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.


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.


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.


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.


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.


HyDrop Bead Generation & PCR Barcoding v1.0

Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.


Microfluidic Chip Production v1.1 V.2

Protocol for producing microfluidic chips used in HyDrop experiment.


HyDrop-ATAC v1.0

Step-by-step protocol for execution of HyDrop-ATAC.


HyDrop-RNA v1.0

Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.


Probedesign pipeline for the inhouse generation of seqFISH probes

The probe design pipeline works by inputting the transcript id’s for which probes have to be designed. Additional probe design parameters such as GC% or melting temperature can be changed via the config file. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.


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.


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.



Section 3: Libraries quality control (QC)

This protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.