oru.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Urology.ORCID iD: 0000-0001-5533-7899
Örebro University, School of Medical Sciences. Department of Urology, Faculty of Medicine and Health, University Hospital, Örebro, Sweden.ORCID iD: 0000-0002-2850-6009
Department of Urology, Faculty of Medicine and Health, University Hospital Örebro, Örebro, Sweden; Örebro University, Örebro, Sweden.
Department of Pathology, F. Addari Institute of Oncology S. Orsola Hospital, Bologna, Italy.
Show others and affiliations
2018 (English)In: BMC Medical Research Methodology, ISSN 1471-2288, E-ISSN 1471-2288, Vol. 18, no 1, article id 161Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: In Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues.

METHODS: In this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent's BioAnalyzer. Student's t-test's and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman's correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality.

RESULTS: Nucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids.

CONCLUSIONS: To conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.

Place, publisher, year, edition, pages
BioMed Central, 2018. Vol. 18, no 1, article id 161
Keywords [en]
Archival formalin-fixed paraffin-embedded tissue, Nucleic acid isolation kits, Prostate biopsies, RNA integrity number
National Category
Urology and Nephrology Cancer and Oncology
Identifiers
URN: urn:nbn:se:oru:diva-70618DOI: 10.1186/s12874-018-0628-1ISI: 000452277900002PubMedID: 30518332Scopus ID: 2-s2.0-85058594763OAI: oai:DiVA.org:oru-70618DiVA, id: diva2:1269388
Funder
Swedish Cancer Society, CAN 2011/825
Note

Funding Agencies:

Italian Association for Cancer Research (IARC)  

Örebro county council research committee  

Lions cancer research foundation in Uppsala/Örebro 

Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2019-01-07Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records BETA

Carlsson, JessicaDavidsson, SabinaAndrén, Ove

Search in DiVA

By author/editor
Carlsson, JessicaDavidsson, SabinaAndrén, Ove
By organisation
School of Medical SciencesÖrebro University Hospital
In the same journal
BMC Medical Research Methodology
Urology and NephrologyCancer and Oncology

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 77 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf