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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.
Report
README guide for code
The purpose of this document is to provide guidance on how to write README files for code.
Article
The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1
Published: The authors identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity. View original preprint.
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.
Themes
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.
Themes
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.
Themes
Article
The pathogenesis of Parkinson’s disease
This review is the second in a series of three papers about Parkinson’s disease published in the Lancet.
Themes
Code
egustavsson / GBA_GBAP1_manuscript
Code used to generate the plots used in manuscript, “The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1” (DOI: 10.1126/sciadv.adk1296).
Themes
Dataset
Targeted long-read RNA-seq
Targeted long-read RNAseq of SNCA, GBA1, and GBAP1. The sequencing data is PacBio Sequel IIe targeted Iso-Seq where enrichment was performed using hybridization probes. Three datasets are available: (i) human brain (ii) iPSC-derived astrocytes microglia neurons and (iii) iPSC-derived midbrain dopaminergic neurons.
Themes
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.
Themes
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.
Themes
Article
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease at Chr16q11.2 and on the MAPT H1 allele
Published: Genome-wide association studies have increased our understanding of PD by identifying genetic variants. The authors used a mitophagy screening assay to evaluate the functional significance of these variants and found two new regulators of PINK-dependent mitophagy, KAT8, and KANSL1. View original preprint.
Teams
Themes
Article
Association between the LRP1B and APOE loci and the development of Parkinson’s disease dementia
Published: Dementia is an important feature of late-stage PD. The authors used an unbiased, genome-wide approach to identify genetic polymorphisms that associate with faster development of dementia in PD patients. They identified four genetic regions that are associated with progression to dementia in PD, including APOE and three previously unknown regions. View original preprint (https://www.medrxiv.org/content/10.1101/2022.05.23.22275465v1).
Teams
Themes
Protocol
LRRK2 Immunofluorescent staining
Protocol for immunofluorescent staining for LRRK2 in cultured cells using the MJFF2 (c41-2) antibody.
Teams
Themes
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.
Teams
Themes