Freezing complete polymerase chain reaction master mix reagents for routine molecular diagnostics

The potential of storing complete frozen real-time polymerase chain reactions (PCRs) and real-time reverse transcription PCRs (RT-PCRs), which require only thawing and the addition of template nucleic acid before PCR cycling, was examined. Master mixes containing all necessary reagents at working concentration (except template nucleic acid) were aliquoted into single-reaction volumes and stored at -70 degrees C for periods of up to 8 months. Reactions were removed from storage and nucleic acid template was added and amplified using different real-time PCR instruments. Threshold cycle values were used to monitor changes in assay performance after storage. Results for hybridization probe and TaqMan probe assays showed that freezing complete real-time PCR and RT-PCR reaction mixes was possible without deterioration in assay performance. This approach has advantages for routine molecular diagnostics in areas such as convenience, test consistency, quality control, and ease of use by nonspecialist staff.

In silico comparison of real-time PCR probes for detection of pathogens

Rapid diagnostics and risk assessment of the pathogens is possible by Real-Time Polymerase Chain Reaction (PCR) probes like TaqMan, Molecular Beacon (MB) and FRET. However, validation of such probes for real-life samples is an expensive and time consuming proposition. Hence, development and comparison of real-time probes in silico can be the first step in selection of most appropriate probe chemistry. The virulence genes specific for a model pathogen, Escherichia coli O157:H7, transmitted worldwide by contaminated water and food, were chosen to compare probe chemistries. MB was observed to be the best probe chemistry for virulence genes stx1, stx2 and eae, while FRET was preferred for hlyA gene, based on Tm and free energy values for self-dimer, hairpin and cross-dimer. Secondary structure analysis indicated that MB design was flexible and less dependent on nucleotide arrangement and repetitive sequences in the genes compared to TaqMan and FRET probes. In addition, multiplexed MB probes could be a feasible option using a single non-fluorescent quencher for high throughput diagnostics.

Polycythemia vera is not initiated by JAK2V617F mutation

OBJECTIVE

The somatic JAK2(V617F) mutation is seen in most polycythemia vera (PV) patients; however, it is not clear if JAK2(V617F) is the PV-initiating mutation.

METHODS

In order to examine this issue, we developed a novel real-time quantitative allele-specific PCR, in which allelic discrimination is enhanced by the synergistic effect of a mismatch in the -1 position, and a locked nucleic acid (LNA) nucleoside at the -2 position.

RESULTS

Determination of allelic frequencies was reproducible (SD = 1.5%) and sensitive--0.1% mutant allele detected in 40 ng of DNA. The JAK2(V617F) frequency in clonal granulocytes from 3 PV females was less than 50% (27.5 +/- 11) and in 7 females greater than 50% (75 +/- 10.5). We also found that wild-type JAK2 BFU-E colonies from PV patients can grow without erythropoietin. The identification of the primary genetic lesion resulting in PV is essential for the development of novel therapeutic strategies.

CONCLUSION

Our studies correlating the frequency of JAK2(V617F) mutant allele and clonality, as well as the presence of homozygous wild-type JAK2 erythropoietin-independent erythroid colonies, provide compelling evidence that the JAK2(V617F) is not the PV-initiating mutation. This supports a model wherein the JAK2(V617F) mutation arises as a secondary genetic event. Furthermore, our results indicate that an undefined molecular lesion, preceding JAK2(V617F), is responsible for clonal hematopoiesis in PV. We conclude that development of therapeutic strategies that target the JAK2(V617F) clonal cells may not be sufficient for eradication of PV.

Entamoeba histolytica: inflammatory process during amoebic liver abscess formation involves cyclooxygenase-2 expression in macrophages and trophozoites

It has been demonstrated that expression of cyclooxygenase-2 (COX-2) isoform is induced by Entamoeba histolytica in macrophages and polymorphonuclear cells during amoebic liver abscess (ALA) formation in hamsters. Trophozoites present in the lesion were also positive for COX-2 signal. However, no cross reactivity of the anti-COX-2 antibody with protein extract of cultivated trophozoites was found. To clarify if trophozoites are involved in PGE(2) production during ALA development, COX-2 expression was detected by in situ hybridization and RT-PCR in liver tissue from intrahepatically infected hamsters. COX-2 mRNA was in polymorphonuclear cells since 4h postinfection, and subsequently, local macrophages expressed COX-2 mRNA in a similar way. Additionally, a positive signal for COX-2 mRNA expression was detected in E. histolytica trophozoites, suggesting that, in vivo, parasite COX expression may be an important mechanism to promote inflammation.

