ESTIMATION OF CELL LINEAGE TREES BY MAXIMUM-LIKELIHOOD PHYLOGENETICS.
Ann Appl Stat
; 15(1): 343-362, 2021 Mar.
Article
in En
| MEDLINE
| ID: mdl-35990087
ABSTRACT
CRISPR technology has enabled cell lineage tracing for complex multicellular organisms through insertion-deletion mutations of synthetic genomic barcodes during organismal development. To reconstruct the cell lineage tree from the mutated barcodes, current approaches apply general-purpose computational tools that are agnostic to the mutation process and are unable to take full advantage of the data's structure. We propose a statistical model for the CRISPR mutation process and develop a procedure to estimate the resulting tree topology, branch lengths, and mutation parameters by iteratively applying penalized maximum likelihood estimation. By assuming the barcode evolves according to a molecular clock, our method infers relative ordering across parallel lineages, whereas existing techniques only infer ordering for nodes along the same lineage. When analyzing transgenic zebrafish data from McKenna, Findlay and Gagnon et al. (2016), we find that our method recapitulates known aspects of zebrafish development and the results are consistent across samples.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Language:
En
Journal:
Ann Appl Stat
Year:
2021
Document type:
Article
Publication country:
EEUU
/
ESTADOS UNIDOS
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ESTADOS UNIDOS DA AMERICA
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EUA
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UNITED STATES
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UNITED STATES OF AMERICA
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US
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USA