Collection of Genomic DNA by Buccal Swabs for Polymerase Chain Reaction-Based Biomarker Assays

Walker, A. H. C.; Najarian, Derek; White, David L.; Jaffe, Julie M.; Kanetsky, Peter A.; Rebbeck, Timothy R.

doi:10.2307/3434392

Cited by 21 publications

(26 citation statements)

References 4 publications

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“…Genomic DNA was extracted from whole blood using GENERATION Capture Columns (Gentra Systems, Minneapolis, Minn.) or from buccal samples using a published protocol (Walker et al 1999). Sample DNA was coamplified with the heteroduplex generator pHGI7 using 1 U AmpliTaq Gold, 1× manufacturer's PCR buffer containing 15 mM MgCl 2 , 0.2 mM dNTP, and 0.4 μM each of the primers TIVS7F and TIVS7R.…”

Section: Laboratory Methodsmentioning

confidence: 99%

The human T locus and spina bifida risk

et al. 2004

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The transcription factor T is essential for mesoderm formation and axial development during embryogenesis. Embryonic genotype for a single-nucleotide polymorphism in intron 7 of T ( TIVS7 T/C) has been associated with the risk of spina bifida in some but not all studies. We developed a novel genotyping assay for the TIVS7 polymorphism using heteroduplex generator methodology. This assay was used to genotype spina bifida case-parent trios and the resulting data were analyzed using the transmission disequilibrium test and log-linear analyses. Analyses of these data demonstrated that heterozygous parents transmit the TIVS7-C allele to their offspring with spina bifida significantly more frequently than expected under the assumption of Mendelian inheritance (63 vs 50%, P=0.02). Moreover, these analyses suggest that the TIVS7-C allele acts in a dominant fashion, such that individuals carrying one or more copies of this allele have a 1.6-fold increased risk of spina bifida compared with individuals with zero copies. In silico analysis of the sequence surrounding this polymorphism revealed a potential target site for olfactory neuron-specific factor-1, a transcription factor expressed in the neural tube during development, spanning the polymorphic site. Several other putative, developmentally important and/or environmentally responsive transcription factor-binding sites were also identified close to the TIVS7 polymorphism. The TIVS7 polymorphism or a variant that is in linkage disequilibrium with the TIVS7 polymorphism may, therefore, play a role in T gene expression and influence the risk of spina bifida.

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Section: Laboratory Methodsmentioning

confidence: 99%

The human T locus and spina bifida risk

et al. 2004

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“…Genomic DNA was collected from saliva and extracted according to modified standard procedures (Walker et al, 1999). Rs2023239 genotype was determined with an Applied Biosystems (Life Technologies, Carlsbad, CA) thermocycler and a Taqman (Invitrogen, Carlsbad, CA) polymerase chain reaction assay, run in triplicate.…”

Section: Genotypingmentioning

confidence: 99%

Associations between Cannabinoid Receptor-1 (CNR1) Variation and Hippocampus and Amygdala Volumes in Heavy Cannabis Users

Schacht

Hutchison

Filbey

2012

Neuropsychopharmacol

111

102

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Heavy cannabis users display smaller amygdalae and hippocampi than controls, and genetic variation accounts for a large proportion of variance in liability to cannabis dependence (CD). A single nucleotide polymorphism in the cannabis receptor-1 gene (CNR1), rs2023239, has been associated with CD diagnosis and intermediate phenotypes, including abstinence-induced withdrawal, cue-elicited craving, and parahippocampal activation to cannabis cues. This study compared hippocampal and amygdalar volumes (potential CD intermediate phenotypes) between heavy cannabis users and healthy controls, and analyzed interactions between group, rs2023239 variation, and the volumes of these structures. Ninety-four heavy cannabis users participated, of whom 37 (14 men, 23 women; mean age=27.8) were matched to 37 healthy controls (14 men, 23 women; mean age=27.3) for case-control analyses. Controlling for total intracranial volume and other confounding variables, matched cannabis users had smaller bilateral hippocampi (left, p=0.002; right, p=0.001) and left amygdalae (p=0.01) than controls. When genotype was considered in the case-control analyses, there was a group by genotype interaction, such that the rs2023239 G allele predicted lower volume of bilateral hippocampi among cannabis users relative to controls (both p<0.001). This interaction persisted when all 94 cannabis users were compared to controls. There were no group by genotype interactions on amygdalar volume. These data replicate previous findings of reduced hippocampal and amygdalar volume among heavy cannabis users, and suggest that CNR1 rs2023239 variation may predispose smaller hippocampal volume after heavy cannabis use. This association should be tested in future studies of brain volume differences in CD.

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“…Genomic DNA was obtained from buccal swabs using a protocol described in detail by Walker and colleagues [20]. The CYP2C9*2 (rs1799853) allele denotes a C430T transition in exon 3 and results in the loss of an AvaII restriction digest site.…”

Section: Genotypingmentioning

confidence: 99%