Evaluation of probe chemistries and platforms to improve the detection limit of real-time PCR

A validated PCR-based Salmonella method targeting a 94-bp sequence of the ttr gene was used as a model to compare six different combinations of reporter and quencher dyes of a TaqMan probe, on three different instruments, to improve the detection limit in a real-time PCR assay with the aim of a same-day analysis. The use of locked nucleic acids (LNA) and Scorpion probes were also tested. The combination FAM-BHQ1 or Cy5-BHQ3, both dark quenchers, gave the best results (Cycle threshold (Ct) of 25.42+/-0.65 and 24.47+/-0.18 at 10(3) DNA copies). When comparing different probe technologies, the LNA probe (FAM-BHQ1) was the most sensitive with the strongest fluorescence signal (dR last 48066), resulting in 0.6 to 1.1 lower Ct values than a DNA TaqMan probe, and 1.9 to 4.0 lower Ct than the Scorpion system (FAM-BHQ1). The RotorGene real-time PCR instrument gave 0.4-1.0 lower Ct values (more sensitive) than the Mx3005p, and 1.5-3.0 lower than the ABI 7700. Using the LNA in a RotorGene instrument, we detected the following Salmonella DNA copies in 1-ml pre-enriched samples: fishmeal (100 copies), chicken rinse (100 copies) and pig feces (10 copies). The detection probability of the final assay on inoculated fecal samples was 100% at 2x10(4) copies per ml. In conclusion, the LNA probe with annealing temperature of 65 degrees C could be useful for more sensitive detection limits.

Species- and strain-specific probes derived from repetitive DNA for distinguishing Entamoeba histolytica and Entamoeba dispar

Entamoeba histolytica and Entamoeba dispar are two morphologically indistinguishable species that are found in the human gut. Of the two, E. histolytica is considered to be pathogenic while E. dispar is nonpathogenic. To generate molecular probes to detect and distinguish between the two species, we utilized repeat sequences present in Entamoeba genome. We have developed probes and primers from rDNA episomes, and unidentified Entamoeba EST1 repeat for this purpose, and used them for dot blot hybridization and PCR amplification. To investigate the possible existence of invasive and noninvasive strains of E. histolytica, the ability to differentiate individual isolates is necessary. For this purpose, we have utilized a modification of the AFLP procedure called 'Transposon display,' which generates and displays large number of genomic bands associated with a transposon. We have used the abundant retrotransposon, EhSINE1, for this purpose,and demonstrated its potential as a marker to study strain variation in E. histolytica. This technique could suitably be employed in carrying out significant molecular epidemiological studies and large-scale typing of this parasite.

Alternative mapping of probes to genes for Affymetrix chips

BACKGROUND

Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available.

METHODS

We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays.

RESULTS

In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data.

CONCLUSIONS

While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis.

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements

Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms.

Primer design for automated DNA sequencing in a core facility

We assessed the quality of nine standard primers for automated fluorescent dye terminator DNA sequencing by whether their melting temperatures (Tms) were in the optimal range for DNA sequencing, and the degree to which their sequences matched the sequences of 36 common vectors. The M13F (-21/-20), M13F (-41/-40), M13R, and T7R primers showed optimal physicochemical characteristics and were not redesigned. The M13R (-41/-40), T3, and SP6 primers showed mismatches and/or Tm values outside of the optimal range and were redesigned by these two criteria. With few exceptions, the redesigned primers did not significantly improve DNA sequencing quality as assessed by Phred scores compared to the corresponding original primer. However, both redesigned T7 primers, which were also redesigned to function as pET primers, strikingly improved sequencing on pET vectors. The original and redesigned T7 primers also improved the sequence quality for the Bluescript family of vectors compared to the original and redesigned M13R (-41/-40) primers. The mismatch-redesigned T7, SP6, and M13R (-41/-40) primers marginally improved the sequence quality over the corresponding original primers for specific vector types. Within limits, decreasing the %GC and Tm below reported optimal levels did not affect the sequence quality. Commercially available standard vector primers were surveyed.

Summaries of Affymetrix GeneChip probe level data

High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.

Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies

The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the specificity of hybridisation. SAFE (specificity assessment from fractionation experiments) is a novel method to discriminate between non- specific cross-hybridisation and specific signals. We applied in situ fractionation of hybridised target on DNA-chips by means of repeated washes with increasing stringencies. Different fractions of hybridised target are washed off at defined stringencies and the collected fluorescence intensity data at each step comprise the fractionation curve. Based on characteristic features of the fractionation curve, unreliable data can be filtered and eliminated from subsequent analyses. The approach described here provides a novel experimental tool to identify probes that produce specific hybridisation signals in DNA-chip expression profiling approaches. The iterative use of the SAFE procedure will result in increasingly reliable sets of probes for microarray experiments and significantly improve the overall efficiency and reliability of RNA expression profiling data from DNA-chip experiments.

