Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines

The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this s...

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Autores principales: Rojas, Mark, Golovko, Georgiy, Khanipov, Kamil, Albayrak, Levent, Chumakov, Sergei, Pettitt, B. Montgomery, Strongin, Alex Y., Fofanov, Yuriy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454691/
https://www.ncbi.nlm.nih.gov/pubmed/26039084
http://dx.doi.org/10.1371/journal.pone.0127799
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author Rojas, Mark
Golovko, Georgiy
Khanipov, Kamil
Albayrak, Levent
Chumakov, Sergei
Pettitt, B. Montgomery
Strongin, Alex Y.
Fofanov, Yuriy
author_facet Rojas, Mark
Golovko, Georgiy
Khanipov, Kamil
Albayrak, Levent
Chumakov, Sergei
Pettitt, B. Montgomery
Strongin, Alex Y.
Fofanov, Yuriy
author_sort Rojas, Mark
collection PubMed
description The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data.
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spelling pubmed-44546912015-06-09 Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines Rojas, Mark Golovko, Georgiy Khanipov, Kamil Albayrak, Levent Chumakov, Sergei Pettitt, B. Montgomery Strongin, Alex Y. Fofanov, Yuriy PLoS One Research Article The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data. Public Library of Science 2015-06-03 /pmc/articles/PMC4454691/ /pubmed/26039084 http://dx.doi.org/10.1371/journal.pone.0127799 Text en © 2015 Rojas et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Rojas, Mark
Golovko, Georgiy
Khanipov, Kamil
Albayrak, Levent
Chumakov, Sergei
Pettitt, B. Montgomery
Strongin, Alex Y.
Fofanov, Yuriy
Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title_full Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title_fullStr Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title_full_unstemmed Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title_short Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines
title_sort secondary analysis of the nci-60 whole exome sequencing data indicates significant presence of propionibacterium acnes genomic material in leukemia (rpmi-8226) and central nervous system (sf-295, sf-539, and snb-19) cell lines
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454691/
https://www.ncbi.nlm.nih.gov/pubmed/26039084
http://dx.doi.org/10.1371/journal.pone.0127799
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