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A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

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Published on: December 18, 2015

Theoretical guarantees for phylogeny inference from single-cell lineage tracing.

Robert Wang¹, Richard Zhang², Alex Khodaverdian²

¹Algorithms and Complexity Group, David R. Cheriton School of Computer Science, University of Waterloo, Waterloo ON N2L 3G1, Canada.

Proceedings of the National Academy of Sciences of the United States of America

|March 17, 2023

Summary

This study introduces new algorithms for reconstructing cell lineages using CRISPR-Cas9 technology. These methods improve the accuracy of tracing cell relationships during development, offering insights for experimental design.

Keywords:

Crispr-Cas9 computational phylogenetics single-cell lineage tracing

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Published on: May 8, 2020

Area of Science:

Genomics
Developmental Biology
Computational Biology

Background:

CRISPR-Cas9 genome editing enables lineage tracing for single-cell developmental studies.
Reconstructing clonal relationships is challenging due to data complexities like cutting rates and indel diversity.

Purpose of the Study:

Develop algorithms for accurate single-cell phylogenetic tree reconstruction.
Establish theoretical bounds on recording sites needed for precise phylogeny.
Analyze how experimental parameters affect reconstruction difficulty.

Main Methods:

Developed two theoretically grounded algorithms for phylogenetic reconstruction.
Derived asymptotic bounds for the number of recording sites.
Conducted simulations to evaluate algorithm performance and bound validity.

Main Results:

Algorithms demonstrate effective reconstruction of single-cell phylogenetic trees.
Asymptotic bounds provide guidance on necessary recording sites for accurate phylogeny.
Simulations confirm empirical performance aligns with theoretical trends.

Conclusions:

This work offers a theoretical framework for phylogenetic reconstruction in CRISPR-Cas9 lineage tracing.
Findings have implications for optimizing experimental design in developmental studies.
The developed algorithms and bounds enhance the utility of CRISPR-Cas9 for lineage tracing.