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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances.

Nika Abdollahi^1,2, Lucile Jeusset^1,3, Anne de Septenville³

¹UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne University, Paris, France.

BMC Bioinformatics

|February 28, 2023

Summary

ClonalTree efficiently reconstructs B cell lineage trees by incorporating genotype abundance into phylogenetic methods. This approach accurately reflects B cell affinity maturation dynamics, outperforming existing algorithms for high-throughput sequencing data.

Keywords:

B cell receptor repertoire Lineage Tree phylogenetics

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Published on: December 28, 2015

Area of Science:

Immunology
Computational Biology
Evolutionary Biology

Background:

B cell receptor (BCR) genes undergo somatic hypermutations and selection during affinity maturation, creating diverse antibody lineages.
Cellular genotype abundance offers insights into the evolutionary dynamics of B cell populations.
Existing phylogenetic methods for B cell lineage reconstruction are often time-consuming or neglect cellular abundance data.

Purpose of the Study:

To develop a novel, computationally efficient, and accurate method for constructing B cell lineage trees.
To integrate cellular genotype abundance into phylogenetic tree inference for B cell affinity maturation.
To provide a tool suitable for analyzing high-throughput BCR sequencing data in biomedical research.

Main Methods:

Introduced ClonalTree, a low-complexity algorithm integrating genotype abundances into minimum spanning tree (MST) algorithms.
Utilized simulated and experimental B cell population data for method validation.
Compared ClonalTree's performance against existing MST-based and exhaustive tree-generating methods.

Main Results:

ClonalTree accurately reconstructs B cell lineage trees, outperforming standard MST algorithms.
The method demonstrates comparable accuracy to exhaustive tree-generating approaches.
ClonalTree significantly reduces computational time, being hundreds to thousands of times faster.

Conclusions:

ClonalTree offers an accurate and highly efficient solution for B cell lineage tree construction.
The method's speed and accuracy make it ideal for large-scale, high-throughput BCR sequencing data analysis.
ClonalTree facilitates deeper insights into B cell evolutionary dynamics in biomedical applications.