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. 2024 May 15;212(10):1579-1588.
doi: 10.4049/jimmunol.2300851.

Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser

Cole G Jensen  1 , Jacob A Sumner  1   2 , Steven H Kleinstein  1   3   4 , Kenneth B Hoehn  3
Affiliations

Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser

Cole G Jensen et al. J Immunol. .

Abstract

Abs are vital to human immune responses and are composed of genetically variable H and L chains. These structures are initially expressed as BCRs. BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated H and L chains, but advancements in single-cell sequencing now pair H and L chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired H and L chain sequences to build phylogenetic trees. We found that incorporating L chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree-building methods and persisted even when mixing bulk and single-cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some L chains were missing, such as when mixing single-cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for H and L chain gene partitions. Thus, we recommend using maximum likelihood methods with separate H and L chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.

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Conflict of interest statement

Disclosures

S.H.K. receives consulting fees from Peraton. K.B.H. receives consulting fees from Prellis Biologics. The remaining authors have no competing interests.

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