cohort studies:
| Cohort | Description | |--------|-------------| | [PPMI](/datasets/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.
Key Statistics
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
Data Harmonization Process
AMP-PD employs rigorous data harmonization protocols to ensure cross-cohort compatibility:
Genomics Harmonization
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)
Proteomics Harmonization
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
Research Applications
Biomarker Discovery
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
The following diagram shows the key molecular relationships involving AMP-PD: Accelerating Medicines Partnership: Parkinson's Disease and Related Disorders discovered through SciDEX knowledge graph analysis: