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A comparison between CARLIN and DNA Typewriter in CRISPR-mediated lineage tracing
Fengshuo Liu1, Xiang Zhang2, Yipeng Yang3
1Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
BMC Bioinformatics
|May 29, 2026
Summary
DNA Typewriter demonstrates superior performance in CRISPR-based lineage tracing compared to CARLIN, especially with more cell divisions and sufficient recording targets. This method offers reduced ambiguity for accurate lineage inference.
Area of Science:
- CRISPR technology
- Molecular biology
- Systems biology
Background:
- CRISPR-based lineage tracing is crucial for understanding cellular processes.
- CARLIN and DNA Typewriter are key technologies in this field.
- Comparative analysis is needed for effective experimental design.
Purpose of the Study:
- To systematically compare the performance of CARLIN and DNA Typewriter.
- To provide quantitative benchmarks for CRISPR lineage tracing strategies.
- To guide experimental design in lineage tracing studies.
Main Methods:
- Utilized a unified stochastic simulation framework.
- Modeled CRISPR editing dynamics, barcode evolution, and cell division.
- Evaluated performance using Robinson-Foulds and triplet accuracy metrics.
Main Results:
- DNA Typewriter consistently outperformed CARLIN in lineage reconstruction accuracy.
- Sufficient recording targets and cell divisions favored DNA Typewriter.
- CARLIN's effectiveness was limited in long-term tracing due to rapid exhaustion of recording potential.
Conclusions:
- DNA Typewriter offers higher accuracy and reduced ambiguity in lineage inference.
- Triplet accuracy is a more informative metric than Robinson-Foulds accuracy for partial sampling.
- The findings provide critical insights for optimizing CRISPR lineage tracing experiments.
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