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Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments

Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell s...

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Autores principales: N. M., Prashant, Liu, Hongyu, Dillard, Christian, Ibeawuchi, Helen, Alsaeedy, Turkey, Chan, Hang, Horvath, Anelia Dafinova
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8535975/
https://www.ncbi.nlm.nih.gov/pubmed/34680953
http://dx.doi.org/10.3390/genes12101558
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author N. M., Prashant
Liu, Hongyu
Dillard, Christian
Ibeawuchi, Helen
Alsaeedy, Turkey
Chan, Hang
Horvath, Anelia Dafinova
author_facet N. M., Prashant
Liu, Hongyu
Dillard, Christian
Ibeawuchi, Helen
Alsaeedy, Turkey
Chan, Hang
Horvath, Anelia Dafinova
author_sort N. M., Prashant
collection PubMed
description Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell scRNA-seq data, wherein the alignments are split by cellular barcode prior to the variant call. We also reanalyze publicly available data on the MCF7 cell line during anticancer treatment. We assessed SNV calls by three variant callers—GATK, Strelka2, and Mutect2, in combination with a method for the cell-level tabulation of the sequencing read counts bearing variant alleles–SCReadCounts (single-cell read counts). Our analysis shows that variant calls on individual cell alignments identify at least a two-fold higher number of SNVs as compared to the pooled scRNA-seq; these SNVs are enriched in novel variants and in stop-codon and missense substitutions. Our study indicates an immense potential of SNV calls from individual cell scRNA-seq data and emphasizes the need for cell-level variant detection approaches and tools, which can contribute to the understanding of the cellular heterogeneity and the relationships to phenotypes, and help elucidate somatic mutation evolution and functionality.
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spelling pubmed-85359752021-10-23 Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments N. M., Prashant Liu, Hongyu Dillard, Christian Ibeawuchi, Helen Alsaeedy, Turkey Chan, Hang Horvath, Anelia Dafinova Genes (Basel) Article Currently, the detection of single nucleotide variants (SNVs) from 10 x Genomics single-cell RNA sequencing data (scRNA-seq) is typically performed on the pooled sequencing reads across all cells in a sample. Here, we assess the gaining of information regarding SNV assessments from individual cell scRNA-seq data, wherein the alignments are split by cellular barcode prior to the variant call. We also reanalyze publicly available data on the MCF7 cell line during anticancer treatment. We assessed SNV calls by three variant callers—GATK, Strelka2, and Mutect2, in combination with a method for the cell-level tabulation of the sequencing read counts bearing variant alleles–SCReadCounts (single-cell read counts). Our analysis shows that variant calls on individual cell alignments identify at least a two-fold higher number of SNVs as compared to the pooled scRNA-seq; these SNVs are enriched in novel variants and in stop-codon and missense substitutions. Our study indicates an immense potential of SNV calls from individual cell scRNA-seq data and emphasizes the need for cell-level variant detection approaches and tools, which can contribute to the understanding of the cellular heterogeneity and the relationships to phenotypes, and help elucidate somatic mutation evolution and functionality. MDPI 2021-09-30 /pmc/articles/PMC8535975/ /pubmed/34680953 http://dx.doi.org/10.3390/genes12101558 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
N. M., Prashant
Liu, Hongyu
Dillard, Christian
Ibeawuchi, Helen
Alsaeedy, Turkey
Chan, Hang
Horvath, Anelia Dafinova
Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title_full Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title_fullStr Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title_full_unstemmed Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title_short Improved SNV Discovery in Barcode-Stratified scRNA-seq Alignments
title_sort improved snv discovery in barcode-stratified scrna-seq alignments
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8535975/
https://www.ncbi.nlm.nih.gov/pubmed/34680953
http://dx.doi.org/10.3390/genes12101558
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