title: Encoding PCR products with batch-stamps and barcodes.
abstract: 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.
authors.affiliation: Department of Biology, University of Washington, Box 351800, Seattle, WA 98195-0002, USA.
authors.forename: Megan L
authors.initials: ML
authors.lastname: McCloskey
authors.forename: Reinhard
authors.initials: R
authors.lastname: Stöger
authors.forename: R Scott
authors.initials: RS
authors.lastname: Hansen
authors.forename: Charles D
authors.initials: CD
authors.lastname: Laird
mesh_terms: D051860:Fragile X Messenger Ribonucleoprotein 1 / Q000235:genetics*; D006801:Humans; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D040641:Quantitative Trait Loci / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D051860:Fragile X Messenger Ribonucleoprotein 1; D009841:Oligonucleotides; C497683:FMR1 protein, human