title: Allelic Dropout During Polymerase Chain Reaction due to G-Quadruplex Structures and DNA Methylation Is Widespread at Imprinted Human Loci.
abstract: Loss of one allele during polymerase chain reaction (PCR) amplification of DNA, known as allelic dropout, can be caused by a variety of mechanisms. Allelic dropout during PCR may have profound implications for molecular diagnostic and research procedures that depend on PCR and assume biallelic amplification has occurred. Complete allelic dropout due to the combined effects of cytosine methylation and G-quadruplex formation was previously described for a differentially methylated region of the human imprinted gene,MESTWe now demonstrate that this parent-of-origin specific allelic dropout can potentially occur at several other genomic regions that display genomic imprinting and have propensity for G-quadruplex formation, includingAIM1,BLCAP,DNMT1,PLAGL1,KCNQ1, andGRB10These findings demonstrate that systematic allelic dropout during PCR is a general phenomenon for regions of the genome where differential allelic methylation and G-quadruplex motifs coincide, and suggest that great care must be taken to ensure biallelic amplification is occurring in such situations.
authors.affiliation: Department of Pathology, University of Otago, Christchurch 8140, New Zealand.
authors.forename: Aaron J
authors.identifier: 0000-0001-9148-8045
authors.initials: AJ
authors.lastname: Stevens
authors.affiliation: Department of Pathology, University of Otago, Christchurch 8140, New Zealand.
authors.forename: Millie G
authors.initials: MG
authors.lastname: Taylor
authors.affiliation: Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
authors.forename: Frederick Grant
authors.initials: FG
authors.lastname: Pearce
authors.affiliation: Department of Pathology, University of Otago, Christchurch 8140, New Zealand martin.kennedy@otago.ac.nz.
authors.forename: Martin A
authors.identifier: 0000-0002-6445-8526
authors.initials: MA
authors.lastname: Kennedy
mesh_terms: D000483:Alleles; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D054856:G-Quadruplexes; D056426:Genetic Loci; D015894:Genome, Human; D018392:Genomic Imprinting; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D013698:Templates, Genetic
chemical_list: D004247:DNA
keywords: G-quadruplex; PCR; allelic dropout; methylation; polymerase chain reaction