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Published August 18, 2021 | Supplemental Material + Published
Journal Article Open

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees


The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.

Additional Information

© 2021 The Author(s). Published by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 21 August 2020, Revised 1 February 2021, Accepted 11 May 2021, Available online 18 June 2021. Funding: the research was funded by the Paul G. Allen Frontiers Group Prime Awarding Agency and HFSP (RGP0002/2016) to I.S.-M. and M.J.T. Author contributions. A.A.G., I.S.-M., O.R., Y.G., Z.L., N.Y., J.S., M.J.T., E.S., M.B.E., and P.M. designed research; A.A.G., O.R., I.S.-M., W.G., J.H., H.Z., R.R., M.G.J., and P.M. analyzed data; K.-H.K.C., I.-Y.K., Al.P., Au.P., A.K., R.Z., S.R., R.W., P.R., V.G.S., N.S., A.R., T.J., R.S., J.P., L.H., and X.S. analyzed data; A.A.G., O.R., I.S., W.G., J.H., H.Z., R.R., M.G.J., and P.M., wrote the manuscript. Data and software availability. We compiled all the challenge related methods in a wiki: https://github.com/Lineage-Reconstruction-DREAM-Challenge/hub/wiki. Data availability. All challenge datasets and participants submissions are available at: https://www.synapse.org/#!Synapse:syn20821809. The authors declare no competing interests.

Attached Files

Published - 1-s2.0-S2405471221001940-main.pdf

Supplemental Material - 1-s2.0-S2405471221001940-mmc1.pdf

Supplemental Material - 1-s2.0-S2405471221001940-mmc2.txt

Supplemental Material - 1-s2.0-S2405471221001940-mmc3.rtf

Supplemental Material - 1-s2.0-S2405471221001940-mmc4.rtf

Supplemental Material - 1-s2.0-S2405471221001940-mmc5.pdf


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August 22, 2023
December 22, 2023