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PubMed1992

Development, multiplexing, and application of ARMS tests for common mutations in the CFTR gene.

The amplification refractory mutation system (ARMS) is a simple, rapid and reliable method for the detection of any mutation involving single base changes or small deletions. We have applied ARMS methodology to the detection of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Single ARMS tests have been developed for 11 CFTR mutations found in the northwest of England. ARMS reactions for the most common mutations have been multiplexed to give a test which will detect the presence of the delta F508, G551D, G542X, and 621 + 1G----T mutations in a DNA sample. The multiplex test has been validated by the analysis of over 500 previously genotyped samples and has been found to be completely accurate. The rapid detection of the most common mutations has enabled early molecular confirmation of suspected cystic fibrosis in neonates, rapid typing of cystic fibrosis patients and their relatives, and testing of sperm and egg donors.

Base Sequence↗
PubMed2003

[Application of multiplex polymerase chain reaction in rapid identification of Mycobacterium bovis BCG].

OBJECTIVE: To establish a method for the rapid identification of Mycobacterium bovis BCG. METHODS: A genomic region designated RD1 was found to be deleted from BCG strains, but present in other strains of Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTC) including Mycobacterium tuberculosis, Mycobacterium africanum, and Mycobacterium microti. With this information, a multiplex PCR method, developed to detect the deletion of RD1, was used to differentiate BCG strains from other strains of Mycobacterium bovis and other members of MTC. RESULTS: RD1 was shown to be absent in 5 BCG vaccine strains and 2 BCG strains isolated from an infant who died of systemic disseminated infection induced by BCG vaccination, but it was present in 3 Mycobacterium bovis standard strains, 6 Mycobacterium bovis strains isolated from diseased cows, deer or patients with pulmonary tuberculosis and other MTC strains including Mycobacterium tuberculosis H(37)Rv and H(37)Ra strains, 48 Mycobacterium tuberculosis strains isolated from patients with pulmonary tuberculosis, and 3 Mycobacterium africanum standard strains. CONCLUSION: The multiplex PCR method is simple, rapid, and specific for the identification of BCG among strains of MTC, and is applicable in clinical laboratories.

Mycobacterium bovis↗
PubMed2004

[A population study of three Y-STR loci by multiplexing in Han population in Chengdu, China].

OBJECTIVE: To establish a better method determining three Y-STR loci. METHODS: A multiplex of Y-STRs and amplify simultaneously three Y-STRs loci. RESULTS: Establish successfully a multiplexing system of three Y-STR loci (DYS390, DYS391 and DYS393) followed by a population genetic study of Han population in Chengdu, China. CONCLUSION: The diversity of haplotype is 0.8965, the value of discrimination and the chance of exclusion chance is 0.8965 with the standard error 0.0081. This established system is one of the good tools in personnel identification and genetic study.

China↗
PubMed2004

Development of a multiplex PCR (m-PCR) test for rapid identification of genes encoding heat-labile (LTI) and heat-stable (STI and STII) toxins of enterotoxigenic Escherichia coli (ETEC) with internal control of amplification.

A multiplex PCR system was developed for specific identification of genes encoding heat-labile (LTI) and heat-stable (STI and STII) toxins of enterotoxigenic Escherichia coli (ETEC) strains. In addition, primers specific for the E. coli gene coding for 16S rRNA were used as an internal control of the DNA amplification. The specificity of the method was validated by single PCR tests performed with reference to E. coli strains as well as pig-isolated bacteria and 100% correlation was observed. The developed multiplex PCR allowed rapid and specific identification of enterotoxin-positive E. coli and may be used as a sensitive and specific method for a direct determination of ETEC and to differentiate them from other E. coli isolates.

Bacterial Toxins↗
PubMed2004

[A novel oligonucleotide arrays-based multiplex amplifiable probe hybridization technology].

Multiplex amplifiable probe hybridization (MAPH) has recently been developed to detect gene copy number changes in total genome in several genetic disease. Here we reported a novel oligonucleotide arrays-based multiplex amplifiable probe hybridization technology for DNA fragment copy number measurement. A set of amplifiable probes were prepared by locus-specific forward and reverse primers synthesized with the T7 and T3 promoter sites at their respective 5'-ends to the interest DNA fragments and purified by Qiagen PCR products purification kit. The set of probes were then hybridized with genome DNA immobilized on the nylon membrane. The selective probes after MAPH were collected with streptavidin coated magnetic beads and amplified by a biotin labeled universal primers. The biotinylated PCR products were then intended for hybridization to the corresponding oligonucleotide arrays consisted of 10 exons of DMD gene probes and positive,negative control probes immobilized on glass slides. After hybridization, the slides were washed by hybridization buffer and stained by streptavidin-Cy3. The hybridization fluorescence images were scanned by the ScanArray software and further quantitatively analyzed by the ImageJ software. Here we used oligonucleotide array technology to replace the agarose gel analysis for detecting the biotinylated PCR products so that extendable ability of parallel assay in our method had greatly been improved. One control female, one control male and one DMD patient were tested in this study. The results demonstrate the feasibility of high-throughput detection and relative quantification of DNA fragment copy numbers changes in total genome DNA combination of MAPH and high-density oligonucleotide arrays in single reaction.

