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SCReadCounts: Estimation of cell-level SNVs from scRNA-seq data [article]

NM Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan John Edwards, Anelia Horvath
2020 bioRxiv   pre-print
demonstrate its application to estimate cell level expression of somatic mutations and RNA-editing on cancer datasets.  ...  Summary: SCReadCounts is a method for a cell-level estimation of the sequencing read counts bearing a particular nucleotide at genomic positions of interest from barcoded scRNA-seq alignments.  ...  Vu,T.N. et al. (2019) Cell-level somatic mutation detection from single-cell RNA sequencing. Bioinformatics.  ... 
doi:10.1101/2020.11.23.394569 fatcat:c6g7yjl77vf7vbhy5zwd4dca5u

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

Wenge Li, R. Brent Calder, Jessica C. Mar, Jan Vijg
2015 Mutation research  
Here, we present an integrative method, termed Single-Cell Transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells.  ...  This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells.  ...  Acknowledgments We thank Shahina Maqbool of Einstein's Epigenomic Core Facility for her assistance in RNA-seq and Jennifer Bae and her colleagues in Axeq/Macrogen for their assistance in WES.  ... 
doi:10.1016/j.mrfmmm.2015.01.002 pmid:25733965 pmcid:PMC4342853 fatcat:7vfv6ifcf5f4xhggzeo322qzo4

Detecting expressed cancer somatic mutations from single-cell RNA sequencing data [article]

Tianyun Zhang, Ning Shen
2021 bioRxiv   pre-print
Identifying expressed somatic mutations directly from single-cell RNA sequencing (scRNA-seq) data is challenging but highly valuable.  ...  Therefore, RESA could provide novel views in the study of intratumor heterogeneity and relate genetic alterations to transcriptional changes at single cell level.  ...  This work was funded by the Starting Fund from Zhejiang University.  ... 
doi:10.1101/2021.10.08.463191 fatcat:hec64k2z3ffw5dqgajigtosnfi

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

Lili Wang, Jean Fan, Joshua M. Francis, George Georghiou, Sarah Hergert, Shuqiang Li, Rutendo Gambe, Chensheng W. Zhou, Chunxiao Yang, Sheng Xiao, Paola Dal Cin, Michaela Bowden (+9 others)
2017 Genome Research  
from thousands of single cells from five CLL samples.  ...  Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells, leading to increased understanding  ...  We also thank the excellent technical support of the MRC Protein Phosphorylation and Ubiquitylation Unit (PPU) Reagents team for DNA sequencing, cloning, and antibody production from University of Dundee  ... 
doi:10.1101/gr.217331.116 pmid:28679620 pmcid:PMC5538547 fatcat:4jgb64mxcjdj7jv7xpgoh472wm

Exome versus transcriptome sequencing in identifying coding region variants

Chee-Seng Ku, Mengchu Wu, David N Cooper, Nasheen Naidoo, Yudi Pawitan, Brendan Pang, Barry Iacopetta, Richie Soong
2012 Expert Review of Molecular Diagnostics  
Because the transcriptome from a specific tissue/cell only represents a subset of the exome, only the variants in the expressed genes or transcripts in that tissue can be detected by RNA-seq.  ...  It is likely that deleterious somatic mutations, such as nonsense/protein-truncating mutations in expressed genes, are more likely to be functionally important.  ...  Most of the studies that have detected somatic mutations in the cancer genome (utilizing genomic DNA extracted from cancer tissues or cell lines) have adopted either WES or WGS approaches.  ... 
doi:10.1586/erm.12.10 pmid:22468815 fatcat:wseg6s5ocnbzrertqrdxe6bcwy

Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data

August Yue Huang, Eunjung Alice Lee
2022 Frontiers in Aging  
An alternative way to study somatic mutations, especially those present in an extremely small number of cells or even in a single cell, is to sequence single-cell genomes after whole-genome amplification  ...  Thus, sensitive bioinformatic methods are required to distinguish mutant alleles from sequencing and base calling errors in bulk tissue samples.  ...  Cell-level Somatic Mutation Detection from Single-Cell RNA Sequencing.  ... 
doi:10.3389/fragi.2021.800380 pmid:35822012 pmcid:PMC9261417 fatcat:hsnhvbshibeqvalwrhcbaqvn2m

Single-cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia

Jolien De Bie, Sofie Demeyer, Llucia Alberti-Servera, Ellen Geerdens, Heidi Segers, Michaël Broux, Kim De Keersmaecker, Lucienne Michaux, Peter Vandenberghe, Thierry Voet, Nancy Boeckx, Anne Uyttebroeck (+1 others)
2018 Leukemia  
Analysis of CD34 + CD38 − cells and myeloid progenitors revealed that in half of the cases somatic mutations were detectable in multipotent progenitor cells.  ...  We demonstrate that targeted single-cell sequencing can elucidate the order of mutation acquisition in T-ALL and that T-ALL development can start in a multipotent progenitor cell.  ...  Acknowledgements This study was supported by the KU Leuven FACS core facility, a fellowship from the FWO-Vlaanderen (JDB and MB), and by grants from the European Research Council (JC), KU Leuven (PF/10  ... 
doi:10.1038/s41375-018-0127-8 pmid:29740158 pmcid:PMC5990522 fatcat:tavbvhun5bf3xdox3dzy5cfowq

