MQuad enables clonal substructure discovery using single cell mitochondrial variants

Aaron Wing Cheung Kwok, Chen Qiao, Rongting Huang, Mai-Har Sham, Joshua W. K. Ho () and Yuanhua Huang ()
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Aaron Wing Cheung Kwok: The University of Hong Kong
Chen Qiao: The University of Hong Kong
Rongting Huang: The University of Hong Kong
Mai-Har Sham: The Chinese University of Hong Kong
Joshua W. K. Ho: The University of Hong Kong
Yuanhua Huang: The University of Hong Kong

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Mitochondrial mutations are increasingly recognised as informative endogenous genetic markers that can be used to reconstruct cellular clonal structure using single-cell RNA or DNA sequencing data. However, identifying informative mtDNA variants in noisy and sparse single-cell sequencing data is still challenging with few computation methods available. Here we present an open source computational tool MQuad that accurately calls clonally informative mtDNA variants in a population of single cells, and an analysis suite for complete clonality inference, based on single cell RNA, DNA or ATAC sequencing data. Through a variety of simulated and experimental single cell sequencing data, we showed that MQuad can identify mitochondrial variants with both high sensitivity and specificity, outperforming existing methods by a large extent. Furthermore, we demonstrate its wide applicability in different single cell sequencing protocols, particularly in complementing single-nucleotide and copy-number variations to extract finer clonal resolution.

Date: 2022
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DOI: 10.1038/s41467-022-28845-0

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