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

Gong, Wuming and Granados, Alejandro A. and Hu, Jingyuan and Jones, Matthew G. and Raz, Ofir and Salvador-Martínez, Irepan and Zhang, Hanrui and Chow, Ke-Huan K. and Kwak, Il-Youp and Retkute, Renata and Prusokas, Alidivinas and Prusokas, Augustinas and Khodaverdian, Alex and Zhang, Richard and Rao, Suhas and Wang, Robert and Rennert, Phil and Saipradeep, Vangala G. and Sivadasan, Naveen and Rao, Aditya and Joseph, Thomas and Srinivasan, Rajgopal and Peng, Jiajie and Han, Lu and Shang, Xuequn and Garry, Daniel J. and Yu, Thomas and Chung, Verena and Mason, Michael and Liu, Zhandong and Guan, Yuanfang and Yosef, Nir and Shendure, Jay and Telford, Maximilian J. and Shapiro, Ehud and Elowitz, Michael B. and Meyer, Pablo (2021) Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees. Cell Systems, 12 (8). pp. 810-826. ISSN 2405-4712. doi:10.1016/j.cels.2021.05.008. https://resolver.caltech.edu/CaltechAUTHORS:20210628-191053293

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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.cels.2021.05.008DOIArticle
https://github.com/Lineage-Reconstruction-DREAM-Challenge/hub/wikiRelated ItemWiki
https://www.synapse.org/#!Synapse:syn20821809Related Itemchallenge datasets and participants submissions
ORCID:
AuthorORCID
Granados, Alejandro A.0000-0002-6275-9800
Chow, Ke-Huan K.0000-0002-7317-2669
Elowitz, Michael B.0000-0002-1221-0967
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.
Funders:
Funding AgencyGrant Number
Paul G. Allen Frontiers GroupUNSPECIFIED
Human Frontier Science ProgramRGP0002/2016
Subject Keywords:cell lineage tracing; intmemoir; CRISPR; C. elegans; crowdsourcing; benchmarking; machine learning; simulation; lineage reconstruction; M. musculus
Issue or Number:8
DOI:10.1016/j.cels.2021.05.008
Record Number:CaltechAUTHORS:20210628-191053293
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210628-191053293
Official Citation:Wuming Gong, Alejandro A. Granados, Jingyuan Hu, Matthew G. Jones, Ofir Raz, Irepan Salvador-Martínez, Hanrui Zhang, Ke-Huan K. Chow, Il-Youp Kwak, Renata Retkute, Alidivinas Prusokas, Augustinas Prusokas, Alex Khodaverdian, Richard Zhang, Suhas Rao, Robert Wang, Phil Rennert, Vangala G. Saipradeep, Naveen Sivadasan, Aditya Rao, Thomas Joseph, Rajgopal Srinivasan, Jiajie Peng, Lu Han, Xuequn Shang, Daniel J. Garry, Thomas Yu, Verena Chung, Michael Mason, Zhandong Liu, Yuanfang Guan, Nir Yosef, Jay Shendure, Maximilian J. Telford, Ehud Shapiro, Michael B. Elowitz, Pablo Meyer, Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees, Cell Systems, Volume 12, Issue 8, 2021, Pages 810-826.e4, ISSN 2405-4712, https://doi.org/10.1016/j.cels.2021.05.008.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109625
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:29 Jun 2021 14:33
Last Modified:24 Aug 2021 18:12

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