Detection and genotyping of human papillomaviruses from archival formalin-fixed tissue samples

Koenraad Van Doorslaer; Zigui Chen; Alison A. McBride

doi:10.1002/cpmc.16

Detection and genotyping of human papillomaviruses from archival formalin-fixed tissue samples

Koenraad Van Doorslaer, Zigui Chen, Alison A. McBride

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Pathology departments routinely process and store formalin-fixed, paraffinembedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades’ worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus.

Original language	English (US)
Pages (from-to)	14B.9.1-14B.9.20
Journal	Current Protocols in Microbiology
Volume	2016
DOIs	https://doi.org/10.1002/cpmc.16
State	Published - 2016
Externally published	Yes

Keywords

Cancer
Cervix
Degenerate primers
FFPE
Formalin
HPV
Neoplasia
PCR
Papillomavirus
Sequencing

ASJC Scopus subject areas

Parasitology
Microbiology
Virology

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10.1002/cpmc.16

Cite this

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title = "Detection and genotyping of human papillomaviruses from archival formalin-fixed tissue samples",

abstract = "Pathology departments routinely process and store formalin-fixed, paraffinembedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades{\textquoteright} worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus.",

keywords = "Cancer, Cervix, Degenerate primers, FFPE, Formalin, HPV, Neoplasia, PCR, Papillomavirus, Sequencing",

author = "{Van Doorslaer}, Koenraad and Zigui Chen and McBride, {Alison A.}",

note = "Funding Information: This work was supported by the Intramu ral Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health. We are very grateful to Bostjan Kocjan for advice on the protocol and manuscript. Publisher Copyright: {\textcopyright} 2016 by John Wiley & Sons, Inc.",

year = "2016",

doi = "10.1002/cpmc.16",

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T1 - Detection and genotyping of human papillomaviruses from archival formalin-fixed tissue samples

AU - Van Doorslaer, Koenraad

AU - Chen, Zigui

AU - McBride, Alison A.

N1 - Funding Information: This work was supported by the Intramu ral Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health. We are very grateful to Bostjan Kocjan for advice on the protocol and manuscript. Publisher Copyright: © 2016 by John Wiley & Sons, Inc.

PY - 2016

Y1 - 2016

N2 - Pathology departments routinely process and store formalin-fixed, paraffinembedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades’ worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus.

AB - Pathology departments routinely process and store formalin-fixed, paraffinembedded (FFPE) tissue samples for clinical diagnosis. These collections often contain decades’ worth of samples and represent a treasure trove of specimens that can be analyzed for retrospective epidemiological studies, diagnostics, and pathogen discovery. Accurate amplification and sequencing of DNA from these samples is critical for the usability of these FFPE samples. Here we present a collection of protocols that describe extraction of DNA from FFPE tissues, PCR amplification of human papillomavirus DNA, and subsequent genotyping of the infecting virus.

KW - Cancer

KW - Cervix

KW - Degenerate primers

KW - FFPE

KW - Formalin

KW - HPV

KW - Neoplasia

KW - PCR

KW - Papillomavirus

KW - Sequencing

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SP - 14B.9.1-14B.9.20

JO - Current Protocols in Microbiology

JF - Current Protocols in Microbiology

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Detection and genotyping of human papillomaviruses from archival formalin-fixed tissue samples

Abstract

Keywords

ASJC Scopus subject areas

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