title: Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics.
abstract: Amplification of genomic sequences flanked by delta elements of retrotransposons TY1 and TY2 is a reliable method for characterization of Saccharomyces cerevisiae strains. The aim of this study is to evaluate the usefulness of microfluidic electrophoresis (Caliper LabChip) to assess the factors that affect interlaboratory reproducibility of interdelta sequence typing for S. cerevisiae strain delimitation. We carried out experiments in two laboratories, using varying combinations of Taq DNA polymerases and thermal cyclers. The reproducibility of the technique is evaluated using non-parametric statistical tests and we show that the source of Taq DNA polymerase and technical differences between laboratories have the highest impact on reproducibility, whereas thermal cyclers have little impact. We also show that the comparative analysis of interdelta patterns is more reliable when fragment sizes are compared than when absolute and relative DNA concentrations of each band are considered. Interdelta analysis based on a smaller fraction of bands with intermediate sizes between 100 and 1000 bp yields the highest reproducibility.
authors.affiliation: CBMA (Centre of Molecular and Environmental Biology)/Department of Biology/University of Minho, Braga, Portugal.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Franco-Duarte
authors.forename: Inês
authors.initials: I
authors.lastname: Mendes
authors.forename: Ana Catarina
authors.initials: AC
authors.lastname: Gomes
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
authors.forename: Bruno
authors.initials: B
authors.lastname: de Sousa
authors.forename: Dorit
authors.initials: D
authors.lastname: Schuller
mesh_terms: D000704:Analysis of Variance; D001331:Automation; D004587:Electrophoresis, Agar Gel; D019075:Electrophoresis, Capillary; D005838:Genotype; D046210:Microfluidic Analytical Techniques / Q000379:methods*; D010316:Particle Size; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D018626:Retroelements / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D018709:Statistics, Nonparametric
chemical_list: D018626:Retroelements