Rapid method for separation of microsatellite alleles by the PhastSystem

Constructing STR multiplexes for individual identification of Hungarian red deer

Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations.

Detection of errors in dinucleotide repeat typing by nondenaturing electrophoresis

This study shows that consideration of minor bands (heteroduplex, shadow, and faint bands) associated with allele bands in nondenaturing polyacrylamide gel electrophoresis (PAGE) after polymerase chain reaction (PCR) is effective for detecting PCR processing errors that lead to mistyping of heterozygotes as homozygotes. Notably, we show that minor bands in native gels are highly effective for detecting allele dropout and preferential amplification in PCR amplification of dinucleotide repeats. These findings are based on an analysis of Mendelian inheritance patterns in families, and the reproduction of heterozygous band patterns by mixing homozygous DNAs before PCR, for a total of six (AC)n repeats located on human chromosome 11p15. To investigate the utility of our approach, a large population sample of 405 unrelated individuals was genotyped for each (AC)n repeat using minor bands as internal quality controls. Genotype frequencies at each of the six loci were in close agreement with Hardy-Weinberg proportions, which suggests that there were few genotyping errors. Our observations add to the evidence indicating that minor bands in native gels are of diagnostic value in the genotyping of dinucleotide repeats.

Accelerated separation of random complex DNA patterns in gels: comparing the performance of discontinuous and continuous buffers

Complex DNA fragment patterns produced by random amplified polymorphic DNA (RAPD) assays were separated in agarose as well as polyacrylamide gels using a continuous buffer and two discontinuous buffer systems, with and without urea, respectively. The effect of very high field strength/current levels on the duration of separation, the relative mobilities of the selected bands, and the appearance of the pattern was tested. The use of discontinuous buffer systems resulted in sharper bands and better resolution at 30 min duration of separation for DNA fragments in the size range of 200-2000 base pairs. These observations could help researchers in the rapid separation of band patterns produced by polymerase chain reaction (PCR)-based methods utilized in small- to mid-scale genome searches.

Gel electrophoretic restriction fragment length polymorphism analysis of DNA derived from individual nematodes, using the PhastSystem

The DNA sequences constituting the internal transcribed spacer region, located between 18S and 26S rDNA genes within the rRNA operon, derived from single nematodes of two genera (Steinernema and Heterorhabditis) were amplified by polymerase chain reaction (PCR) and subjected to digestion by four restriction enzymes. The digests were analyzed by restriction fragment length polymorphism (RFLP) gel electrophoresis on the PhastSystem, using 7.5%T, 5%C(Bis) polyacrylamide. The downscaling from conventional agarose to PhastSystem gels permitted the analysis to be done on individual nematodes, rather than on mixed samples with average properties. The analysis time was reduced so as to allow for the electrophoretic separation on 200 samples/workday. The resulting patterns of DNA fragments differed from those obtained by agarose gel electrophoresis under conventional conditions by an increased number of detected fragments. The PhastSystem gel analysis provides the basis for taxonomical revisions.

Heteroduplex mobility assay for subtyping HIV-1: improved methodology and comparison with phylogenetic analysis of sequence data

The feasibility of using DNA heteroduplex mobility analysis (HMA) as a rapid and reproducible method for routine subtyping HIV-1 in clinical specimens was examined by comparison with subtype determination by sequencing in both the gag and env genes. The heteroduplexes formed were examined by conventional polyacrylamide gel electrophoresis (PAGE) and also by electrophoresis in the Pharmacia PhastSystem. The significance of the HMA results was determined by the Kruskal-Wallis test, a non-parametric one way analysis of variance. It was possible to obtain an HMA profile rapidly (1-2 days) using fast PCR conditions and the PhastSystem. The HMA bands were generally sharper and more satisfactory on the Phast gels than on conventional polyacrylamide gels and the use of Phast gels was an improvement over conventional PAGE. Non-B subtype viruses could be distinguished from B subtypes, but it was more difficult to distinguish between the non-B subtypes and to assign a subtype to them. Thus, HMA can be adapted to offer a rapid screening method for HIV-1 subtyping, but sequencing is still necessary to assign a definitive subtype. This reflects the empirical nature of the subtype definitions and the quasispecies nature of the HIV genome population.