pMCT 118 (D1S80): a new allelic ladder and an improved electrophoretic separation lead to the demonstration of 28 alleles

Interlaboratory reproducibility of a microsatellite-based typing assay for Aspergillus fumigatus through the use of allelic ladders: proof of concept

An interlaboratory study was performed with the aim of investigating the reproducibility of a multiplex microbial microsatellite-based typing assay for Aspergillus fumigatus in different settings using a variety of experimental and analytical conditions and with teams having variable prior microsatellite typing experience. In order to circumvent problems with exchange of sizing data, allelic ladders are introduced as a straightforward and universally applicable concept for standardization of such typing assays. Allelic ladders consist of mixtures of well-characterized reference fragments to act as reference points for the position in an electrophoretic trace of fragments with established repeat numbers. Five laboratories independently analysed six microsatellite markers in 18 samples that were provided either as DNA or as A. fumigatus conidia. Allelic data were reported as repeat numbers and as sizes in nucleotides. Without the use of allelic ladders, size differences of up to 6.7 nucleotides were observed, resulting in interpretation errors of up to two repeat units. Difficulties in interpretation were related to non-specific amplification products (which were resolved with explanation) and bleed-through of the different fluorescent labels. In contrast, after resolution of technical or interpretive problems, standardization of sizing data by using allelic ladders enabled all participants to produce identical typing data. The use of allelic ladders as a routine part of molecular typing using microsatellite markers provides robust results suitable for interlaboratory comparisons and for deposition in a global typing database.

Molecular typing of Aspergillus species

Aspergillus species are widely distributed fungi that release large amounts of airborne conidia, which are dispersed in the environment. Several Aspergillus species have been described as human pathogens. Molecular techniques have been developed to investigate the epidemiological relation between environmental and clinical isolates. Several typing methods have been described for Aspergillus species, most of them with reference to Aspergillus fumigatus. Here, we summarise all the different available molecular typing techniques for Aspergillus. The performance of these techniques is evaluated with respect to their practical feasibility, and their interpretation and discriminatory power assessed. For A. fumigatus isolates, a large extent of genetic variability is demonstrated and therefore fingerprinting techniques with high discriminatory power and high reproducibility are required for this species. Afut1-restriction fragment length polymorphism and microsatellite typing showed the highest discriminatory power. In addition, the microsatellites show excellent reproducibility. Other typing techniques are still useful for smaller epidemiological problems and for less well-equipped laboratories.

Microsatellite based typing of Aspergillus fumigatus: Strengths, pitfalls and solutions

Microsatellites, or short tandem repeats (STR's), are popular tools to discriminate between microbial isolates. Here, we report on the robustness of a microsatellite panel for discrimination of Aspergillus fumigatus isolates. Two major PCR artefacts (stutter peaks and minus-A peaks) can complicate correct interpretation of STR data. We investigated the effect of alterations to the various components of the PCR amplification mixtures on these PCR artefacts and on the reproducibility of this assay. Some extreme conditions led to a loss of signal, but, under all conditions where a signal was obtained, identical typing results were produced. Furthermore, pitfalls with the exchange of results between labs are discussed. These pitfalls are primarily associated with sizing of the obtained PCR fragments.

Characterization of a novel D1S80 pseudoallele

During a D1S80 population study conducted for databasing purposes in the New York City Ashkenazi Jewish population, eight out of 96 samples were typed with a band corresponding to the position of a #15 allele. In seven of the eight samples, three bands appeared. Further investigation was needed to explain the high frequency of an allele considered so rare that it is not included in the commercially provided allelic ladder. After extraction of the putative D1S80 15-repeat amplicon band from the 6% polyacrylamide genotyping gel, the amplicon bands were reamplified with D1S80 primers. After retyping as putative 15 alleles, these samples underwent Southern hybridization with a D1S80 locus-specific probe followed by DNA sequence analysis. Sequence analysis revealed that these bands did not arise from true D1S80 15 alleles. However, the PCR product was of a size that fell within the allelic ladder region corresponding to the 15 band and contained end sequences with strong homology to the D1S80 primers. An alignment search of the sequenced product revealed that a portion of the amplicons contained 72% identity to a known gene. These results emphasize the importance of sequencing analysis when questions arise about the authenticity of an allele.

D1S80 subtyping by PCR-RFLP: new nomenclature and further characterization

In a previous study, we screened out sequence variations within alleles at the D1S80 locus of a Japanese population using PCR-RFLP with EcoRII as a restriction enzyme. In the present study, through analyzing the alleles in a Chinese population, we were able to demonstrate four new electrophoretic band patterns that were complementary to the Japanese data. After summarizing the band patterns and sequencing results of these two populations, we established a new nomenclature for the PCR-RFLP band patterns, closely relating them to their corresponding sequences so that the new types could be designated easily and accurately. After PCR-RFLP subtyping, nineteen alleles in the Chinese population were revealed to have a total of thirty-seven subtypes. The discrimination power of this locus in the Chinese population was elevated from 0.974 to 0.988, and the Hardy-Weinberg equilibrium in this population showed no deviation when checked. Two samples typed as homozygotes 24/24 and 30/30 were identified to be actually heterozygous according to their band patterns. The result was supported by the sequencing analysis of the two samples in which overlapping of eight and eleven repeat units, respectively, were revealed. The heterozygosity was thus elevated from 0.85 to 0.87. The present study proved that PCR-RFLP was an effective method for subtyping D1S80 alleles in the Chinese.

