News & Updates

AMP PD’s latest v4 dataset release introduces a new data type: plasma RNA sequencing of neuron‑derived extracellular vesicles (NDEVs). This release adds 1,062 EV plasma RNASeq samples from approximately 356 participants within the PDBP cohort collected at baseline, 12-month, and 24-month timepoints. These data were processed with GENCODE version 45, underwent multi-modal quality control, and were integrated into the existing unified dataset. The new EV RNASeq data expand AMP PD’s transcriptomic coverage to include plasma-derived extracellular vesicles, providing additional insight into extracellular RNA expression and potential biomarkers of disease progression across participants with overlapping genomics, whole-blood transcriptomics, and proteomics data in the unified dataset.

New Data Type

Extracellular Vesicle (EV) Plasma RNASeq

Overview:
Neuron-derived extracellular vesicles (NDEVs) were isolated using NeuroDex’s proprietary ExoSORT procedure. Plasma EV RNA was processed using Takara Bio’s SMART-Seq Stranded Kit (Cat. No. 634492) and SMARTer RNA Unique Dual Index Kit (Cat. No. 634452 & 634457). Each sample (≤2 ng total RNA input) underwent library synthesis, RNA fragmentation (94°C × 2 min), 5-cycle indexing PCR, ribosomal cDNA depletion, and 16-cycle enrichment PCR.

Sequencing Workflow:
Libraries were quality-controlled using Agilent High Sensitivity D1000 ScreenTape, pooled, and sequenced in two stages:

• Initial iSeq Run: Library balancing and validation at 101×8×8×101 cycles.
• Final NovaSeqX Run: 100×8×8×100 cycles at 180 pM final concentration, targeting ≥50 M read pairs per sample.