Ultra-rapid DNA analysis using HyBeacon probes and direct PCR amplification from saliva

We describe a novel probe technology, termed HyBeacons, which provides a new homogeneous method for fluorescence-based sequence detection and allele discrimination. Employing a single nucleotide polymorphism located in the N-acetyltransferase 2 gene as a model system, we demonstrate the utility of HyBeacon probes for rapid and reliable sequence analysis. We also demonstrate that homozygous and heterozygous samples may be accurately identified using a single HyBeacon oligonucleotide. Polymorphic DNA sequences were detected and differentiated by real-time PCR and melt peak methodologies, without performing extraction of genomic DNA prior to target amplification. Employing a combination of homogeneous HyBeacon analysis, the rapid thermal cycling conditions of the LightCycler and direct amplification from saliva, allowed samples to be genotyped within 30 min. Such rapid non-invasive diagnostic technologies may permit 'point-of-care' genetic testing to be performed in hospitals and doctor's surgeries.

Seryl-histidine as an alternative DNA nicking agent in nick translation yields superior DNA probes and hybridizations

Nick translation is a commonly used method for labeling DNA to make DNA hybridization probes. In this approach, the use of DNase I to generate nicks in double-stranded DNA presents an inherent drawback, because the enzyme's high rate of reaction causes significant fragmentation and shortening of the hybridization probes. Based on our recent findings regarding the nucleolytic activity of the dipeptide seryl-histidine (Ser-His) and generation of free 3' hydroxyl and 5' phosphate groups at the cleavage sites of the substrate DNA by Ser-His, it was hypothesized that this disadvantage may be overcome by using Ser-His in place of DNase I as an alternative DNA nicking agent. In this study we demonstrate that like DNase I, Ser-His randomly nicks DNA, but the dipeptide has a much lower rate of reaction that enables more complete labeling of the DNA probes with less fragmentation. DNA probes labeled through nick translation using Ser-His as the DNA nicking agent were consistently larger in size and exhibited significantly higher specific activities, and enhanced hybridization signals in Southern blot analyses compared to control DNA probes that were made using DNase I as the nicking agent. Furthermore, the degree of nicking and consequently the quality of the probes could be easily controlled by adjusting the temperature and time of the Ser-His nicking reaction. These results affirm our hypothesis that Ser-His can serve as an alternative DNA nicking agent in nick translation to yield superior DNA probes and hybridization results and suggest the possible general utility of Ser-His for wide range of biological and biomedical applications that require more moderated nicking of nucleic acids. Based upon these and computer modeling results of Ser-His, a mechanism of action is proposed to explain how Ser-His may nick DNA.

Quantitative assessment of minimal residual disease in childhood lymphoid malignancies using an allele-specific oligonucleotide real-time quantitative polymerase chain reaction

We developed an assay using a real-time quantitative polymerase chain reaction (RQ-PCR) for the quantitative assessment of minimal residual disease (MRD) in childhood lymphoid malignancies by using a consensus V-region probe combining a allele-specific oligonucleotide (ASO) reverse primer. Our strategy employs a set consisting of a consensus V-region probe, an ASO reverse primer, and a patient-specific forward primer for clonal antigen-receptor (IgH, immunoglobulin heavy chain; TCR, T-cell receptor) gene rearrangements (IgH-ASO and TCR-ASO RQ-PCR assays). The limit of detection in both assays was 5 copies of the target/10(5) cell equivalents. We tested the assays in 17 childhood malignancies (14 cases of acute lymphoblastic leukemia and 3 of non-Hodgkin's lymphoma). High correlation coefficients of the standard curves (>0.980) and PCR efficiency (>0.95) were achieved with all primer/probe sets. In 2 (12%) of the 17 patients, ASO primers could not be designed because there was no junctional N-sequence. The quantitative data suggest that the copy number of clonal antigen receptors markedly decreased after induction therapy in 15 of 17 patients and that 1 patient relapsed and died of the disease. Consensus probes make it possible to examine a large number of patients with only a limited number of probes. The strategy used for IgH-ASO and TCR-ASO RQ-PCR assays is accurate and reliable in the clinical prospective study of MRD in childhood lymphoid malignancies.