Gene Dosage↗
PubMed2004

High-throughput protein analysis by multiplexed sodium dodecyl sulfate capillary gel electrophoresis with UV absorption detection.

We have developed a novel, high-throughput approach for molecular mass determination of proteins from 14 200 to 116 000 based upon multiplexed, absorbance-based capillary electrophoresis. Via capillary multiplexing, 96 samples were analyzed simultaneously within 30 min. Detection with ultraviolet light obviates the need for protein staining or derivatization. The detection limit of the system was estimated at 5 microg/ml bovine serum albumin (BSA) when sampled from 12.5 mM Tris-HCl. The linear dynamic range was over two orders of magnitude from 5 microg/ml to 1000 microg/ml for BSA. Better than 5% sizing accuracy for protein molecular mass determination and excellent run-to-run and day-to-day reproducibility was obtainable with the described method.

Electrophoresis, Capillary↗
PubMed2004

Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples.

The molecular genotyping of individuals and reconstruction of kinship through short and high polymorphic DNA markers, so-called short tandem repeats (STR), has become an important and efficient method in anthropology and forensic science. The here introduced experimental design describes a multiplex PCR capable of simultaneously amplifying 16 STRs and the sex determinant locus amelogenin in a short fragment lengths range from 84 bp to 275 bp. Thus, the design depends predominantly on the routines for DNA typing of historical samples with highly degraded ancient DNA. It is shown, that the newly designed multiplex PCR is suitable for successful typing of both forensic and historical material.

Alleles↗
PubMed2005

[The multiplex analysis of epigenetic markers and genetic markers by post-digestion mutagenically separated PCR].

OBJECTIVE: To establish a novel method for the multiplex analysis of the methylation and single nucleotide polymorphism (SNP). METHODS: The imprinted SNP rs220028 was chosen as a model. Genomic DNA, after being digested with methylation sensitive restriction enzyme, were typed by mutagenically separated PCR (MS-PCR). The polymorphism of restriction site was excluded by PCR-RFLP. RESULTS: By post-digestion MS-PCR, the methylated allele was detected selectively, the maternal origin of which was confirmed by pedigree analysis; A=0.5085, G=0.4915,PIC=0.3749. CONCLUSION: The multiplex analysis of methylation markers and SNP can be achieved by post-digestion MS-PCR. The imprinted SNP locus rs220028 is a potentially useful marker in screening Prader-Willi/Angelman syndrome.

DNA Methylation↗
PubMed2005

Detection of homozygous and heterozygous SMN deletions of spinal muscular atrophy in a single assay with multiplex ligation-dependent probe amplification.

OBJECTIVE: Spinal muscular atrophy(SMA), an autosomal recessive neuromuscular degeneration of the anterior horn cells of the spinal cord and brain stem, results in one of the most common diseases with muscle fatigue and atrophy. Most SMA cases including all the types are due to the homozygous deletion of at least exon 7 within the survival motor neuron 1 (SMN-1) gene. Although a "golden standard" assay (PCR with mismatch primer followed by enzyme digestion) is very reliable for the identification of homozygous SMN-1 deletion, the carrier detection of heterozygous SMN-1 deletion remains a challenge. METHODS: Some PCR-based gene dosage assays or multiplex PCR allow for the determination of the copy number of SMN-1 gene to identify heterozygous deletion, but these procedures are often time consuming and available on a limited clinical basis. Recently developed MLPA (multiplex ligation-dependent probe amplification) is an efficient procedure that can accurately analyze relative quantification to establish the copy number of the SMN gene. We performed a validation for simultaneous detection of homozygous SMN-1 deletions of SMA patients and heterozygous SMN-1 deletions of SMA carriers in a simple assay using a MLPA-SMA assay specific reagent. RESULTS: Six out of 20 patients with SMA were found to have homozygous SMN-1 deletion, confirmed by the PCR/digestion assay. All 4 parents of the children with SMA had heterozygous SMN-1 deletion, confirmed by an independent relative quantitative analysis. CONCLUSION: MLPA provides a simple, rapid and accurate method of simultaneously detecting homozygous deletions and heterozygous deletions in a single assay for both SMN-1 and SMN-2 genes.

Cyclic AMP Response Element-Binding Protein↗
PubMed2004

[Multiplex PCR assay against E. coli O157 in foodstuffs].

