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PubMed2005

A new "miniSTR-multiplex" displaying reduced amplicon lengths for the analysis of degraded DNA.

A multiplex PCR was designed for the loci D2S1338, D16S539, D18S51, TH01 and FGA using redesigned primers in order to reduce the lengths of the amplification products compared to the designs used in commercially available multiplex PCR kits, also including amelogenin. The new PCR primers were used to amplify highly degraded DNA from casework samples, which had shown no or only poor results for these loci in previous analyses with standard primer sets. The application of the new miniSTR-multiplex resulted in an increased overall typing success rate for degraded DNA samples. In a concordance study between the conventional and the newly designed primers, no genotype differences were revealed in 124 randomly selected individuals.

Amelogenin↗

PubMed2002

Bacterial etiology of otitis media with effusion; focusing on the high positivity of Alloiococcus otitidis.

The etiology of otitis media with effusion (OME) is unclear. The bacterial analyses of middle ear effusion (MEE) in OME may reveal important information regarding its etiology. Alloiococcus otitidis, Heamophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis were investigated by using microbiologic culture and a multiplex PCR method in the middle ear fluid of 32 children (54 samples) with chronic OME. PCR yielded positive results in 18 (33.3%) middle ear effusions while culture resulted positive for 3 (5.6%). The PCR method detected A. otitidis in 10 (18.5%) specimens, H. influenzae in 7 (13%), M. catarrhalis in 4 (7.4%) and S. pneumoniae in 2 (3.7%) specimens. The multiplex PCR method enhances the detection rate significantly compared to that of the conventional culture method. A. otitidis is the most common detected pathogen in the MEE of the OME.

Adolescent↗

PubMed1998

Emergence of vancomycin-resistant enterococci in Australia: phenotypic and genotypic characteristics of isolates.

Enterococci with resistance to glycopeptides have recently emerged in Australia. We developed multiplex PCR assays for vanA, vanB, vanC1, and vanC2 or vanC3 in order to examine the genetic basis for vancomycin resistance in Australian isolates of vancomycin-resistant Enterococcus faecium and E. faecalis (VRE). The predominant genotype from human clinical E. faecium isolates was vanB. The PCR van genotype was consistent with the resistance phenotype in all but six cases. One vanA E. faecalis isolate had a VanB phenotype, one vanB E. faecium isolate had a VanA phenotype, and four E. faecalis isolates were consistently negative for vanA, vanB, vanC1, and vanC2 or vanC3, even though they exhibited a VanB phenotype. These four isolates were subsequently examined for the presence of vanD by published methods and were found to be negative. No vancomycin-susceptible strains produced a PCR product. On the basis of our findings the epidemiology of VRE in Australia appears to be different from that in either the United States or Europe. Our multiplex PCR assays gave a rapid and accurate method for determining the genotype and confirming the identification of glycopeptide-resistant enterococci. Rapid and accurate methods are essential, because laboratory-based surveillance is critical in programs for the detection, control, and prevention of the transmission of glycopeptide-resistant enterococci.

Anti-Bacterial Agents↗

PubMed2004

AutoDimer: a screening tool for primer-dimer and hairpin structures.

The ability to select short DNA oligonucleotide sequences capable of binding solely to their intended target is of great importance in developing nucleic acid based detection technologies. Applications such as multiplex PCR rely on primers binding to unique regions in a genome. Competing side reactions with other primer pairs or template DNA decrease PCR efficiency: Freely available primer design software such as Primer3 screens for potential hairpin and primer-dimer interactions while selecting a single primer pair. The development of multiplex PCR assays (in the range of 5 to 20 loci) requires the screening of all primer pairs for potential cross-reactivity. However, a logistical problem results due to the number of total number of comparisons required. Comparing the primer set for a 10-plex assay (20 total primer sequences) results in 210 primer-primer combinations that must be screened. The ability to screen sets of candidate oligomers rapidly for potential cross-reactivity reduces overall assay devlelopment time. Here we report the application of a familiar sliding algorithm for comparing two strands of DNA in an overlapping fashion. The algorithm has been employed in a software package wherein the user can compare multiple sequences in a single computational run. After the screening is completed, a score is assigned to potential duplex interactions exceeding a user-defined threshold. Additional criteria of predicted melting temperature (Tm) and free energy of melting (deltaG) are included for further ranking. Sodium counterion and total stand concentrations can be adjusted for the Tm and deltaG calculations. The predicted interactions are saved in a text file for further evaluation.

