Next generation lineage tracing and its applications to unravel development

Spencer Short; Rodrigo Garcia-Tejera; Linus J Schumacher; Daniel L. Coutu

doi:10.1038/s41540-025-00542-w

Next generation lineage tracing and its applications to unravel development

Spencer Short
, Rodrigo Garcia-Tejera
, Linus J Schumacher
, Daniel L. Coutu^*

^*Corresponding author for this work

Research output: Contribution to journal › Review article › peer-review

Abstract

Lineage tracing remains an essential approach towards understanding cell fate, tissue formation, and human development. Herein, we review advancements in lineage tracing techniques, the integration of sequencing and imaging technologies, and computational tools for analysis. We report on recent lineage tracing applications including integrative techniques (MADM-CloneSeq), in situ hybridization (DART-FISH), and modern workflows (BaSISS), which hold an essential role in our aim to unravel lineage hierarchies and, ultimately, human development.

Original language	English
Article number	60
Journal	npj Systems Biology and Applications
Volume	11
DOIs	https://doi.org/10.1038/s41540-025-00542-w
Publication status	Published - 5 Jun 2025

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10.1038/s41540-025-00542-wLicence: Creative Commons: Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND)

npj VHD lineage tracing review manuscript (pr_Linus Schumacher (1)Accepted author manuscript, 0.98 MB
s41540-025-00542-wFinal published version, 1.01 MBLicence: Creative Commons: Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND)

Cite this

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title = "Next generation lineage tracing and its applications to unravel development",

abstract = "Lineage tracing remains an essential approach towards understanding cell fate, tissue formation, and human development. Herein, we review advancements in lineage tracing techniques, the integration of sequencing and imaging technologies, and computational tools for analysis. We report on recent lineage tracing applications including integrative techniques (MADM-CloneSeq), in situ hybridization (DART-FISH), and modern workflows (BaSISS), which hold an essential role in our aim to unravel lineage hierarchies and, ultimately, human development.",

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AU - Short, Spencer

AU - Garcia-Tejera, Rodrigo

AU - Schumacher, Linus J

AU - Coutu, Daniel L.

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Y1 - 2025/6/5

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AB - Lineage tracing remains an essential approach towards understanding cell fate, tissue formation, and human development. Herein, we review advancements in lineage tracing techniques, the integration of sequencing and imaging technologies, and computational tools for analysis. We report on recent lineage tracing applications including integrative techniques (MADM-CloneSeq), in situ hybridization (DART-FISH), and modern workflows (BaSISS), which hold an essential role in our aim to unravel lineage hierarchies and, ultimately, human development.

U2 - 10.1038/s41540-025-00542-w

DO - 10.1038/s41540-025-00542-w

M3 - Review article

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VL - 11

JO - npj Systems Biology and Applications

JF - npj Systems Biology and Applications

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ER -

Next generation lineage tracing and its applications to unravel development

Abstract

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