Effect of oligonucleotide truncation on single-nucleotide distinction by solid-phase hybridization

Oligonucleotide microarrays are used to analyze target sequences on the basis of differences in hybridization stability between matched and mismatched probe-target duplexes. DNA microarray manufacture via photolithographic synthesis generates a minority of full-length oligonucleotide probes along with a series of 5'-truncated contaminants. In a model experiment, we now investigate the effect of truncated oligonucleotides on the ability to distinguish target sequence variants that differ in a single nucleotide position. A series of oligonucleotides, mixed in proportions simulating stepwise synthetic yields of between 82 and 100%, were bound to a solid support and allowed to hybridize to a target molecule. The extent of hybridization was monitored over a range of temperatures via the fluorescence of a double-strand-specific dye. The discriminatory power of pure oligonucleotide probes was found to be significantly greater than that of a population of truncated probes, but only over a limited temperature interval. We conclude that at optimal temperatures greater oligonucleotide quality can improve the performance of oligonucleotide hybridization microarrays.

Direct DNA hybridization detection based on the oligonucleotide-functionalized conductive polymer

Electrochemical methods for DNA hybridization detection have many advantages that are very fast to detect hybridization and can be directly applied for a portable DNA sensor. In this paper, an electrochemical method to directly detect DNA hybridization was developed on the basis of a new conductive polymer, which was polymerized on the glassy carbon electrode with a terthiophene monomer having a carboxyl group (3'-carboxyl-5,2',5',2"-terthiophene). The ss-DNA probe was made by chemically bonding an amine-linked C6 alkyl group to the 5' terminus of oligonucleotide (19-mer). The probe moiety was immobilized on the polymer through covalent bonding with a catalyst, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. A difference in admittance was observed before and after hybridization as a result of the reduction of the resistance after hybridization. The highest difference in admittance was observed around 1 kHz before and after hybridization. Hybridization amounts of end two-base and center one-base mismatched sequences were obtained only in a 14.3% response when compared to that for the complementary matched sequence.

Trypanosoma vivax: characterization of the spliced-leader gene of a Brazilian stock and species-specific detection by PCR amplification of an intergenic spacer sequence

The sequence of the spliced-leader gene repeat of a Brazilian Trypanosoma vivax stock from cattle showed high similarity to sequences of West African T. vivax in both intron and intergenic sequences. This is the first evidence based on DNA sequences of close-relatedness between Brazilian and West African T. vivax stocks. A T. vivax-specific diagnostic PCR assay based on spliced-leader gene intergenic sequences was able to amplify DNA from T. vivax stocks from South America (Brazil, Bolivia, and Colombia) and West Africa. Species-specificity of this method was confirmed by results obtained by testing 15 other trypanosomes, including other species and subspecies that can also infect cattle. The PCR assay developed presented high sensitivity, detecting the DNA content of only one parasite and also revealing T. vivax infection in asymptomatic animals without detectable parasitemia by microhematocrit or in Giemsa-stained blood smears. Use of crude preparations from field-blood samples collected on both filter paper and glass slides as DNA template suggested that this method could be useful for the diagnosis of T. vivax in large epidemiological studies.

Evaluation of nonisotopic DNA hybridization methods for detection of the tdh gene of vibrio parahaemolyticus

Production of the thermostable direct hemolysin (TDH) by Vibrio parahaemolyticus is associated with pathogenicity of the organism and is encoded by the tdh gene. The timely resolution of seafood-associated outbreaks requires rapid and accurate detection of pathogenic V. parahaemolyticus. The specificity of alkaline phosphatase- and digoxigenin-labeled tdh gene probes was evaluated against 61 strains of V. parahaemolyticus (including isolates from recent outbreaks involving oysters from the Pacific Northwest, Texas, and New York), 85 strains of other vibrios, and 7 strains of non-vibrio species from clinical and environmental sources. The probes were specific for detection of the V. parahaemolyticus tdh gene.

Competitive cytokeratin 19 RT-PCR for quantification of breast cancer cells in blood cell suspensions

Detection of residual tumor cells in BM and PBPC products has been correlated with worse outcome of breast cancer patients. Still, there is a considerable demand for studies investigating the influence of the actual tumor cell number on prognosis, as quantification routinely has been cumbersome and time consuming and, thus, was evaded. We developed and evaluated a competitive RT-PCR-ELISA assay for cytokeratin 19 (CK19) with standard curve quantification that allows quantification of multiple samples within a working day; mRNA isolation, RT-PCR reaction, and automated ELISA detection were carried out using commercial kits. Results were expressed as OD420nm ratios of CK19 and an internal competitor. Values were then converted into tumor cell numbers using a standard curve of MCF-7 tumor cells. The assay had high specificity because of primers and capture probes with great heterogeneity to both published pseudogenes, which was confirmed by BLAST sequence alignment. We achieved a sensitivity of detecting 1 tumor cell per 10(6) mononuclear cells (MNC). Between-batch precision (n = 8) for quantification was consistent and reasonable, with a coefficient of variation around 25%. Therefore, this assay should be suitable and sufficient for routine quantification of tumor cell numbers in BM or PBPC samples.

