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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.
Article
The annotation and function of the Parkinson’s and Gaucher disease-linked gene GBA1 has been concealed by its protein-coding pseudogene GBAP1
Here, 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.
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.
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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.
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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.
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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.
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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.
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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.
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Article
From structure to ætiology: a new window on the biology of leucine-rich repeat kinase 2 and Parkinson’s disease
Review: This review summarizes LRRK2 structure both in a historical and current context, highlighting new insights into the structure of LRRK2 and complexes it forms.
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Article
Vesicular dysfunction and pathways to neurodegeneration
In this review, the pathways that have emerged as being critical for neuronal survival in the human brain is be discussed – illustrating the diversity of proteins and cellular events with three molecular case studies drawn from different neurological diseases.
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Lab Resource
Lentivirus plasmid: pLV[Exp]-U6>KAT8_P1_Seq1-hPGK>mApple
Plasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter.
Generated by Vectorbuilder in the pLV[Exp] backbone.
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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.
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Article
Combining biomarkers for prognostic modeling of 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.
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