Sequence variation of allele 27 at the D1S80 locus

In 180 unrelated Japanese individuals 18 examples of allele 27 were detected at the locus D1S80 (MCT118). On 6% polylacrylamide gels 5 out of these 18 alleles were found to migrate between allele 26 and allele 27, but closer to allele 27, and thus were labelled variants of allele 27. All 18 examples of allele 27 were sequenced and the results were compared. Although all had the same number of base pairs (578 bp) the five variants could be subdivided into three types. V1, V2 and V3. The variants and the standard allele were composed of the same kinds of repeat units, but the order of arrangement was different. We investigated whether it was possible to distinguish the standard allele 27, and the variants V1, V2, and V3 by PCR-RFLP. EcoRII and MspI which have restriction sites within the repeat units were adopted as restriction enzymes. The variants could be discriminated from each other after treatment of the PCR fragments with EcoRII or MspI, followed by PAG electrophoresis.

Optimization of single-strand conformation polymorphism analysis in the presence of polyethylene glycol

We report optimization of single-strand conformation polymorphism (SSCP) analysis in the presence of polyethylene glycol. The protocol developed separates single-strand conformers in a much shorter time (1–3 h) than conventional SSCP protocols and broadens the applicability of SSCP analysis from 150 to as much as 500 bp of DNA by different percentages of GC content present. We conclude that addition of polyethylene glycol helps improve the differential separation of conformers and, in combination with high-resolution polyacrylamide gel electrophoresis, offers an alternative to previous SSCP analysis protocols. This protocol should be very useful for clinical applications in routine detection of mutations as well as for research purposes.

Allele frequency distributions of D1S80 in the Polish population

The polymorphism of the D1S80 locus has been analyzed in a population sample of 208 unrelated individuals in the Southeast Poland and 103 mother/child pairs. PCR amplified alleles were separated by a vertical discontinuous polyacrylamide gel electrophoresis system. Nineteen different alleles and 52 phenotypes could be distinguished. The alleles 18 (f = 0.267) and 24 (f = 0.300) were most common in Poland. D1S80 genotype frequencies of Poland population do not deviate from Hardy-Weinberg equilibrium. All mother/child pairs shared at least one D1S80 allele.

Sequence determination of an allele ladder for the STR polymorphism at the CD4 locus and application of the ladder in testing an Austrian Caucasian population sample

The short tandem repeat (STR) polymorphism at the CD4 locus, designated HUMCD4, was examined by PCR, native polyacrylamide electrophoresis and subsequent silver staining using an allelic ladder of eight distinguishable alleles occurring in an Austrian Caucasian population sample as a standard size marker. The ladder was produced by pooling equal concentrations of eluted, separately amplified and sequenced alleles, which were previously identified by their different electrophoretical migration. Components of the ladder are in regular intervals of five basepairs. Alleles 4 to 8 were designated according to the number of AAAAG repeat units. The four longer alleles 8' to 11 showed a stable A to G transition in one of the repeat units and were designated counting the AAAGG unit for a AAAAG. Allele 8' was not included in the ladder because it showed the same electrophoretic mobility as allele 8. This ladder proved to be a precise and reliable tool in the analysis of 600 chromosomes of the Austrian population. The population investigated showed no deviation from Hardy-Weinberg equilibrium (P = 0.23).

Human phylogenetic relationships according to the D1S80 locus

By analyzing the allelic frequencies at the D1S80 locus in 43 human populations, we show that the locus is polymorphic globally and that it can be used to discriminate between major racial groups and subpopulations through phylogenetic analysis. Although the use of informative multiple loci generally provides more accurate phylogenetic relationships, in instances where time and/or target DNA availability is limited, D1S80 could provide useful data to discriminate between human groups. Also, knowledge of which loci independently provide accurate phylogenetic relationships, such as the D1S80, can be used to design more accurate multi-locus combinations. In addition, allele frequencies at the locus are reported, for the first time, for Bahamian individuals of African origin and for Chimila, Bari, and Navajo (Cañoncito Valley) native Americans. Allelic data was obtained using standard polymerase chain reaction (PCR) techniques. In the four new populations, 65 genotypes and 20 segregating alleles were observed. All populations conformed to Hardy-Weinberg expectations except the Chimila.