In-situ detection of Aspergillus fumigatus

An in-situ hybridisation (ISH) technique to detect Aspergillus fumigatus in infected tissues was developed in which 568-bp, 333-bp and 154-bp PCR products of the alkaline proteinase gene were employed. Dot-blot hybridisation with the 568-bp probe on a membrane containing genomic DNA from several different fungi including A. flavus, A. niger, Penicillium spp., Mucor racemosus or Pseudallescheria boydii gave negative results. ISH was done on formalin-fixed, paraffin-embedded pulmonary tissues from rats infected with A. fumigatus and renal tissues from mice infected with A. fumigatus, A. flavus or A. niger. The 568-bp probe reacted strongly in ISH with both A. fumigatus and A. flavus, and weakly with A. niger. The 333-bp probe also reacted in ISH with A. fumigatus and A. flavus, although the intensity was weaker. However, in ISH with the 154-bp probe, there was no positive signal with any Aspergillus spp. These results demonstrate that A. fumigatus and A. flavus can be specifically detected in infected tissues by ISH with the 568-bp probe. This technique could be applicable to clinical specimens for molecular diagnosis of aspergillus infections.

DNA probe for beta-hemolytic group B Streptococcus. Diagnostic accuracy in threatened preterm labor

OBJECTIVE

To determine the diagnostic accuracy of a DNA probe for beta-hemolytic group B Streptococcus (GBS) in women with threatened preterm labor.

STUDY DESIGN

Two identical vaginal/perianal samples were collected from 75 pregnant women who were being evaluated for threatened preterm labor. One sample was managed in the traditional manner, with direct plating onto blood agar followed by plating after 8 and 24 hours of LIM broth enhancement. The "gold standard" was 24 hours of LIM broth enhancement followed by blood agar plating. The second sample was placed in LIM broth, and DNA probe testing was performed after incubation for 8 and 24 hours.

RESULTS

The prevalence of GBS colonization by the gold standard culture was 32%. After 8 hours of incubation in LIM broth, the DNA probe had poor sensitivity (79%); however, after 24 hours of incubation in LIM broth the DNA probe sensitivity rose to 96%. The DNA probe demonstrated only one false negative result after 24 hours of LIM broth enhancement. All DNA probe results were known 25 hours after sample collection.

CONCLUSION

This DNA probe gave results nearly identical to those of standard cultures and allowed a substantial saving of time.

Development of internal controls for probe-based nucleic acid diagnostic assays

A method is described for the design, evaluation, and application of internal control targets and probes for use in probe-based nucleic acid diagnostic assays (i.e., PCR-ELISA). The technique is a modified version of oligonucleotide-directed mutagenesis in conjunction with PCR amplification to develop a novel probe-annealing sequence in a cloned IS1111a gene fragment of Coxiella burnetii. The internal control probe-recognition site with its complementary probe was identical to the wild-type-specific probe in length, base composition, location, and annealing temperature. Neither the internal control nor the wild-type probes annealed to the recognition sequence of the other. As both of the amplified nucleic acid fragments, internal control and wild type, were identical in length and base composition, the amplification conditions for the diagnostic assay were not affected. This allowed small copy numbers of the internal control clone to be loaded into a diagnostic assay without negatively affecting it. In a single reaction we were able to differentiate between an assay reporting a true or false-negative signal. A negative signal is defined as the absence of detectable pathogen genetic material (true) or inhibition/failure of the reaction (false).

Different behavior of two Trypanosoma cruzi major clones: transmission and circulation in young Bolivian patients

Specificity of two widespread Trypanosoma cruzi clonal genotypes or "clonets" (20 and 39) was first analyzed by hybridization with a large set of T. cruzi stocks characterized by multigenic study relying on both MLEE and RAPD. Then, these clonets were detected in the blood of Chagasic children from a Bolivian endemic area by a combination of polymerase chain reaction and clonet-specific DNA hybridization. The distribution of these clonets in patients was significantly different from that observed in the vectors of the same area (Triatoma infestans). In vectors, clonets 20 and 39 are found with comparable frequencies (0.69 and 0.67, respectively) in contrast with patients, in whom clonet 20 and mixed infections exhibit low frequencies. The Chagasic population can be divided into acute infections and latent infections above the accepted criterion of parasitemia (direct microscopic examination). The results suggest a limited selection in the transmission of the two clonets and a further drastic control of clonet 20 parasitemia by the immune system of children patients.

