This repository contains codes and pipelines, as well as data used in the analysis of human inhibitory and excitatory neuronal clonal dynamics and lineage relationships, with cell-type-specific mosaic variant barcoding analysis (cMVBA). WGS, MPAS, snMPAS, snRNA-seq data are available from multiple neurotypical postmortem donors. Raw WGS, MPAS, snMPAS, snRNAseq sequences from cortical regions, subregions from ID01, ID05, ID06, ID07, and ID08 are available at the NDA website under accession number 919 and SRA under accession numbers PRJNA736951 and PRJNA799597. WGS panel of normal data is available here.
WGS data processing is following this pipeline.
Germline heterozygous variants are called with HaplotypeCaller following this pipeline.
Sample-unique variant calling with Mutect2 and Strelka paired mode is carried out following this pipeline.
Sample-specific variant calling is first carried with this pipeline using Mutect2 single mode (full panel of normal). Followed with DeepMosaic is carried out following the official guidelines and MosaicForecast using this pipeline.
Sample-unique and sample-specific variants are further called without control using MosaicHunter following this pipeline and the 300x properties file.
Variants were further combined and annotations were performed using this pipeline.
Single nucleus transcriptome sequencing analysis with ResolveOME RNA seq pipeline is provided here.
Single nucleus transcriptome sequencing analysis with a 10x Genomics RNA seq pipeline is provided here.
Cell identity was determined as described here.
2. Pipelines for the process of Massive Parallel Amplicon Sequencing (MPAS) and single-nuclei Massive Parallel Amplicon Sequencing (snMPAS)
Alignment and processing of MPAS and snMPAS were carried out following this pipeline
After alignment, candidate variants were further combined and genotyped using this pipeline in every sample detected with MPAS and snMPAS.
Quality control were carried out for WGS and MPAS MAFs measured in ID01 and ID05.
3.1 Pipelines for methylome analysis using BisMark
3.2 Statical analysis combining published standards to identify the cell types
Variant annotation for ID01 and ID05 are provided separately.
UpSet plot for ID01 and ID05 variants.
Fig.1 Single-nucleus RNA sequencing results for cell type identification of sorted nuclei, Number of MVs categorized by location detected in each donor ID01 or ID05
Fig.2 Heatmaps, dendrograms, and contour plots with kernel density estimation plots for strong Hippocampal lineage restriction: ID01, ID05
Fig.3 Bootstraps, AF Heatmaps and dendrograms and for sorted cortical excitatory and inhibitory neuronal pools: ID01, ID05
Fig.4 ResolveOME analysis: Cell type identification, oncoplot, Peudobulk analysis, Permutation test, DEG analysis between InN1 and InN2
Fig.5 AF Heatmap, dendrogram, contour plots with kernel density estimation plots for restricted clonal spread in a parietal lobe of ID05 is here
Pearson correlation analysis for ID01 and ID05
Lolliplot and geoclones for ID01; ID05 lollipolt and geoclones.
UMAP for variant AF for ID01 and ID05. Simulated contamination and deconvolution for ID01, ID05_contamination, ID05 deconvolution. Estimating the contribution of dorsal and ventral origin for DLX1+ inhibitory neurons for ID01 and ID05
📧 Changuk Chung: chchung@health.ucsd.edu
📧 Xiaoxu Yang: u6055394@utah.edu, xiaoxuyanglab@gmail.com, xiy010@health.ucsd.edu
📧 Joseph Gleeson: jogleeson@health.ucsd.edu, or the Gleeson lab gleesonlab@health.ucsd.edu
Chung C, Yang X, et al., Gleeson JG. Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain. 2024. (Nature, DOI: 10.1038/s41586-024-07292-5, PMID: 38600385 )