title: Multiplex polymerase chain reaction for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA: application in human identification.
abstract: Human forensic casework requires sensitive quantitation of human nuclear (nDNA), mitochondrial (mtDNA), and male Y-chromosome DNA from complex biomaterials. Although many such systems are commercially available, no system is capable of simultaneously quantifying all three targets in a single reaction. Most available methods either are not multiplex compatible or lack human specificity. Here, we report the development of a comprehensive set of human-specific, target-specific multiplex polymerase chain reaction (PCR) assays for DNA quantitation. Using TaqMan-MGB probes, our duplex qPCR for nDNA/mtDNA had a linear quantitation range of 100 ng to 1 pg, and our triplex qPCR assay for nDNA/mtDNA/male Y DNA had a linear range of 100-0.1 ng. Human specificity was demonstrated by the accurate detection of 0.05 and 5% human DNA from a complex source of starting templates. Target specificity was confirmed by the lack of cross-amplification among targets. A high-throughput alternative for human gender determination was also developed by multiplexing the male Y primer/probe set with an X-chromosome-based system. Background cross-amplification with DNA templates derived from 14 other species was negligible aside from the male Y assay which produced spurious amplifications from other nonhuman primate templates. Mainstream application of these assays will undoubtedly benefit forensic genomics.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Walker
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Perodeau
authors.forename: Kate E
authors.initials: KE
authors.lastname: Landry
authors.forename: Nadica
authors.initials: N
authors.lastname: Stoilova
authors.forename: Meredith E
authors.initials: ME
authors.lastname: Laborde
authors.forename: Jaiprakash
authors.initials: J
authors.lastname: Shewale
authors.forename: Sudhir K
authors.initials: SK
authors.lastname: Sinha
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D041321:Chromosomes, Human, X; D041322:Chromosomes, Human, Y / Q000235:genetics; D004247:DNA / Q000032:analysis* / Q000592:standards; D016172:DNA Fingerprinting / Q000379:methods*; D015342:DNA Probes; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: D015342:DNA Probes; D004272:DNA, Mitochondrial; D004247:DNA