Encoding PCR Products with Batch-stamps and Barcodes
Polymerase chain reaction (PCR) has become the mainstay of DNA sequence analysis. Yet there is always uncertainty concerning the source of the template DNA that gave rise to a particular PCR product. The risks of contamination, biased amplification, and product redundancy are especially high when limited amounts of template DNA are used. We have developed and applied molecular encoding principles to solve this source-uncertainty problem for DNA sequences generated by standard PCR. Batch-stamps specify the date and sample identity, and barcodes detect template redundancy. Our approach thus enables classification of each PCR-derived sequence as valid, contaminant, or redundant, and provides a measure of sequence diversity. We recommend that batch-stamps and barcodes be used when amplifying irreplaceable DNAs and cDNAs available for forensic, clinical, single cell, and ancient DNA analyses.
KeywordsPCR Contamination Redundancy Batch-stamp Barcode Source DNA Populations of molecules
This work was supported by the National Institutes of Health grants GM 53805, HD 02274, and by the Washington Research Foundation. The method presented here is included in United States Patent Application 20070020640, filed by the University of Washington. We thank Carl Bergstrom, Alice Burden, Diane Genereux, Brooks Miner, and Jessica Sneeden for helpful suggestions and discussion.
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