AMP PD Research Plan

AMP PD Research Plan Summary

Starting in January, 2018, the AMP PD program was created to identify and validate diagnostic, prognostic, and progression biomarkers in order to improve clinical trial design, patient stratification, monitoring of disease progression, and contribute to the identification of new pathways for therapeutic development. The AMP PD effort is organized into three (3) primary stages:

  • Stage 1: Focusing on the harmonization of clinical data across multiple cohorts to CDISC standards, establish the AMP PD Knowledge Platform to handle existing WGS, RNA seq, and clinical datasets, utilize existing pipelines from ongoing large scale -omics projects, and analysis of whole transcriptomics from 7,700 longitudinal blood-derived RNA samples.
  • Stage 2: Pursue additional large-scale biomarker discovery (exRNA, proteomics, metabolomics) on 2,200 matched CSF and Plasma samples and single cell RNA seq analysis from 2 regions in 200 brains.
  • Stage 3: Dissect new targets and disease subtypes; track and predict disease progression.

Research Plan Timeline

  1. Stage 1 (Began January 2018, 0-18 months)
    • Establish Working Groups

      Data working group will be the central organizing unit of WGs:

      1. Transcriptomics - Policies
      2. WGS-Portal-Clinical Data Harmonization
    • Develop operation and data processing SOPs
    • Harmonization datasets

      Participant Type: 3,000 PD cases & 1,000 controls
      Biosamples: 3,313 CSF, 15,430 RNA, 10,392 Plasma, 4,000 DNA, and PBMCs

      1. PPMI (MJFF)
      2. PDBP HBS, BioFIND, Verily
    • Launch AMP PD Knowledge Portal (Beta Version)

      Includes: Clinical data, WGS, and RNA Seq

  2. Stage 2 (12-48 months)
    • Adaptive Design
      Current Stage/Status

      Strategy development for finalizing Stage 2 data: Plasma & CSF

    • Platform Analysis
      1. Extracellular RNA (exRNA) seq
      2. Proteomics (targeted and unbiased)
      3. Metabolomics (TBD)
      4. Methylome study (TBD)
    • Brain Platform

      Feasibility Study -- identification of brain samples for scRNA seq and epigenome analysis

      1. RFA(s)/Contracts/Prize Challenge
  3. Stage 3 (36-60 months)
    • RFA(s)/Contracts/Prize Challenge
      1. Longitudinal cohort analysis of successful platforms from Stage 2
      2. RFA for data analysis, tool development, disease modeling
    • NINDS Clinical Trial Data
      1. Add data from 2 Phase III clinical trials to AMP PD knowledge portal
      2. WGS
      3. Plasma samples