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

被引：30

作者：

Gong, Wuming ^{[1
]}

Granados, Alejandro A. ^{[2
]}

Hu, Jingyuan ^{[3
]}

Jones, Matthew G. ^{[4
,5
]}

Raz, Ofir ^{[6
]}

Salvador-Martinez, Irepan ^{[7
]}

Zhang, Hanrui ^{[8
]}

Chow, Ke-Huan K. ^{[2
]}

Kwak, Il-Youp ^{[9
]}

Retkute, Renata ^{[10
]}

Prusokiene, Alisa ^{[11
]}

Prusokas, Augustinas ^{[12
]}

Khodaverdian, Alex ^{[4
]}

Zhang, Richard ^{[4
]}

Rao, Suhas ^{[4
]}

Wang, Robert ^{[4
]}

Rennert, Phil ^{[13
]}

Saipradeep, Vangala G. ^{[14
]}

Sivadasan, Naveen ^{[14
]}

Rao, Aditya ^{[14
]}

Joseph, Thomas ^{[14
]}

Srinivasan, Rajgopal ^{[14
]}

Peng, Jiajie ^{[15
]}

Han, Lu ^{[15
]}

Shang, Xuequn ^{[15
]}

Garry, Daniel J. ^{[1
]}

Yu, Thomas ^{[16
]}

Chung, Verena ^{[16
]}

Mason, Michael ^{[16
]}

Liu, Zhandong ^{[3
]}

Guan, Yuanfang ^{[8
]}

Yosef, Nir ^{[4
]}

Shendure, Jay ^{[17
,18
,19
,20
]}

Telford, Maximilian J. ^{[7
]}

Shapiro, Ehud ^{[6
]}

Elowitz, Michael B. ^{[2
]}

Meyer, Pablo ^{[21
]}

机构：

[1] Univ Minnesota, Lillehei Heart Inst, 2231 6th St SE,4-165 CCRB, Minneapolis, MN 55114 USA

[2] CALTECH, Pasadena, CA 91125 USA

[3] Baylor Coll Med, Program Quantitat & Computat Biosci, Houston, TX 77030 USA

[4] Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA

[5] Univ Calif San Francisco, Integrat Program Quantitat Biol, San Francisco, CA 94143 USA

[6] Weizmann Inst Sci, Dept Comp Sci & Appl Math, IL-761001 Rehovot, Israel

[7] UCL, Ctr Lifes Origins & Evolut, Dept Genet Evolut & Environm, Gower St, London WC1E 6BT, England

[8] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[9] Chung Ang Univ, Coll Business & Econ, Dept Appl Stat, 84 Heukseok Ro, Seoul, South Korea

[10] Univ Cambridge, Dept Plant Sci, Downing St, Cambridge CB2 3EA, England

[11] Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England

[12] Imperial Coll London, Dept Life Sci, London SW7 2AZ, England

[13] EC Wise Inc, 1299 4th St 505, San Rafael, CA 94901 USA

[14] Tata Consultancy Serv, TCS Res & Innovat, Hyderabad 500019, India

[15] Northwestern Polytech Univ, Sch Comp Sci, Xian, Peoples R China

[16] Sage Bionetworks, 2901 3rd Ave 330, Seattle, WA 98121 USA

[17] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[18] Allen Discovery Ctr Cell Lineage Tracing, Seattle, WA USA

[19] Brotman Baty Inst Precis Med, Seattle, WA USA

[20] Howard Hughes Med Inst, Seattle, WA USA

[21] IBM Corp, Healthcare & Life Sci, TJ Watson Res Ctr, 1101 Kitchawan Rd 10598, Yorktown Hts, NY 10598 USA

来源：

CELL SYSTEMS | 2021年 / 12卷 / 08期

关键词：

benchmarking; C; elegans; cell lineage tracing; CRISPR; crowdsourcing; intmemoir; lineage reconstruction; M; musculus; machine learning; simulation;

D O I：

10.1016/j.cels.2021.05.008

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：810 / +

页数：21

共 42 条

[31] COMPARISON OF PHYLOGENETIC TREES [J].

ROBINSON, DF ;

FOULDS, LR .