Algorithms↗

PubMed1998

[Search for microdeletions in the long arm of chromosome Y in 48 infertile men].

About 30% of infertilities are from male origin. They appear in some cases de novo and considered idiopathic. The aim of our work is to evaluate, in these cases, the Y chromosome long arm microdeletion prevalence within the AZF a, b and c regions by molecular biology technics. Were excluded from our study, azoo-oligospermia from hereditary, endocrine, obstructive origins or with a constitutional cytogenetic abnormality. 48 infertile men with a spermogram-proven azoo-oligospermia were studied. Among them, 30 were idiopathics, 8 out of them exhibited a genital infection past history or biological abnormalities suggesting partial obtruction of the genito-urinary tractus. 8 cases of varicocela and 10 of cryptorchidia were also studied. Peripheral blood DNA was extracted from each patient, then amplified by multiplex PCR with STS genomic markers from the 3 Y chromosome AZF zones. PCR products were then analysed on agarose gels. Considering the difficulty to affirm the absence of a signal in molecular biology, each suspicion of deletion was checked by multiplex PCR complication with the SRY marker. 5 Y chromosome long arm microdeletions were diagnosed among our 48 patients. All of them included the AZFc zone and the intragenic DAZ gene markers. Moreover a larger Y chromosome deletion encompassing the 3 AZF zones was diagnosed, and confirmed by the cytogenetic analysis. All the Y chromosome microdeletions were observed in the 22 truly idiopathic azoo/oligospermia, corresponding to a proportion of 22.7% which falls to 10.4% considering the whole population of 48 studied people (closer to the published data). The relatively high proportion of microdeletions found in our series, underlines the need of a strict patient selection to avoid unnecessary search for long arm Y chromosome microdeletions.

Chromosome Deletion↗

PubMed2001

Usefulness of blood and urine samples collected on filter paper in detecting cytomegalovirus by the polymerase chain reaction technique.

A rapid test for the diagnosis of congenital CMV infection is still needed. This study evaluated the usefulness of dried blood and urine samples collected on filter paper for detecting cytomegalovirus (CMV) by the polymerase chain reaction (PCR) assay compared with the use of liquid urine. Samples were obtained from 332 infants aged 1-7 days. Liquid urine samples were collected into bags, cultured in human fibroblasts, and processed using a multiplex PCR technique. Dried urine samples were obtained by placing a piece of filter paper in contact with the infant's genitals. The heels of neonates were punctured and capillary blood was blotted onto filter paper and dried. Dried blood and urine specimens were analyzed by multiplex PCR and nested-PCR assays. A diagnosis of congenital CMV infection was established by isolating the virus, and by detecting viral DNA in the liquid urine. Of the 332 liquid urine samples collected from 332 neonates, seven (2.1%) were positive for CMV and 325 were negative, by both cell culture and PCR assay. In dried samples, CMV DNA was detectable only with a nested PCR assay. Compared with known CMV infection status, 5/7 (71.4%) neonates were positive for congenital CMV infection using dried blood samples. All 325 uninfected neonates were negative. In the dried urine samples, 4/4 CMV-infected infants gave positive tests, and all 262 uninfected infants were negative. Although further improvements in sample collection and/or processing are still needed, PCR testing on dried urine or blood collected on filter paper is a promising approach in the diagnosis of neonatal CMV infection.

Blood Specimen Collection↗

PubMed2003

Detection of rhinovirus and enterovirus in upper respiratory tract samples using a multiplex nested PCR.

