Work

SNPmanifold: detecting single-cell clonality and lineages from single-nucleotide variants using binomial variational autoencoder

Year: 2025

Type: article

Abstract: Single-nucleotide-variant (SNV) clone assignment of high-covariance single-cell lineage tracing data remains a challenge due to hierarchical mutation structure and many missing signals. We develop SNPmanifold, a Python package that learns an SNV embedding manifold using a binomial variational autoencoder to give an efficient and interpretable cell-cell distance metric. We demonstrate that SNPmanifold is a suitable tool for analysis of complex, single-cell SNV mutation data, such as in the context of demultiplexing a large number of donors and somatic lineage tracing via mitochondrial SNV data and can reveal insights into single-cell clonality and lineages more accurately and comprehensively than existing methods.

Source: Genome biology

DOI: 10.1186/s13059-025-03803-3

Authors: Hoi Man Chung, Yuanhua Huang

Institution: University of Hong Kong

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490

Funders: National Natural Science Foundation of China, University of Hong Kong