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns

Martin Enge, H. Efsun Arda, Marco Mignardi, John Beausang, Rita Bottino, Seung K. Kim, Stephen R. Quake
2017 Cell  
Our results demonstrate the feasibility of using singlecell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue  ...  We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift.  ...  Acknowledgments The authors thank Norma Neff and Gary Mantalas for assistance with sequencing and Spyros Darmanis, Geoff Stanley, and Felix Horns for helpful discussions.  ... 
doi:10.1016/j.cell.2017.09.004 pmid:28965763 pmcid:PMC6047899 fatcat:ltzv3flkwzemvp5zbsa73sj24i

Subclonal identification of driver mutations and copy number variations from single-cell DNA sequencing of tumors

Chrysanthi Ainali, Manimozhi Manivannan, Sombeet Sahu, Adam Sciambi, Anup Parikh
2020 Journal of Biomolecular Techniques  
Here, we present a dynamic solution that we developed to simultaneously characterize point mutations, small indels and gene-level CNVs from the same single-cell.  ...  Single-cell sequencing elucidates unique insights in understanding intratumor heterogeneity and clonal evolution.  ...  Methods: Here, we present a dynamic solution that we developed to simultaneously characterize point mutations, small indels and gene-level CNVs from the same single-cell.  ... 
pmid:32831677 pmcid:PMC7424661 fatcat:qv72hghnkfcdndhu5hlcr563ii

Multiomic technologies for analyses of inborn errors of immunity: from snapshot of the average cell to dynamic temporal picture at single-cell resolution

Yusuke Kawashima, Ryuta Nishikomori, Osamu Ohara
2021 Inflammation and Regeneration  
gene at the nucleotide sequence level.  ...  In this review, we first overview current technologies for multiomic analysis, particularly focusing on RNA and protein profiling of bulk cell ensembles.  ...  absolute counting of RNA molecules [4] and (2) RNA sequencing at a single-cell resolution [5] .  ... 
doi:10.1186/s41232-021-00169-4 fatcat:aay4pc3x2jfyjhh7jifjjz2cfy

Longitudinal assessment of clonal mosaicism in humanhematopoiesis via mitochondrial mutation tracking

Caleb A. Lareau, Leif S. Ludwig, Vijay G. Sankaran
2019 Blood Advances  
Key Points Tracking of somatic mtDNA mutations in the peripheral blood enables the longitudinal assessment of clonal dynamics.  ...  of somatic mutation dynamics from bulk RNA-seq data.  ...  To these ends, we processed 57 RNA-seq datasets that had been serially sampled over the course of 161 weeks from a single individual.  ... 
doi:10.1182/bloodadvances.2019001196 pmid:31841597 pmcid:PMC6929387 fatcat:7rt4jpl3g5gopi4kt56czchxd4

Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint

Sören Müller, Aaron Diaz
2017 Frontiers in Genetics  
Single cell mRNA sequencing (scRNA-seq) has enabled unprecedented studies of intra-tumor heterogeneity and its role in cancer progression, metastasis, and treatment resistance.  ...  This combination can be used to reliably distinguish neoplastic from non-neoplastic cells, to correlate paracrine-signaling pathways between neoplastic cells and stroma, and to map expression signatures  ...  (C) Left: Circos-plot of somatic SNVs detected by Mutect from exome-seq, for all autosomes. Middle: Histogram of somatic SNVs (y-axis) detected in single cells (x-axis).  ... 
doi:10.3389/fgene.2017.00073 pmid:28620412 pmcid:PMC5450061 fatcat:macjeytgafb7jkscdkqnhv74ky

Emerging concepts in liquid biopsies

Samantha Perakis, Michael R. Speicher
2017 BMC Medicine  
We address normal and detectable mutation levels in the context of our current knowledge regarding the gradual accumulation of mutations during aging and in light of technological limitations.  ...  Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components.  ...  In fact, nucleosome positions inferred from whole-genome sequencing of plasma DNA strongly correlated with plasma RNA levels in cancer-free subjects.  ... 
doi:10.1186/s12916-017-0840-6 pmid:28381299 pmcid:PMC5382440 fatcat:z32lyn663bbjplcyquxck4dceq

Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes

J. D. Merker, K. M. Roskin, D. Ng, C. Pan, D. G. Fisk, J. J. King, R. Hoh, M. Stadler, L. M. Okumoto, P. Abidi, R. Hewitt, C. D. Jones (+10 others)
2013 Haematologica  
Additional mutations in three genes (CAP2, SOX30, and MFRP) were also evident, albeit with no support for expression at the RNA level.  ...  Interfacing of whole-genome DNA sequence data with RNA expression data identified three somatic mutations of potential functional significance: i) a nonsense mutation in CARD6, implicated in modulation  ...  Genome sequencing of myelofibrosis haematologica | 2013; 98 (11)  ... 
doi:10.3324/haematol.2013.092379 pmid:23872309 pmcid:PMC3815168 fatcat:ugx7psuevvfaxk3wst3jab7jri

Germline and somatic mtDNA mutations in mouse aging

Hong Ma, Yeonmi Lee, Tomonari Hayama, Crystal Van Dyken, Nuria Marti-Gutierrez, Ying Li, Riffat Ahmed, Amy Koski, Eunju Kang, Hayley Darby, Thanasup Gonmanee, Younjung Park (+4 others)
2018 PLoS ONE  
Remarkably, no acquired somatic mutations were detected in tested tissues.  ...  The accumulation of acquired mitochondrial genome (mtDNA) mutations with aging in somatic cells has been implicated in mitochondrial dysfunction and linked to age-onset diseases in humans.  ...  We are indebted to Yibing Jia for help in whole mtDNA genome sequencing.  ... 
doi:10.1371/journal.pone.0201304 pmid:30040856 pmcid:PMC6057648 fatcat:3do737ihabde5gd2yfx5g6sbe4
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