Human enteroviruses and rhinoviruses are respiratory pathogens whose role in acute respiratory infection is underestimated due to the use of diagnostic procedures with poor sensitivity. To determine the prevalence of these two pathogens in the upper respiratory tract infections, a multiplex procedure was developed that both detect and differentiate rhinoviruses and enteroviruses. This sensitive procedure allowed the detection of both pathogens from archival material (nasal swabs) collected during the previous winters and differentiated rhinoviruses from enteroviruses. This procedure can be used to determine the role of these pathogens in mild or severe upper respiratory tract infections.

Animals↗

PubMed1999

An accurate and rapid gender determination assay in single cells by the capillary polymerase chain reaction method.

PURPOSE: In preimplantation genetic diagnosis (PGD), a rapid and accurate assay has been required. We have therefore developed a capillary polymerase chain reaction (PCR) method using rapid thermal cycling programs to determine the gender of single amniocytes. METHODS: Single amniocytes from each amniotic fluid sample were isolated by micromanipulation and their gender was determined by a multiplex PCR assay in a capillary tube, using primers that amplify a 308-bp DXZ1 and a 154-bp DYZ1 repeat sequence on the X and Y chromosomes, respectively. RESULTS: All four thermal cycling programs, which took 180, 150, 120, and 90 min, were 100% accurate in diagnosing the gender of single amniocytes. No DNA contamination was observed in any samples. CONCLUSIONS: The multiplex PCR assay was rapid and accurate in diagnosing gender in single cells and may be clinically applicable in PGD.

Amnion↗

PubMed2000

Validation of a simple Yq deletion screening programme in an ICSI candidate population.

This study reports on the validation of a diagnostic screening programme for Yq deletions in a population of infertile men. First, an unselected group of 402 intracytoplasmic sperm injection (ICSI) candidate patients was screened prospectively by means of three polymerase chain reactions (PCR) each with one marker in the region AZFa, AZFb or AZFc. With this screening strategy, eight males (2.2%) were found to carry a deletion in Yq11. Secondly, a subgroup of males were further analysed by multiplex PCR with 27 sequence-tagged sites. In this group of 229 cytogenetically normal males with azoospermia, cryptozoospermia or extreme oligozoospermia, including some patients with varicocele or a history of cryptorchidism, only one additional microdeleted patient was found with the multiplex PCR. Hence we obtained a frequency of 2.2% (9/402) or 4% (9/229) in the unselected and selected patient groups respectively. We conclude that in a diagnostic programme for Yq deletions in ICSI candidates it might be sufficient to use only four markers representing the three AZF regions and a more distal region in AZFc. In this way, it is possible to detect most, if not all, Yq deletions which might be the causal factor in the patient's infertility.

Gene Deletion↗

PubMed2004

QF-PCR-based prenatal detection of aneuploidy in a southeast Asian population.

OBJECTIVES: We have investigated the efficacy of using quantitative fluorescent polymerase chain reaction (QF-PCR) for the prenatal recognition of aneuploidy in chromosomes 13, 18, 21, X and Y. A total of 1115 samples, from mainly southeast Asian patients, were analysed and compared in a blind trial to the results previously obtained cytogenetically. METHODS: A multiplex PCR involving 15 short tandem repeat (STR) sequences was used. The probability of two or more of these markers being informative was calculated, and this required the multiplex PCR to be modified. RESULTS: The QF-PCR and previous cytogenetic results concurred, except for two products of conception (POC). One of these may be a case of complete uniparental disomy that was not recognized cytogenetically. The other was tetraploid, and as such appeared normal using QF-PCR. A mosaic trisomy 18 was correctly identified. The population sample was of a mainly Chinese, ethnic origin, and the allele frequency, size and heterozygosity appeared more restricted than the population groups analysed hitherto. CONCLUSION: The QF-PCR methodology is an efficient cost-effective method of screening for major chromosome aneuploidy, and, for certain referral categories, could be used alone. It also appears to be applicable to patients of different ethnic origins.

Alleles↗

PubMed2003

Detection and quantification of Escherichia coli O157:H7 in environmental samples by real-time PCR.

