Skip Navigation

Nucleic Acids Research 2005 33(13):e119; doi:10.1093/nar/gni126
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (63K) Freely available
Right arrow Screen PDF (63K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Dickson, P. A.
Right arrow Articles by James, M. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dickson, P. A.
Right arrow Articles by James, M. R.
Related Collections
Right arrow Genomics
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 29 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan

Peter A. Dickson, Grant W. Montgomery, Anjali Henders, Megan J. Campbell, Nicholas G. Martin and Michael R. James*

Queensland Institute of Medical Research Brisbane 4029 Australia

*To whom correspondence should be addressed. Tel: +61 3362 0277; Fax: +61 3362 0101; Email: michaelJ{at}qimr.edu.au

Received May 31, 2005. Revised June 29, 2005. Accepted July 19, 2005.

Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA–DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, despite their inherent instability during DNA replication, and the obvious challenge that this presents to WGA techniques. Here, we aimed to assess the applicability of MDA in STR genotyping by conducting a genome-wide scan of 768 STR markers for MDAs of 15 high quality genomic DNAs. We found that MDA genotyping call and accuracy rates were only marginally lower than for genomic DNA. Pooling of three replicate MDAs resulted in a small increase in both call rate and genotyping accuracy. We identified 34 STRs (4.4% of total markers) of which five essentially failed with MDA samples, and 29 of which showed elevated genotyping failures/discrepancies in the MDAs. We emphasise the importance of DNA and MDA quality checks, and the use of appropriate controls to identify problematic STR markers.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
J. M. Cunningham, T. A. Sellers, J. M. Schildkraut, Z. S. Fredericksen, R. A. Vierkant, L. E. Kelemen, M. Gadre, C. M. Phelan, Y. Huang, J. G. Meyer, et al.
Performance of Amplified DNA in an Illumina GoldenGate BeadArray Assay
Cancer Epidemiol. Biomarkers Prev., July 1, 2008; 17(7): 1781 - 1789.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. J. Salipante and M. S. Horwitz
Phylogenetic fate mapping
PNAS, April 4, 2006; 103(14): 5448 - 5453.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.