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: Parkinson’s disease likely reflects a complex interaction among genetic and environmental factors. Here, the role of nicotine, SV2 and the alpha-synuclein were examined. The study suggests that SV2 may be needed for the protection nicotine provides from Parkinson’s-related neurotoxicity. View original preprint.

Article

Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease at 16q11.2 and MAPT H1 loci

These results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.

Article

Splicing accuracy varies across human introns, tissues, and age

This in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.

Code

Long-read RNA seq analysis using Talon

This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts. It is forked from ANNSeq. The link includes the dag of the pipeline.

Article

Pseudogenes limit the identification of novel common transcripts generated by their parent genes

Preprint: Genetic analyses are often complicated by genomic sequences with high sequence similarity. Here, the authors examined the role of pseudogenes on transcriptomic analyses using GB1 and GBAP1 as examples.

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

Article

Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias

Published: Hereditary Spastic Paraplegias are a group of neurodegenerative disorders with diverse clinical presentation and genetic variability. The authors used validated human data to create a protein-protein interaction map using causative genes to identify core proteins and processes. View original preprint.

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

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.

Lab Resource

Plasmid: pLV[Exp]-EF1A>V5/hKAT8[NM_032188.3]:IRES:Puro

Human KAT8 gene with N-terminal V5 tag cloned into the pLV[Exp] plasmid backbone under a EF1a promoter and including IRES puromycin selection cassette by Vectorbuilder.

Code

huw-morris-lab/PDD_GWSS

Code used in the analysis from the manuscript Real et al., Association between the LRP1B and APOE loci and the development of Parkinson’s disease dementia (2022): https://doi.org/10.1101/2022.05.23.22275465

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.

Article

Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases

Preprint: Analysis of local genetic correlations can identify genomic regions that associate with more than one trait which can provide a better mechanistic understanding of disease. The authors identified several local genetic correlations between common neurodegenerative and neuropsychiatric diseases.