Usefulness of hepatitis C virus RNA counts by second generation HCV bDNA-probe in chronic hepatitis C based on the HCV genotype

Detection of hepatitis C virus (HCV) RNA by a second generation (ver 2) HCV bDNA-probe method (bDNA-probe) was compared with detection by the first generation (ver 1) assay. The two assays were performed simultaneously with the same serum samples of HCV genotypes 1b, 2a, 2b, 3a, and 3b. The positive rates with ver 1 were 82% for HCV genotype 1b (type 1b), 57.6% for HCV genotype 2a (type 2a), 75.0% for HCV genotype 2b (type 2b), 55.6% for HCV genotype 3a (type 3a), and 93.8% for HCV genotype 3b (type 3b). The positive rates with ver 2 were 95.0% for type 1b, 93.9% for type 2a, 83.3% for type 2b, 100% for type 3a, and 93.8% for type 3b. With Fisher's exact test, the detection rate for type 2a was significantly higher (P = 0.001) with ver 2 than with ver 1. We obtained regression lines using the HCV counts measured by bDNA-probe on the y axis and the HCV counts obtained by an HCV reverse transcriptase (RT)-competitive polymerase chain reaction method (competitive PCR) on the x axis. The gradients for types 1b, 2a, and 3b were greater with ver 2 compared to ver 1. The gradients for types 2a and 3b were the highest: for type 2a, y = 0.135x + 0.6 with ver 1 and y = 0.248x + 0.1 with ver 2; for type 3b, y = 0.366x + 0.1 with ver 1 and y = 0.727x + 0.3 for ver 2. In addition, HCV-RNA counts for all the genotypes tested in this study were significantly higher with ver 2 than with ver 1. Hence, we conclude that ver 2 of the bDNA-probe measures HCV-RNA counts closer to those obtained with competitive PCR than the ver 1 assay.

Sensitive and specific detection of Trypanosoma vivax using the polymerase chain reaction

The nucleic acid probes that are currently in use detect and distinguish Trypanosoma vivax parasites according to their geographic origin. To eliminate the need for using multiple DNA probes, a study was conducted to evaluate the suitability of a tandemly reiterated sequence which encodes a T. vivax diagnostic antigen as a single probe for detection of this parasite. The antigen is recognized by monoclonal antibody Tv27 currently employed in antigen detection ELISA (Ag-ELISA). A genomic clone which contained a tetramer of the 832-bp cDNA sequence was isolated and shown to be more sensitive than the monomer. Oligonucleotide primers were designed based on the nucleotide sequence of the 832-bp cDNA insert and used in amplifying DNA sequences from the blood of cattle infected with T. vivax isolates from West Africa, Kenya, and South America. The polymerase chain reaction (PCR) product of approximately 400 bp was obtained by amplification of DNA from all the isolates studied. The oligonucleotide primers also amplified DNA sequences in T. vivax-infected tsetse flies. Subsequently, PCR was evaluated for its capacity to detect T. vivax DNA in the blood of three animals experimentally infected with the parasite. T. vivax DNA was detectable in the blood of infected animals as early as 5 days post-infection. Blood and serum samples from the three cattle and from six other infected animals were also examined for the presence of trypanosomes and T. vivax-specific diagnostic antigen. Trypanosomes appeared in the blood 7-12 days post-challenge, while the antigenemia was evident on Days 5-20 of infection. Analysis of the data obtained in the three animals during the course of infection revealed that the buffy coat technique, Ag-ELISA, and PCR revealed infection in 42, 55, and 75% of the blood samples, respectively. PCR amplification of genomic DNA of T. vivax is thus superior to the Ag-ELISA in the detection of T. vivax. More importantly, both the T. vivax diagnostic antigen and the gene encoding it are detectable in all the T. vivax isolates examined from diverse areas of Africa and South America.

[Evaluation of non radioactive DNA probe (Affirm DP) for detecting periodontopathic bacteria]

The purpose of this investigation was to evaluate the potential of application of non-radioactive DNA probe method (Affirm DP) in clinical diagnosis and evaluation of treatment efficacy. Sensitivity and specificity of two different cut-off levels (10(4), 5 x 10(5)) of the method with bacterial culture in detection of Bacteroides forsythus, Porphyromonas gingivalis, and Actinobacillus actinomycetemcomitans were compared. Those bacteria were obtained from bacterial cultures and clinical samples from healthy subjects and patients with periodontal disease. The results showed that detection percentage of DNA probe method with 10(4) cut-off was equal to or higher than the culture method for Bacteroides forsythus and Porphyromonas gingivalis detection. Therefore, it is suggested to be a useful chairside DNA probe kit as an aid in clinical diagnosis and evaluation of treatment efficacy.

