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.