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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
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
This study demonstrates that the authors’ semi-automated protocol is suitable for shotgun metagenomic analysis, by significantly producing higher DNA fragment sizes while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
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Detection of mosaic and population-level structural variants with Sniffles2
Published: The authors developed Sniffles2, a faster and more accurate method to analyze long-ready structural variation calling. This method also solves the problem of family to population-level SV calling to produce fully genotyped VCF files. View original preprint.
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Article
Multiple genome alignment in the telomere-to-telomere assembly era
Published: This review provides an overview of the algorithmic template that most multiple genome alignment methods follow. We also discuss prospective areas of improvement of multiple genome alignment for keeping up with continuously arriving high-quality T2T assembled genomes and for unlocking clinically-relevant insights.
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Article
More of less: novel multi-ome profiling of single human neurons
Review: Epigenetic modifications to DNA and chromatin interact to influence gene expression and cellular phenotypes, but defining these omics layers in complex tissues is a daunting task. In this issue of Cell Genomics, Luo et al. describe a novel single-cell multi-omic method, simultaneously profiling transcriptome, DNA methylome, and chromatin accessibility, to shed light on human neurons.
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Article
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads. Article
Published: The data available in this repository can be used to replicate all the figures in the authors’ manuscript using their data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis.
View original preprint.
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Article
Sex distribution of GBA1 variant carriers with dementia with Lewy Bodies and Parkinson’s disease
Sex distribution of GBA1 variant carriers with dementia with Lewy Bodies and Parkinson’s disease.
Article
Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics
Existing spatial transcriptomics techniques are either limited by capture array density or are cost-prohibitive for large-scale atlasing. Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells enables customized, low-cost, flexible, and high-resolution spatial profiling of large tissue sections.
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Article
Response to: “Is Gauchian genotyping of GBA1 variants reliable?”
Preprint: To understand the cause of these discrepancies, the team reviewed their data, and concluded that they are misinterpreting Gauchian results in 8 of the 11 discrepant samples, and incorrectly using Gauchian to analyze low-coverage 1kGP samples.
Article
Methods and applications for single-cell and spatial multi-omics
In this review, the authors highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across molecular layers.
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