Robustness of single-base extension against mismatches at the site of primer attachment in a clinical assay.

DNA genotyping is important for epidemiological and clinical studies and diagnosis for individuals. Genotyping error can strongly influence the outcome of such investigations. One possible reason for genotyping error is additional DNA sequence variation, which can lead to allelic dropout. Based on a published study where allelic dropout occurred in genotyping the cholesteryl ester transfer protein TaqIB polymorphism by a TaqMan-based method, we investigated the susceptibility of the single-base extension (SBE)-based GenoSNIP method to additional sequence variation at the primer attachment site. SBE genotyping was applied to 147 patient samples with known alleles and to synthetic SBE templates. Variables were positions of nucleotide mismatches, yield of SBE reactions, primer design, and ratio of alleles in the template. No allelic dropout occurred when genotyping the TaqIB polymorphism regardless of the reported nucleotide mismatch. Yields of SBE assays critical for allelic dropout were decreased in the presence of the reported nucleotide mismatch depending on SBE assay design. In a systematic mutation scan, only the position immediately adjacent to the polymorphism caused allelic dropout under standard conditions. Depending on SBE assay design, changes in allelic ratio due to a nucleotide mismatch were similar in appearance to changes due to sample mixture or copy number variation. In conclusion, we found the SBE genotyping assays to be relatively robust against interfering DNA variations. The importance of appropriate design and validation of assays, especially in regard to critical yields and potentially interfering nucleotide mismatches, should be emphasized particularly in clinical settings. Care should be taken when interpreting observed changes in the allelic ratio, which could be caused by nucleotide mismatches, sample mixtures, or copy number variation.

Hibernation model of tau phosphorylation in hamsters: selective vulnerability of cholinergic basal forebrain neurons - implications for Alzheimer's disease.

Neurofibrillar tangles made up of 'paired helical filaments' (PHFs) consisting of hyperphosphorylated microtubule-associated protein tau are major hallmarks of Alzheimer's disease (AD). Tangle formation selectively affects certain neuronal types and systematically progresses throughout numerous brain areas, which reflects a hierarchy of neuronal vulnerability and provides the basis for the neuropathological staging of disease severity. Mechanisms underlying this selective neuronal vulnerability are unknown. We showed previously that reversible PHF-like phosphorylation of tau occurs during obligate hibernation. Here we extend these findings to facultative hibernators such as Syrian hamsters (Mesocricetus auratus) forced into hibernation. In this model, we showed in the basal forebrain projection system that cholinergic neurons are selectively affected by PHF-like phosphorylated tau, while gamma-aminobutyric acid (GABA)ergic neurons are largely spared, which shows strong parallels to the situation in AD. Formation of PHF-tau in these neurons apparently does not affect their function as pacemaker for terminating hibernation. We conclude that although formation of PHF-like phosphorylated tau in the mammalian brain follows a certain hierarchy, affecting some neurons more frequently than others, it is not necessarily associated with impaired neuronal function and viability. This indicates a more general link between PHF-like phosphorylation of tau and the adaptation of neurons under conditions of a 'vita minima'.