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scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq

View ORCID ProfileGiovanni Quinones Valdez, View ORCID ProfileTing Fu, Tracey Chan, View ORCID ProfileXinshu (Grace) Xiao
doi: https://doi.org/10.1101/2022.03.29.486330
Giovanni Quinones Valdez
1Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
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Ting Fu
2Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA 90095, USA
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Tracey Chan
3Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095, USA
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Xinshu (Grace) Xiao
1Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
2Molecular, Cellular and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA 90095, USA
3Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA 90095, USA
4Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA
5Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
6Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
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  • For correspondence: gxxiao@ucla.edu
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Abstract

Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq data set, scAllele identified variants with strong allelic linkage to alternative splicing, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted March 30, 2022.
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scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Giovanni Quinones Valdez, Ting Fu, Tracey Chan, Xinshu (Grace) Xiao
bioRxiv 2022.03.29.486330; doi: https://doi.org/10.1101/2022.03.29.486330
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scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Giovanni Quinones Valdez, Ting Fu, Tracey Chan, Xinshu (Grace) Xiao
bioRxiv 2022.03.29.486330; doi: https://doi.org/10.1101/2022.03.29.486330

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