Catalog

ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.

Article

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

Published: The authors present ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts from long-read sequences. This tool is an extension of ggplot2. View original preprint.

Article

Evaluation Of The Rims2 Locus As A Risk Locus For Parkinson’s Disease Dementia

Preprint: Genome-wide association studies have identified several risk loci for PD, providing insights into the mechanisms of disease initiation. Previously, the RIMS2 locus was identified as a determinant of dementia in PD. The authors evaluated 2536 individuals evaluated it, but found no association between RIMS2 and development of PD-related dementia.

Protocol

Western blotting for LRRK2 signalling in macrophages

This protocol describes the immunoblotting for components of the LRRK2 signalling pathway (LRRK2, LRRK2 pS935 and phospho-Rabs) using Invitrogen NuPage SDS-PAGE reagents and the BioRad Turbo Blot transfer system.

Article

Serum neurofilament light as a biomarker for prognosis in patients with newly diagnosed Parkinson’s disease

Published: Disease progression in PD patients is variable, but blood biomarkers may be useful. The authors evaluated serum neurofilament light (NfL) as a potential prognostic biomarker for PD. They found that serum NfL provided an objective measure of neurodegeneration in PD patients. View original preprint.

Code

Code for making forest plots for top GWAS loci

This repository contains the script used to create forest plots for top loci [part of code for the PD progression survival GWAS to mortality, Hoehn and Yahr stage 3 or greater (H&Y3+), and dementia].

Article

A step forward for LRRK2 inhibitors in Parkinson’s disease

Review: A discussion on learnings from phase 1 clinical trial for kinase inhibitors targeting LRRK2 that can provide the foundations for moving towards testing the efficacy of LRRK2 kinase inhibition in Parkinson’s disease.

Protocol

LRRK2 Immunofluorescent staining

Protocol for immunofluorescent staining for LRRK2 in cultured cells using the MJFF2 (c41-2) antibody.

Article

The Emerging Role of LRRK2 in Tauopathies

Review: Authors review the emerging evidence and discuss the potential impact of LRRK2 dysfunction on tau aggregation, lysosomal function, and endocytosis and exocytosis.

Protocol

Glucosylceramidase Beta (GBA) Genotyping

This protocol has been adapted from the PRoBaND Clinical Consortium (incorporating methods described by Neuman et al., 2009 and Stone et al., 2000) and has been used for all publications for PRoBaND / Tracking Parkinson’s describing clinical data and outcomes with respect to GBA status.

Protocol

Sample Collection and Measurement of Serum Neurofilament Light (NfL)

This protocol details the steps for the preparation of serum from human blood samples and the measurement of NfL concentration using the NF-Light Advantage kit on the HD-X Analyzer (Quanterix, Billerica, MA).

Protocol

SNP Genotyping and ApoE Genotyping

This protocol details the steps for DNA extraction from a human blood sample, quality control, and SNP and APOE genotyping. The protocol has been adapted from the PRoBaND SNP Genotyping and ApoE Genotyping Protocol

Protocol

Protein interaction network analysis for Mendelian diseases

This protocol describes the steps to use experimentally validated human data to create a protein-protein interaction network (PPIN) based on disease causative genes. Network analysis (combination of topological functional analyses) will lead to the identification of biological processes relevant for disease and disease endophenotypes.

Protocol

Analysis of glycosphingolipids from human plasma

The original qualitative method was published in 2004 and measured the oligosaccharides selectively released from glycosphingolipids using a ceramide glycanase enzyme derived from the medicinal leech. This is an updated protocol with the focus on achieving sensitive and reproducible quantitation of glycosphingolipids from human plasma samples