Cargando…
Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level
Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Investigative Pathology
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351127/ https://www.ncbi.nlm.nih.gov/pubmed/32247862 http://dx.doi.org/10.1016/j.jmoldx.2020.02.013 |
_version_ | 1783735905746419712 |
---|---|
author | Lu, Shan Chang, Chia-Jung Guan, Yinghui Szafer-Glusman, Edith Punnoose, Elizabeth Do, An Suttmann, Becky Gagnon, Ross Rodriguez, Angel Landers, Mark Spoerke, Jill Lackner, Mark R. Xiao, Wenzhong Wang, Yulei |
author_facet | Lu, Shan Chang, Chia-Jung Guan, Yinghui Szafer-Glusman, Edith Punnoose, Elizabeth Do, An Suttmann, Becky Gagnon, Ross Rodriguez, Angel Landers, Mark Spoerke, Jill Lackner, Mark R. Xiao, Wenzhong Wang, Yulei |
author_sort | Lu, Shan |
collection | PubMed |
description | Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1), multiple displacement amplification (Repli-g), and hybrid PCR- and multiple displacement amplification–based [multiple annealing and loop-based amplification cycling (MALBAC)] is reported herein. To demonstrate clinical utilities, copy number variations (CNVs) in single CTCs isolated from four patients with squamous non–small-cell lung cancer were profiled. Results indicate that MALBAC and Repli-g WGA have significantly broader genomic coverage compared with GenomePlex and Ampli1. Furthermore, MALBAC coupled with low-pass whole genome sequencing has better coverage breadth, uniformity, and reproducibility and is superior to Repli-g for genome-wide CNV profiling and detecting focal oncogenic amplifications. For mutation analysis, none of the WGA methods were found to achieve sufficient sensitivity and specificity by whole exome sequencing. Finally, profiling of single CTCs from patients with non–small-cell lung cancer revealed potentially clinically relevant CNVs. In conclusion, MALBAC WGA coupled with low-pass whole genome sequencing is a robust workflow for genome-wide CNV profiling at single-cell level and has great potential to be applied in clinical investigations. Nevertheless, data suggest that none of the evaluated single-cell sequencing workflows can reach sufficient sensitivity or specificity for mutation detection required for clinical applications. |
format | Online Article Text |
id | pubmed-8351127 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Society for Investigative Pathology |
record_format | MEDLINE/PubMed |
spelling | pubmed-83511272021-08-23 Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level Lu, Shan Chang, Chia-Jung Guan, Yinghui Szafer-Glusman, Edith Punnoose, Elizabeth Do, An Suttmann, Becky Gagnon, Ross Rodriguez, Angel Landers, Mark Spoerke, Jill Lackner, Mark R. Xiao, Wenzhong Wang, Yulei J Mol Diagn Regular Article Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1), multiple displacement amplification (Repli-g), and hybrid PCR- and multiple displacement amplification–based [multiple annealing and loop-based amplification cycling (MALBAC)] is reported herein. To demonstrate clinical utilities, copy number variations (CNVs) in single CTCs isolated from four patients with squamous non–small-cell lung cancer were profiled. Results indicate that MALBAC and Repli-g WGA have significantly broader genomic coverage compared with GenomePlex and Ampli1. Furthermore, MALBAC coupled with low-pass whole genome sequencing has better coverage breadth, uniformity, and reproducibility and is superior to Repli-g for genome-wide CNV profiling and detecting focal oncogenic amplifications. For mutation analysis, none of the WGA methods were found to achieve sufficient sensitivity and specificity by whole exome sequencing. Finally, profiling of single CTCs from patients with non–small-cell lung cancer revealed potentially clinically relevant CNVs. In conclusion, MALBAC WGA coupled with low-pass whole genome sequencing is a robust workflow for genome-wide CNV profiling at single-cell level and has great potential to be applied in clinical investigations. Nevertheless, data suggest that none of the evaluated single-cell sequencing workflows can reach sufficient sensitivity or specificity for mutation detection required for clinical applications. American Society for Investigative Pathology 2020-06 /pmc/articles/PMC8351127/ /pubmed/32247862 http://dx.doi.org/10.1016/j.jmoldx.2020.02.013 Text en © 2020 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Regular Article Lu, Shan Chang, Chia-Jung Guan, Yinghui Szafer-Glusman, Edith Punnoose, Elizabeth Do, An Suttmann, Becky Gagnon, Ross Rodriguez, Angel Landers, Mark Spoerke, Jill Lackner, Mark R. Xiao, Wenzhong Wang, Yulei Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title | Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title_full | Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title_fullStr | Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title_full_unstemmed | Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title_short | Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level |
title_sort | genomic analysis of circulating tumor cells at the single-cell level |
topic | Regular Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351127/ https://www.ncbi.nlm.nih.gov/pubmed/32247862 http://dx.doi.org/10.1016/j.jmoldx.2020.02.013 |
work_keys_str_mv | AT lushan genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT changchiajung genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT guanyinghui genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT szaferglusmanedith genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT punnooseelizabeth genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT doan genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT suttmannbecky genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT gagnonross genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT rodriguezangel genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT landersmark genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT spoerkejill genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT lacknermarkr genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT xiaowenzhong genomicanalysisofcirculatingtumorcellsatthesinglecelllevel AT wangyulei genomicanalysisofcirculatingtumorcellsatthesinglecelllevel |