D1S80 VNTR locus genotypes in population of south Poland; meta-analysis pointer to genetic disequilibrium of human populations

A highly variable number of tandem repeats (VNTRs) in a human locus D1S80 can prove to be useful for forensic science purposes. As with other genetic polymorphisms, a database of a local population allelic frequencies is needed to ensure that no departure from genetic equilibrium exists. DNA from the locus D1S80 was amplified by polymerase chain reaction (PCR) and analyzed by horizontal PAGE followed by silver staining. Samples from 133 unrelated inhabitants of Southern Poland were examined. The amplified fragment length polymorphism (AMP-FLP) analysis of the D1S80 locus demonstrated 21 alleles and heterozygosity of 0.85%. Out of the 231 possible genotypes, 47 were observed. The results were compared to the published D1S80 population studies and a meta-analysis of the genotype frequencies was performed. The G statistics revealed a deviation from genetic equilibrium in the Spanish population. Replicated goodness of fit tests showed highly significant heterogeneity of genotype distribution between tested populations. Therefore, interpretation of the casework on the basis of D1S80 locus typing may be biased by interpopulation differences.

AMPFLP analysis of the VNTR loci D1S80 and ApoB in Hungary

Population data studies for D1S80 and ApoB were carried out on a caucasian population sample from Hungary of 229 and 222 unrelated individuals, respectively. We observed 26 different alleles for D1S80 and 13 for ApoB. The allele frequencies found are similar to those reported in the literature for European caucasians. No evidence of significant deviations from Hardy-Weinberg equilibrium were observed for both AMPFLP systems.

Frequency of D1S80 and HLA DQ alpha alleles in a Chinese population

Allele frequency distributions for the D1S80 (MCT118) and HLA DQ alpha loci were determined in a Chinese population sample using the polymerase chain reaction (PCR). A total of 25 alleles and 100 phenotypes were observed for D1S80. The frequency of allele 18 was higher than allele 24 only in this Chinese population when compared to other reported populations. A total of 6 alleles and 21 possible phenotypes were observed for HLA DQ alpha. The power of discrimination was 0.97 and 0.93 for D1S80 and HLA DQ alpha, respectively.

D1S80 (pMCT118): analysis of 3 ethnic subpopulations living in Brussels

Population genetic studies were carried out on 3 ethnic subpopulations living in Brussels (119 Belgians, 120 Turks and 137 Moroccans). DNA extraction was performed using the Chelex method. After DNA amplification the DNA fragments were separated electrophoretically in horizontal polyacrylamide gels. A total of 32 alleles (between 21 and 25 alleles in each subpopulation) including 8 "interalleles" could be differentiated. The allele frequencies were compared with population data from a German study and no significant differences could be observed.

PCR-amplification of D2S44 alleles

A strategy for PCR-amplification and sequencing of the flanking regions in the polymorphism D2S44 (YNH24) has been developed based on the investigations of Edwards et al. (1991). The flanking regions of the YNH24 probe were successfully amplified and two distinct PCR products with fragment sizes of 180 and 250 bp obtained. After asymmetric PCR and didesoxy-sequencing 60 bp could be determined for every PCR fragment. D2S44-specific primers were constructed which were located at the transition between the flanking and repeat regions. Amplification conditions were optimized using the YNH24 probe, different nuclease S1 concentrations and incubation times. Optimized conditions were applied to the amplification assay of human D2S44 alleles which had been investigated by RFLP analysis.

Analysis of the VNTR locus D1S80 in a Japanese population

A population study on the VNTR locus D1S80 was carried out in a sample of 377 unrelated Japanese individuals living in and around Gifu Prefecture (central region of Japan). A total of 29 different alleles was distinguished. Alleles 18, 24 and 30 were found to be the 3 most common alleles in this population sample and their frequencies were 0.147, 0.200 and 0.162, respectively. Out of the 435 possible phenotypes, 120 were observed. The observed heterozygosity was 0.88 and the power of discrimination was 0.98. No significant deviations from Hardy-Weinberg equilibrium could be found in this Japanese population sample.

Analysis of the locus D1S80 by amplified fragment length polymorphism technique (AMP-FLP). Frequency distribution in Danes. Intra and inter laboratory reproducibility of the technique

DNA from the locus D1S80 was amplified by polymerase chain reaction (PCR) and analyzed by electrophoresis in vertical polyacrylamide gels followed by silverstaining. DNA samples from 119 unrelated Danes and 97 mother/child pairs were examined. The amplified fragment length polymorphism (AMP-FLP) analysis of the D1S80 locus demonstrated 21 alleles and a heterozygosity of 77%. Of the 231 possible phenotypes, 57 were observed. All mother/child pairs shared at least one D1S80 allele. The D1S80 typing results in 70 Danes were compared to the results obtained on the same samples in another laboratory and the results were concordant in all cases.

Allele frequency distribution of the D1S80 (pMCT118) locus polymorphism in the Japanese population by the polymerase chain reaction

Population studies among Japanese were carried out at the D1S80 locus by the polymerase chain reaction and subsequent analysis in agarose gel electrophoresis. A total of 58 genotypes and 25 alleles ranging from 16 to 45 repeat units were observed in a population group of 121 unrelated individuals. The alleles with 18, 24 and 30 repeat units were found to be most common. Some large alleles with more than 42 repeat units were first observed in this study. Statistical tests for Hardy-Weinberg equilibrium showed that no significant deviations could be found in this Japanese population sample. The values of the mean exclusion chance and the discriminating power (DP) were calculated to be 0.76 and 0.91, respectively. The observed heterozygosity was 0.91.