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bioRxiv · 10.1101/2021.10.29.466515

A comprehensive evaluation of CRISPR lineage recorders using TraceQC

Hu, J.·Jeong, H.-H.·Al-Ouran, R.·Bado, I.·Zhang, W.·Zhang, X.·Liu, Z.
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Abstract

The CRISPR-Cas9 genome editing-based lineage tracing system is emerging as a powerful tool to track cell lineages at unprecedented scale and resolution. However, the complexity of CRISPR-Cas9 induced mutations has raised challenges in lineage reconstruction, which requires a unique computational analysis framework. Meanwhile, multiple distinctive CRISPR-based high-throughput lineage recorders have been developed over the years in which the data analysis is incompatible across platforms. To address these challenges, first, we present the TraceQC, a cross-platform open-source package for data processing and quality evaluation of CRISPR lineage tracing data. Second, by using the TraceQC package, we performed a comprehensive analysis across multiple CRISPR lineage recorders to uncover the speed and distribution of CRISPR-induced mutations. Together, this work provides a computational framework for the CRISPR lineage tracing system that should broadly benefit the design and application of this promising technology.

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Hu, J., Jeong, H.-H., Al-Ouran, R., Bado, I., Zhang, W., Zhang, X., Liu, Z.. 2021-10-30. A comprehensive evaluation of CRISPR lineage recorders using TraceQC. https://doi.org/10.1101/2021.10.29.466515

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