bioRxivSystems BiologyPreprint
Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars
Jan Philipp JunkeriD, Bastiaan SpanjaardiD, Josi Peterson-Maduro, Anna AlemanyiD, Bo HuiD, Maria FlorescuiD, Alexander van OudenaardeniD
Abstract
A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scartrace, a strategy for massively parallel clonal analysis based on Cas9 induced genetic scars in the zebrafish.
- organism: zebrafish
- assay: CRISPR screen
- research focus: cell type annotation
- research focus: clustering
- approach: experimental assay
Abstract summary
Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract · CC BY-NC-ND 4.0
scartrace uses Cas9-induced genetic scars for clonal analysis in zebrafish, aiming at lineage reconstruction across many cells at once rather than the small subsets imaging covers.
Lineage tracing by imaging has given detailed results but, in vertebrates, mostly for limited subsets of cells, so organism-scale lineage trees stay out of reach. Marking cells with scars written by Cas9 is put forward as a way to recover clonal relationships from many cells in parallel.
Key results
ClaimedA strategy named scartrace is introduced, in which genetic scars left by Cas9 serve as marks for massively parallel clonal analysis in zebrafish.
Announced in the abstract as the contribution of the work; no numbers of cells, scars or clones, no reconstructed lineage tree, and no validation or error estimate appear in the text available. · Abstract
Methods, data and reproducibility
Cas9 is used to create genetic scars in zebrafish, and those scars are used as marks to assign cells to clones for lineage analysis. The abstract does not state the targeted locus, how scars are read out, or how the lineage analysis is performed.
- zebrafish, the organism in which the scar-based clonal analysis is applied · zebrafish
- Methods & tools
- scartrace, CRISPR/Cas9
Limitations (2)
- The abstract announces the approach without reporting any results: no cell or scar counts, no lineage tree, no comparison with imaging-based tracing and no estimate of error or dropout. · noted in this summary
- Nothing is said about the practical constraints of scar-based tracing, such as which locus is targeted, how scars are read out, scar saturation over development, or independent scars arising identically in unrelated cells. · noted in this summary
Read this if you do lineage tracing and want to see how CRISPR-induced scars were proposed for clonal analysis in zebrafish at a scale imaging-based tracing has mostly not reached.
- Citations
- 43
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