Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

ABSTRACT Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the asso...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Don A. Baldwin, Michael Feldman, James C. Alwine, Erle S. Robertson
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/56bc6903ec1744d2823ec88ef6cc896c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:56bc6903ec1744d2823ec88ef6cc896c
record_format	dspace
spelling	oai:doaj.org-article:56bc6903ec1744d2823ec88ef6cc896c2021-11-15T15:45:54ZMetagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues10.1128/mBio.01714-142150-7511https://doaj.org/article/56bc6903ec1744d2823ec88ef6cc896c2014-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01714-14https://doaj.org/toc/2150-7511ABSTRACT Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases. IMPORTANCE This work describes the design and testing of a PathoChip array containing probes with the ability to detect all known publicly available virus sequences as well as hundreds of pathogenic bacteria, fungi, parasites, and helminths. PathoChip provides wide coverage of microbial pathogens in an economical format. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and sequencing methods. These studies demonstrate that the PathoChip technology is a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.Don A. BaldwinMichael FeldmanJames C. AlwineErle S. RobertsonAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 5 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Don A. Baldwin Michael Feldman James C. Alwine Erle S. Robertson Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
description	ABSTRACT Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases. IMPORTANCE This work describes the design and testing of a PathoChip array containing probes with the ability to detect all known publicly available virus sequences as well as hundreds of pathogenic bacteria, fungi, parasites, and helminths. PathoChip provides wide coverage of microbial pathogens in an economical format. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and sequencing methods. These studies demonstrate that the PathoChip technology is a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.
format	article
author	Don A. Baldwin Michael Feldman James C. Alwine Erle S. Robertson
author_facet	Don A. Baldwin Michael Feldman James C. Alwine Erle S. Robertson
author_sort	Don A. Baldwin
title	Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
title_short	Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
title_full	Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
title_fullStr	Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
title_full_unstemmed	Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues
title_sort	metagenomic assay for identification of microbial pathogens in tumor tissues
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/56bc6903ec1744d2823ec88ef6cc896c
work_keys_str_mv	AT donabaldwin metagenomicassayforidentificationofmicrobialpathogensintumortissues AT michaelfeldman metagenomicassayforidentificationofmicrobialpathogensintumortissues AT jamescalwine metagenomicassayforidentificationofmicrobialpathogensintumortissues AT erlesrobertson metagenomicassayforidentificationofmicrobialpathogensintumortissues
_version_	1718427584405962752

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

Ejemplares similares