AIMS: To apply the real-time Polymerase chain reaction (PCR) method to detect and quantify Escherichia coli O157:H7 in soil, manure, faeces and dairy waste washwater. METHODS AND RESULTS: Soil samples were spiked with E. coli O157:H7 and subjected to a single enrichment step prior to multiplex PCR. Other environmental samples suspected of harbouring E.coli O157:H7 were also analysed. The sensitivity of the primers was confirmed with DNA from E.coli O157:H7 strain 3081 spiked into soil by multiplex PCR assay. A linear relationship was measured between the fluorescence threshold cycle (C T ) value and colony counts (CFU ml(-1)) in spiked soil and other environmental samples. The detection limit for E.coli O157:H7 in the real-time PCR assay was 3.5 x 10(3) CFU ml(-1) in pure culture and 2.6 x 10(4) CFU g(-1) in the environmental samples. Use of a 16-h enrichment step for spiked samples enabled detection of <10 CFU g(-1) soil. E. coli colony counts as determined by the real-time PCR assay, were in the range of 2.0 x 10(2) to 6.0 x 10(5) CFU PCR (-1) in manure, faeces and waste washwater. CONCLUSIONS: The real-time PCR-based assay enabled sensitive and rapid quantification of E. coli O157:H7 in soil and other environmental samples. SIGNIFICANCE AND IMPACT OF THE STUDY: The ability to quantitatively determine cell counts of E.coli O157:H7 in large numbers of environmental samples, represents considerable advancement in the area of pathogen quantification for risk assessment and transport studies.

Colony Count, Microbial↗

PubMed1996

Molecular epidemiology of cystic fibrosis mutations and haplotypes in southern Italy evaluated with an improved semiautomated robotic procedure.

We screened for 22 cystic fibrosis (CF) mutations in DNA from a first cohort of 69 CF patients from southern Italy using a semiautomated allele specific oligonucleotide (ASO) dot blot procedure based on two multiplex PCR amplifications. Seven mutations (delta F508, N1303K, G542X, 1717-1 G-->A, W1282X, 1148T, and R553X) identified 77.6% of CF chromosomes. Detection reached 79.8% with the 2183 AA-->G mutation analysed with the restriction generating PCR method. Thus, we included the 2183 AA-->G mutation in the ASO protocol and set up the conditions to amplify the gene regions that include the eight mutations in a single multiplex PCR reaction. With this method we tested the DNA of the first cohort of 69 CF patients, a second cohort of 63 CF patients, and 300 carrier relatives; we also performed 12 prenatal diagnoses. The results from the 132 CF patients showed differences in the distribution of CF mutations between the south and north of Italy. The XV2c, KM19, and intron 8 VNDR haplotypes suggested the presence, in CF chromosomes bearing undetected mutations, of a limited number of unknown mutations typical of southern Italy. Finally, for six of the eight mutations, we compared the ASO procedure with the methods based on restriction enzymes; the results obtained with the two procedures were identical for all the 57 chromosomes compared.

Carrier State↗

PubMed2004

Genetic diagnosis of claudin-16 deficiency and sex determination in bovine preimplantation embryos.

Renal tubular dysplasia is an autosomal recessively inherited disorder in Japanese black cattle that is due to deletion mutations in the claudin-16 gene and causes chronic renal failure and death of affected animals. Here, we report a multiplex-PCR procedure to determine the genotype for claudin-16 deficiency in preimplantation embryos. The presence or absence of the wild-type and mutant allele(s) was precisely detected with the multiplex-PCR using as little as 5 pg of genomic DNA from leukocytes. When biopsied embryo cells were examined for claudin-16 deficiency, 97.2% of genotypes were consistent with the PCR results obtained for the corresponding embryos. In addition, sexing of embryos by PCR was performed using an aliquot of DNA extracted from biopsied embryo cells, and determination of claudin-16 genotype and sex was successfully achieved with an efficiency of 91.7% for claudin-16 genotyping and 83.3% for sexing. The production of a 100-day fetus that was male and homozygous for claudin-16 deficiency, as expected from the analysis of biopsied embryo cells, gave evidence of the reliability and applicability of this procedure for preventing the transmission of this disease and for enabling advances in animal breeding.