MATHEMATICAL BIOSCIENCES, 1981, 53 (1-2) :131-147

[32] Crowdsourcing biomedical research: leveraging communities as innovation engines [J].

Saez-Rodriguez, Julio ;

Costello, James C. ;

Friend, Stephen H. ;

Kellen, Michael R. ;

Mangravite, Lara ;

Meyer, Pablo ;

Norman, Thea ;

Stolovitzky, Gustavo .

NATURE REVIEWS GENETICS, 2016, 17 (08) :470-486

[33] THE NEIGHBOR-JOINING METHOD - A NEW METHOD FOR RECONSTRUCTING PHYLOGENETIC TREES [J].

SAITOU, N ;

NEI, M .

MOLECULAR BIOLOGY AND EVOLUTION, 1987, 4 (04) :406-425

[34] A community effort to create standards for evaluating tumor subclonal reconstruction [J].

Salcedo, Adriana ;

Tarabichi, Maxime ;

Espiritu, Shadrielle Melijah G. ;

Deshwar, Amit G. ;

David, Matei ;

Wilson, Nathan M. ;

Dentro, Stefan ;

Wintersinger, Jeff A. ;

Liu, Lydia Y. ;

Ko, Minjeong ;

Sivanandan, Srinivasan ;

Zhang, Hongjiu ;

Zhu, Kaiyi ;

Ou Yang, Tai-Hsien ;

Chilton, John M. ;

Buchanan, Alex ;

Lalansingh, Christopher M. ;

P'ng, Christine ;

Anghel, Catalina V. ;

Umar, Imaad ;

Lo, Bryan ;

Zou, William ;

Simpson, Jared T. ;

Stuart, Joshua M. ;

Anastassiou, Dimitris ;

Guan, Yuanfang ;

Ewing, Adam D. ;

Ellrott, Kyle ;

Wedge, David C. ;

Morris, Quaid ;

Van Loo, Peter ;

Boutros, Paul C. ;

Jha, Alokkumar ;

Huang, Tanxiao ;

Yang, Tsun-Po ;

Peifer, Martin ;

Sahinalp, Cenk ;

Malikic, Salem ;

Vazquez-Garcia, Ignacio ;

Mustonen, Ville ;

Yang, Hsih-Te ;

Lee, Ken-Ray ;

Ji, Yuan ;

Sengupta, Subhajit ;

Rudewicz, Justine ;

Nikolski, Macha ;

Schaeverbeke, Quentin ;

Yuan, Ke ;

Markowetz, Florian ;

Macintyre, Geoff .

NATURE BIOTECHNOLOGY, 2020, 38 (01) :97-+

[35] CeLaVi: an interactive cell lineage visualization tool [J].

Salvador-Martinez, Irepan ;

Grillo, Marco ;

Averof, Michalis ;

Telford, Maximilian J. .

NUCLEIC ACIDS RESEARCH, 2021, 49 (W1) :W80-W85

[36] Is it possible to reconstruct an accurate cell lineage using CRISPR recorders? [J].

Salvador-Martinez, Irepan ;

Grillo, Marco ;

Averof, Michalis ;

Telford, Maximilian J. .

ELIFE, 2019, 8

[37] Triplet MaxCut: a new toolkit for rooted supertree [J].

Sevillya, Gur ;

Frenkel, Zeev ;

Snir, Sagi .

METHODS IN ECOLOGY AND EVOLUTION, 2016, 7 (11) :1359-1365

[38] Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars [J].

Spanjaard, Bastiaan ;

Hu, Bo ;

Mitic, Nina ;

Olivares-Chauvet, Pedro ;

Janjuha, Sharan ;

Ninov, Nikolay ;

Junker, Jan Philipp .

NATURE BIOTECHNOLOGY, 2018, 36 (05) :469-+

[39] eSTGt: a programming and simulation environment for population dynamics [J].

Spiro, Adam ;

Shapiro, Ehud .

BMC BIOINFORMATICS, 2016, 17

[40] POST-EMBRYONIC CELL LINEAGES OF NEMATODE, CAENORHABDITIS-ELEGANS [J].

SULSTON, JE ;

HORVITZ, HR .

DEVELOPMENTAL BIOLOGY, 1977, 56 (01) :110-156

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