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Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol

Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represent...

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Autores principales: Carretta, Chiara, Mallia, Selene, Genovese, Elena, Parenti, Sandra, Rontauroli, Sebastiano, Bianchi, Elisa, Fantini, Sebastian, Sartini, Stefano, Tavernari, Lara, Tagliafico, Enrico, Manfredini, Rossella
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7582552/
https://www.ncbi.nlm.nih.gov/pubmed/33036143
http://dx.doi.org/10.3390/ijms21197366
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author Carretta, Chiara
Mallia, Selene
Genovese, Elena
Parenti, Sandra
Rontauroli, Sebastiano
Bianchi, Elisa
Fantini, Sebastian
Sartini, Stefano
Tavernari, Lara
Tagliafico, Enrico
Manfredini, Rossella
author_facet Carretta, Chiara
Mallia, Selene
Genovese, Elena
Parenti, Sandra
Rontauroli, Sebastiano
Bianchi, Elisa
Fantini, Sebastian
Sartini, Stefano
Tavernari, Lara
Tagliafico, Enrico
Manfredini, Rossella
author_sort Carretta, Chiara
collection PubMed
description Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.
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spelling pubmed-75825522020-10-29 Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol Carretta, Chiara Mallia, Selene Genovese, Elena Parenti, Sandra Rontauroli, Sebastiano Bianchi, Elisa Fantini, Sebastian Sartini, Stefano Tavernari, Lara Tagliafico, Enrico Manfredini, Rossella Int J Mol Sci Article Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing. MDPI 2020-10-06 /pmc/articles/PMC7582552/ /pubmed/33036143 http://dx.doi.org/10.3390/ijms21197366 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Carretta, Chiara
Mallia, Selene
Genovese, Elena
Parenti, Sandra
Rontauroli, Sebastiano
Bianchi, Elisa
Fantini, Sebastian
Sartini, Stefano
Tavernari, Lara
Tagliafico, Enrico
Manfredini, Rossella
Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title_full Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title_fullStr Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title_full_unstemmed Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title_short Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol
title_sort genomic analysis of hematopoietic stem cell at the single-cell level: optimization of cell fixation and whole genome amplification (wga) protocol
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7582552/
https://www.ncbi.nlm.nih.gov/pubmed/33036143
http://dx.doi.org/10.3390/ijms21197366
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