Validation of probe EFD52 (D17S26) for forensic DNA analysis

Validation studies that meet TWGDAM (The Working Group on DNA Analysis Methods) and CAC (California Association of Criminalists) guidelines for RFLP (restriction fragment length polymorphism) analysis were performed with the DNA probe EFD52 (D17S26). These studies demonstrate that the probe EFD52 is suitable for forensic casework. No unexpected DNA banding patterns were obtained from controlled studies examining various tissues, sample consistency over many gels, mixtures of body fluids, various substrates, various contaminants and non-human DNA sources. Of all the animal DNAs tested, only one higher primate yielded a single band to EFD52 hybridization. The sensitivity of EFD52 was shown to be comparable to that of other forensic probes. Population frequency distribution tables were prepared from over 4000 alleles and two-locus studies were conducted on nine forensically useful probes. Black, White, Hispanic and Lumbee Indian populations were found to be in Hardy-Weinberg and linkage equilibrium. Comparisons between victim blood standards and epithelial fractions of mixed strains from sexual assault cases were used to demonstrate the robustness of the EFD52 probe in forensic casework.

[DNA profiling for identification purposes]

DNA "fingerprinting" was described for the first time in 1985, and since then DNA profiling has been used increasingly to identify the origin of biological material, such as blood and semen stains. The method is also used in cases of disputed paternity and to help identify dead bodies. In this article we review the methods and their practical use, and discuss various aspects of quality and security.

Identification and enumeration of Listeria monocytogenes by nonradioactive DNA probe colony hybridization

A plasmid containing the cloned listeriolysin gene of Listeria monocytogenes was used as a probe to identify Listeria strains by DNA colony hybridization. The probe DNA was labeled with horseradish peroxidase in the presence of glutaraldehyde. After the hybridization and wash procedures, the hybrid molecules were detected by luminescence, which resulted from the oxidation of luminol by a horseradish peroxidase-hydrogen peroxide-coupled reaction. Of the 150 Listeria strains and 16 non-Listeria strains examined, the probe hybridized only with L. monocytogenes. The technique was also used to enumerate L. monocytogenes in artificially contaminated foods.

Two different multi-locus probes MZ1.3 and (CAC)5 show nearly the same RFLP pattern

The RFLP patterns revealed by 2 different multi-locus probes MZ1.3 and (CAC)5 were compared using 4 different restriction enzymes AluI, MboI, HaeIII, HinfI. Irrespective of the restriction enzyme the fingerprints obtained with MZ1.3 and (CAC)5 were almost identical. The MZ1.3 RFLP pattern showed some extra bands which were absent in the (CAC)5 fingerprint.

DNA single locus profiles: tests for the robustness of statistical procedures within the context of forensic science

We describe a series of experiments, carried out on data from DNA profiles, which have been designed specifically to test the validity of the statistical procedures currently used in the Home Office Forensic Science Service. The tests address issues which have been the subject of topical debate, in particular those of representativeness and band independence. The results confirm the confidence which had already been placed in the established procedures. We recommend that all practitioners in the forensic field should carry out similar testing on their own data collections.

Sex determination and species exclusion in forensic samples with probe cY97

A total of 120 human samples of blood, saliva and semen stains, hair roots, bone and skin fragments, obtained from 30 males and 16 females were analyzed in Southern blots with probe cY97. Only the male samples gave a specific band of 5.7 kb. In dot blot, under high stringency conditions, male DNA gave signals equivalent to a quantity of female DNA eight times higher. Probe cY97 did not react with 9 different vertebrate species but gave a signal for monkey DNA when used at low stringency. The advantage of using a probe specific for the centromeric region for sex determination and species exclusion is discussed.

Problems associated with the DNA analysis of stains

Selected stain cases are presented which highlight various problems associated with DNA investigations on stain materials, especially risks of artefacts. These cases involve stain materials (blood, semen) which were exposed to different external conditions so that the DNA was partially degraded and of variable quantity. One multi locus probe (MLP) and 4-6 single locus probes (SLP's) were used for individualisation but artefacts such as extra bands, band deficiencies or shifts only occurred with the MLP. In one case where only a few spermatozoa were present in the vaginal swab, DNA extraction was carried out without preferential lysis to avoid loss of sperm DNA. The resulting mixed band pattern could be clearly attributed to the bands from the corresponding blood samples after SLP hybridisation.

Report of a European collaborative exercise comparing DNA typing results using a single locus VNTR probe

A collaborative exercise was carried out in 1989 among 12 European forensic laboratories using the single locus VNTR probe pYNH24, the restriction enzyme HinfI, the same set of human genomic DNA samples, and a standardized DNA size marker. The objectives of the exercise were: (1) to study the degree of variation within and between laboratories, (2) to obtain information on requirements for technical standardization allowing the exchange of typing results and (3) to compare different approaches for the identification of allelic DNA fragments of unknown size. Each laboratory carried out up to 10 independent typing experiments using the same DNA samples. The results were analysed independently by two laboratories using three different methods. The results of the exercise demonstrate the correlation of typing that can be achieved within and between laboratories under conditions of minimal standardization.

