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Nucleic Acids Research 2004 32(17):e135; doi:10.1093/nar/gnh132
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Published online 30 September 2004

Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved

Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR

Brooks E. Miner1,*, Reinhard J. Stöger1, Alice F. Burden1, Charles D. Laird1,2 and R. Scott Hansen3

1 Department of Biology, 2 Department of Genome Sciences and 3 Department of Medicine, University of Washington, Seattle, WA 98195, USA

* To whom correspondence should be addressed at Box 351800, Seattle, WA 98195, USA. Tel: +1 206 616 9385; Fax: +1 206 543 3041; Email: miner{at}u.washington.edu
Correspondence may also be addressed to Charles D. Laird. Email: cdlaird{at}u.washington.edu

Received August 12, 2004; Revised and Accepted September 11, 2004

PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular ‘batch-stamps’ that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes.


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