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dc.contributor.authorJohnson, Matthew
dc.contributor.authorHaupt, Larisa
dc.contributor.authorGriffiths, Lyn
dc.date.accessioned2017-05-03T12:15:52Z
dc.date.available2017-05-03T12:15:52Z
dc.date.issued2004
dc.date.modified2014-07-14T05:55:07Z
dc.identifier.issn03051048
dc.identifier.doi10.1093/nar/gnh046
dc.identifier.urihttp://hdl.handle.net/10072/5497
dc.description.abstractWith an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.
dc.description.peerreviewedYes
dc.description.publicationstatusYes
dc.format.extent238176 bytes
dc.format.extent46350 bytes
dc.format.mimetypeapplication/pdf
dc.format.mimetypetext/plain
dc.languageEnglish
dc.language.isoeng
dc.publisherOxford University Press
dc.publisher.placeUK
dc.relation.ispartofpagefrom1
dc.relation.ispartofpageto9
dc.relation.ispartofissue6
dc.relation.ispartofjournalNucleic Acids Research
dc.relation.ispartofvolume32
dc.subject.fieldofresearchEnvironmental sciences
dc.subject.fieldofresearchBiological sciences
dc.subject.fieldofresearchInformation and computing sciences
dc.subject.fieldofresearchcode41
dc.subject.fieldofresearchcode31
dc.subject.fieldofresearchcode46
dc.titleLocked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dcterms.licensehttp://creativecommons.org/licenses/by/3.0/
gro.facultyGriffith Health, School of Medical Science
gro.rights.copyright© 2005 Johnson, Matthew Peter et al. This is an open access paper. http://creativecommons.org/licenses/by/3.0/ license that permits unrestricted use, provided that the paper is properly attributed.
gro.date.issued2004
gro.hasfulltextFull Text
gro.griffith.authorHaupt, Larisa
gro.griffith.authorJohnson, Matthew P.
gro.griffith.authorGriffiths, Lyn


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