Evaluation of biotinylated DNA probes for the detection of gene rearrangements in clinical specimens

To determine whether a nonisotopic procedure is suitable for analyzing clinical specimens for gene rearrangements, the authors hybridized DNA from 15 specimens of lymphoid tissue with biotinylated DNA probes directed to J beta I + J beta II (T-cell receptor beta chain gene), JH (immunoglobulin gene heavy chain J region), and J kappa (immunoglobulin gene kappa light chain J region). Five cases of benign lymphoid hyperplasia, one case of dermatopathic lymphadenopathy, and one case of small noncleaved follicular center cell lymphoma had germline hybridization patterns when digested with Bam HI, Eco RI, and Hind III restriction endonucleases. Four cases of B-cell lymphoma and three cases of T-cell lymphoma had clearly detectable rearrangements of the genes for immunoglobulin or the T-cell receptor or both. One case of dermatopathic lymphadenopathy had a faint, clonal rearrangement of the T-cell receptor after digestion with Eco RI and Bam III. The authors conclude that biotinylated DNA probes can be useful for analyzing gene rearrangements in clinical specimens.

Use of Gen-Probe and Bactec for rapid isolation and identification of mycobacteria. Correlation of probe results with growth index

Gen-Probe culture confirmation tests (Gen-Probe, San Diego, CA) for Mycobacterium tuberculosis complex and Mycobacterium avium complex were performed on 276 mycobacterial isolates. All 138 M. tuberculosis complex isolates and 79 of 80 M. avium complex isolates were identified correctly. No falsely positive test results were obtained; 58 nontuberculous mycobacteria other than M. avium complex were negative by Gen-Probe. In a second phase of testing, Gen-Probe tests were performed using concentrates from 101 patient Bactec 12B cultures. Positive results by Gen-Probe tests were correlated with the growth index (GI) reading on the day of processing as well as the accumulated GI readings. For those 51 with high (greater than or equal to 999) final GIs, 40/40 (100%) M. tuberculosis complex isolates and 9/11 M. avium complex isolates were positive by Gen-Probe, and six other mycobacteria were negative. Of the 25 with moderate final readings (400 less than or equal to GI less than 999), 12/17 M. tuberculosis complex isolates and 1/1 M. avium complex isolates were correctly identified by Gen-Probe; seven other mycobacteria were negative. Of 25 with low readings (GI less than 400), 8/24 M. tuberculosis isolates were correctly identified by Gen-Probe, and no falsely positive test results were obtained with the other probes. All true negative tests on seven other mycobacteria (not M. tuberculosis complex or M. avium complex) had less than 2% hybridization. Of the 24 falsely negative tests on M. tuberculosis complex isolates or M. avium complex isolates, 22 had greater than 2% hybridization with their respective probes. Thus, percent hybridization greater than 2% may be a useful indicator of the need for retesting.

A comparison of biotin- and 35S-based in situ hybridization methodologies for detection of human papillomavirus DNA

In situ hybridization is commonly used for the detection of human papillomavirus (HPV) DNA in genital tract lesions. Systems based on biotin complexes are quicker and easier to use than 35S-based systems, although reportedly less sensitive. We compared three in situ hybridization systems for HPV DNA detection: two biotin [PathoGene DNA probe assay [Enzo Diagnostics] and Viratype in situ HPV probes and HPV tissue hybridization kit [Life Technologies Inc. (LTI)] and one 35S based. By using serial sections from 80 female genital tract lesions with the histologic features of an HPV infection, sequences homologous to HPV DNA were detected in 59 cases (74%) with the LTI system and 25 cases (31%) with the Enzo system. The Enzo system uses a streptavidinbiotinylated horseradish peroxidase complex and 2% 3-amino-9-ethylcarbazole as the chromogen. The LTI system uses a streptavidin alkaline phosphatase conjugate in which the chromogen is 5-bromo-4-chloro-3-indolylphosphate in the presence of nitroblue tetrazolium. Replacing the Enzo detection system with the LTI detection system increased the sensitivity of the Enzo kit. The LTI biotin system was equally sensitive when compared against 35S-labeled HPV probes. The sensitivity with the biotin probes, reported to be less than the 35S probes in a previous study (Lab Invest 58:354, 1988), was increased if the current LTI detection system replaced the detection system used in that study. It is concluded that biotin-labeled DNA probes can be equally sensitive to 35S-labeled DNA probes for the detection of sequences homologous to HPV DNA. The enhanced sensitivity for the biotin system is primarily due to improved detection of the probe/target complex.