Alleles↗

PubMed1994

Sex determination of human embryos using the polymerase chain reaction and confirmation by fluorescence in situ hybridization.

OBJECTIVE: To use fluorescence in situ hybridization to corroborate the polymerase chain reaction (PCR) preimplantation diagnosis of human embryos in three couples carrying a chromosome X-linked disease. SETTING: Clinical and research IVF laboratories. PATIENTS: Individuals undergoing preimplantation diagnosis. RESULTS: Four ETs were performed in couples undergoing preimplantation diagnosis by multiplex PCR or fluorescence in situ hybridization, resulting in the birth of two normal female twins. The result of another is pending. A total of 22 embryos were analyzed by PCR. Embryos that were diagnosed as being at risk of carrying the genetic abnormality (n = 8), embryos that failed diagnosis (n = 4), and genetically normal embryos that arrested development (n = 4) were further analyzed by fluorescence in situ hybridization. The sex of all 16 embryos was determined and confirmed the previous 12 preimplantation diagnoses by multiplex PCR. In addition, fluorescence in situ hybridization analysis allowed the detection of two aneuploid embryos, one XO and one XXY, previously diagnosed by PCR as a normal female and male. Two mosaics were also detected. CONCLUSION: Polymerase chain reaction and fluorescence in situ hybridization are possible for preimplantation sex determination in cases of genetic sex-linked disease. Fluorescence in situ hybridization, however, supplies additional information about sex chromosome aneuploidy and is not susceptible to contamination or misdiagnosis of monosomy X.

Adult↗

PubMed2000

VP7 and VP4 genotyping of human group A rotavirus in Buenos Aires, Argentina.

Specific and sensitive tests for the detection and typing of group A rotavirus strains are needed for a more comprehensive knowledge of the epidemiology of rotaviral infection. In this study 500 stool specimens taken from 1996 to 1998 from children with acute diarrhea in Buenos Aires were examined. Group A rotavirus was unequivocally demonstrated in 62% of the samples tested by enzyme-linked immunosorbent assay (ELISA) for detection of VP6 antigen, polyacrylamide gel electrophoresis of double-stranded RNA, and reverse transcription-PCR (RT-PCR) for amplification of the VP7:G (1, 062 bp) and VP4:P (876 bp) genes. Only five positive specimens were found by RT-PCR but not by ELISA. G and P typing was carried out by nested amplification of variable sequences of the VP7 and the VP4 genes with six G- and five P-type-specific primers (multiplex PCR). Results obtained by this method showed the prevalence of the following G and P types: G1, 39%; G2, 43%; G4, 4%; P[8], 16%; P[4], 71%. Unexpectedly, the G-P type combination most frequently found was G2P[4] (43%) rather than G1P[8] (12%), which is the most commonly found worldwide. Unusual strains of the type G1P[4] accounted for 14% of the total, while mixed infections with more than one type were found in 10% of the samples. Detection of fecal rotavirus-specific immunoglobulin M (IgM) and IgA antibodies in consecutive samples of two patients taken at daily intervals demonstrated that high levels of IgM and IgA antibodies were detected on day 1 after the onset of disease and that the samples remained positive for about 10 days, after which virus shedding was no longer observed. Multiplex PCR offers a sensitive and specific alternative to determine the prevalence of group A rotavirus G and P types and to identify the emergence of uncommon strains, whereas detection of fecal IgM and IgA antibodies represents a useful supplement to virus detection for the diagnosis of current or recently acquired infections.

Antibodies, Viral↗

PubMed2005

PCR method for the detection of potential ochratoxin-producing Aspergillus species in coffee beans.

