# Integrative Analysis and Visualization of AMP-PD Transcriptomic Data

> **NIH NIH U01** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2020 · $441,149

## Abstract

ABSTRACT
The private/public Accelerating Medicine Partnership in Parkinson's disease (AMP PD) is the culmination of an
effort to bring together four major studies into a common computational environment for analysis of uniformly
profiled molecular data and harmonized clinical data. AMP PD includes over 8,300 RNA samples on over 4,200
whole-genome sequenced individuals participating in the NINDS Parkinson's Disease Biomarkers Program
(PDBP), Parkinson's Progression Markers Initiative (PPMI), and the BioFIND cohort. Our overarching objective
is to support the use and analysis of AMP PD data, with a specific focus on integrative visualization and analysis
of RNA transcriptomic data with the existing genomic data. We hypothesize that analysis of whole-blood
transcriptome RNA-seq data together with additional clinical and genomic data can yield insights into disease
diagnosis, progression, and genetic etiology of PD and other neurological disorders. Our work will consist of two
primary aims. First, we will identify changes in RNAs that are predictive for a disease state, subtypes,
progression, clinical correlates, and risk of PD. We will do this using the existing alignments and count-level data.
Additionally, we will conduct new VCF aware alignments allowing us to leverage the paired genomic DNA level
information. The outcome will be more complete analysis examining differential expression, isoform usage, and
splicing. Second, we will implement new tools for visualizing individual and summary level data within the Terra-
based AMP-PD Knowledge Platform. Overall, we believe the tools we develop will help the community identify
biomarkers of Parkinson's progression and assess their potential as targets for therapies. Moreover, we believe
these tools will be of broad utility providing new ways for researchers to understand the genetic etiology of
neurological disease.

## Key facts

- **NIH application ID:** 10130326
- **Project number:** 1U01NS120260-01
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** David W Craig
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $441,149
- **Award type:** 1
- **Project period:** 2020-09-30 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10130326

## Citation

> US National Institutes of Health, RePORTER application 10130326, Integrative Analysis and Visualization of AMP-PD Transcriptomic Data (1U01NS120260-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10130326. Licensed CC0.

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