Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • 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
Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.
Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Health Sciences. Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.
Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Show others and affiliations
2012 (English)In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 425, no 2, 379-83 p.Article in journal (Refereed) Published
Abstract [en]

Personalized cancer treatment requires molecular characterization of individual tumor biopsies. These samples are frequently only available in limited quantities hampering genomic analysis. Several whole genome amplification (WGA) protocols have been developed with reported varying representation of genomic regions post amplification. In this study we investigate region dropout using a φ29 polymerase based WGA approach. DNA from 123 lung cancers specimens and corresponding normal tissue were used and evaluated by Sanger sequencing of the p53 exons 5-8. To enable comparative analysis of this scarce material, WGA samples were compared with unamplified material using a pooling strategy of the 123 samples. In addition, a more detailed analysis of exon 7 amplicons were performed followed by extensive cloning and Sanger sequencing. Interestingly, by comparing data from the pooled samples to the individually sequenced exon 7, we demonstrate that mutations are more easily recovered from WGA pools and this was also supported by simulations of different sequencing coverage. Overall this data indicate a limited random loss of genomic regions supporting the use of whole genome amplification for genomic analysis.

Place, publisher, year, edition, pages
2012. Vol. 425, no 2, 379-83 p.
Keyword [en]
Whole genome amplification, TP53, Mutations, Validation
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:liu:diva-99893DOI: 10.1016/j.bbrc.2012.07.101PubMedID: 22842464OAI: oai:DiVA.org:liu-99893DiVA: diva2:658839
Available from: 2013-10-23 Created: 2013-10-23 Last updated: 2017-12-06

Open Access in DiVA

fulltext(525 kB)160 downloads
File information
File name FULLTEXT01.pdfFile size 525 kBChecksum SHA-512
ec000c42d53e4ed5f5cc72c62ef6fc75729a562391ccd966108e1e79b7f203f96be8ad5f69c7944ddeea782e7fc9f30abd348cbbbf1f37840846dd89617f839f
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Green, Henrik

Search in DiVA

By author/editor
Green, Henrik
By organisation
Division of Drug ResearchFaculty of Health Sciences
In the same journal
Biochemical and Biophysical Research Communications - BBRC
Medical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 160 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 78 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • 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