Ochratoxin A (OA) is a nephrotoxic and carcinogenic mycotoxin that has been found in cereal and food commodities. Currently, Aspergillus carbonarius, A. niger and A. ochraceus have been recognized as the species responsible for OA in coffee beans. With the aim of developing multiplex-PCR for detection of these species in coffee bean samples, we first developed specific primers for A. niger detection. The primer designed (OPX7(372)) provided an amplicon of 372 pb in all A. niger stricto sensu isolates. The PCR assay developed for A. niger identification in pure culture was also successfully used for detecting this species in coffee beans. No cross-reaction was observed using DNA from coffee beans inoculated with closely related black aspergilli species. A multiplex-PCR method for detection of A. carbonarius, A. niger and A. ochraceus species in coffee beans was developed. From a single assay this method detected the amplicons of 809, 372, and 260 pb that represent the three most ochratoxigenic species found in coffee bean samples, i.e., A. carbonarius, A. niger and A. ochraceus, respectively.

Aspergillus↗

PubMed1999

Screening for microdeletions on the long arm of chromosome Y in 53 infertile men.

About 30% of couple infertilities are of male origin. They appear in some cases de novo and are considered idiopathic. The aim of our work was to evaluate, in these cases, the prevalence of microdeletions of the long arm of chromosome Y, within the AZF a, b and c regions using molecular biology techniques. Men with azoospermia or oligozoospermia resulting from hereditary, endocrine or obstructive causes, or with a constitutional cytogenetic abnormality were excluded. Fifty-three infertile men with azoospermia or oligozoospermia, as determined by a spermiogram, were studied. Of these, 34 were idiopathic and 7 exhibited a past history of genital infection or biological abnormalities, suggesting partial obstruction of the genito-urinary tract. A further 8 men had a varicocele and 11 cases with a history of cryptorchidism were also studied. Peripheral blood DNA was extracted from each patient, then amplified by multiplex PCR with STS genomic markers from the three Y chromosome AZF zones. PCR products were then analysed on agarose gels. In view of the difficulty of confirming the absence of a signal in molecular biology, each case suspected of having a deletion was checked by multiplex PCR through coamplification with the SRY marker. Five men with microdeletions of the long arm of the Y chromosome were diagnosed among the 53 patients. All of them included the AZFc zone and the intragenic DAZ gene markers. Furthermore, a larger Y chromosome deletion encompassing the 3 AZF zones was diagnosed, and confirmed by cytogenetic analysis. All Y chromosome microdeletions were observed in the 34 truly idiopathic azoospermia/oligozoospermia cases, corresponding to a proportion of 14.7% (or 9.4% considering the whole population of 53 infertile men). The relatively high proportion of microdeletions found in our series suggests the need for strict patient selection to avoid unnecessary screening for long arm Y chromosome microdeletions.

Adult↗

PubMed2006

Validation of a method for the detection of virulent Yersinia enterocolitica and their distribution in slaughter pigs from conventional and alternative housing systems.

Various methods have been described in the literature for the detection of virulent Yersinia enterocolitica in pigs. The risk factors for pig herd contamination have yet to be determined. The objective of this study was to validate a sensitive method for the detection of Y. enterocolitica and to describe the distribution of the bacteria in pigs at slaughter from conventional and alternative ("organic") housing systems. First, samples were collected from tonsils, caecum with caecal contents, and the caecal lymph nodes of 60 slaughter pigs. These samples were used to compare the sensitivity of six different laboratory culture methods either in common use or described in the literature with that of a polymerase chain reaction with two primer pairs (multiplex PCR). Then, only PCR was used to examine tonsils, caecum and caecal lymph nodes from two groups of slaughter pigs: 210 from six conventional fattening farms and 200 from three with alternative housing. The results of the multiplex PCR were positive in 28 cases. All culture methods proved inferior to PCR in sensitivity. In the second part of the study, PCR detected 36 (18%) positive pigs from alternative housing and 60 (29%) from conventional housing (p<0.05). The highest rate of Y. enterocolitica contamination was found in tonsils (11% alternative, 22% conventional; p<0.05), followed by caecum (5%, 11%) and lymph nodes (2%, 7%). The housing system appears to be one important factor in the prevalence of this common pathogen in pig herds, as we found important differences between the two systems studied here. In the conventional system, the main risk factors appeared to be sourcing pigs from different pig suppliers, use of commercial feed and transportation to slaughter.

Animal Husbandry↗