A multiplex PCR assay for detection of Escherichia coli O157:H7 was developed with 4 pairs primers which focus on its specific fliC, rfbE, SLT I and SLT II genes. The target genes fragments of the PCR assay were 560 bp, 678 bp, 210 bp and 484 bp. The multiplex PCR had very high specificity to match all the 71 tested strains including 58 E. coli strains and other 18 strains. The strain of E. coli O157:H7 was identified in one step, and the type of SLT was also identified as well. With the enrichment procedure, the strain of E. coli O157:H7 were recovered at the detection limit of 0.1 cfu/ml from artificial inoculated pasteurized milk.

Animals↗
PubMed2005

Medical devices; clinical chemistry and clinical toxicology devices; instrumentation for clinical multiplex test systems. Final rule.

The Food and Drug Administration (FDA) is classifying instrumentation for clinical multiplex test systems into class II (special controls). The special control that will apply to the device is the guidance document entitled "Class II Special Controls Guidance Document: Instrumentation for Clinical Multiplex Test Systems." The agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device. Elsewhere in this issue of the Federal Register, FDA is publishing a notice of availability of a guidance document that is the special control for this device.

Chemistry, Clinical↗
PubMed2005

Isolation and identification of Escherichia coli O157:H7 using different detection methods and molecular determination by multiplex PCR and RAPD.

Escherichia coli O157:H7 is recognized as a significant food-borne pathogen, so rapid identification is important for food hygiene management and prompt epidemiological investigations. The limited prevalence data on Shiga toxin-producing E. coli (STEC) and E. coli O157:H7 in foods and animals in Korea made an assessment of the risks difficult, and the options for management and control unclear. The prevalence of the organisms was examined by newly developed kit-E. coli O157:H7 Rapid kit. For the isolation of E. coli O157:H7, conventional culture, immunomagnetic separation, and E. coli O157:H7 Rapid kit were applied, and multiplex PCR and randomly amplified polymorphic DNA (RAPD) were performed for the molecular determination. There was high molecular relatedness among 11 Korean isolates and 17 U.S. strains at 63% level. Additionally, distinct differentiation between pig and cattle isolates was determined. It implied that RAPD had a capacity to distinguish strains with different sources, however it could not discriminate among isolates according to their differences in the degree of virulence. In antimicrobial susceptibility tests, 45.5% of isolates showed antibiotic resistance to two or more antibiotics. Unlike the isolates from other countries, domestic isolates of E. coli O157:H7 was mainly resistant to ampicillin and tetracyclines. In summary, the application of E. coli O157:H7 Rapid kit may be useful to detect E. coli O157:H7 due to its sensitivity and convenience. Moreover, combinational analysis of multiplex PCR together with RAPD can aid to survey the characteristics of isolates.

Abattoirs↗
PubMed2005

[Rapid detection of three common deletional alpha thalassemias in Chinese by single-tube multiplex PCR].

OBJECTIVE: To develop a simple, rapid, accurate, and cost-effective single-0tube multiplex polymerase chain reaction (PCR) assay, which could be used for molecular screening and prenatal diagnosis, for detection of three commonest deletional alpha-thalassemias (-- (SEA), -alpha (3.7) and -alpha (4.2)) in Chinese population. METHODS: Four groups of primers were designed on the basis of gap-PCR, and the PCR reaction condition was optimized systematically with the purpose of amplifying effectively specific DNA fragments that are indicative of the respective genotypes of these three deletional alpha thalassemias. In addition, a pair of primers was designed to amplify LIS1 3' untranslated region (UTR) fragment for use as a separate control for amplification running. A total of 72 blood and prenatal archival DNA samples with various known alpha thalassemia genes or normal alpha globin gene sequence that had been confirmed by Southern blotting analysis or DNA sequencing were collected to test the specificity of this assay by blind analysis. In addition, DNA samples from nine couples at high risk of alpha thalassemia were also analyzed to evaluate the reliability of this technique in prenatal implementation. RESULTS: Homozygote, heterozygote and double heterozygote of the three commonest deletional alpha thalassemias were well detected simultaneously by this established method. For normal allele, a 2.4 kb amplified band as a systematic control and an alpha (2) gene-specific amplicon of 1.8 kb were produced. Besides the two amplified fragments of normal allele, it was found that a 1.3 kb, a 2.0 kb or a 1.6 kb amplified band could be simultaneously shown for representing --(SEA), -alpha (3.7) and -alpha (4.2) alleles, respectively, in the heterozygous states. In a blind test, this technique accurately detected 100% of the DNA samples previously characterized by Southern blotting or DNA sequencing, and it was successfully applied to prenatal diagnosis of alpha thalassemia in nine at-risk families. CONCLUSION: The single-tube multiplex PCR protocol presented in this study is easy-to-handle, rapid, reliable and is cost-effective for detecting --(SEA), -alpha (3.7) and -alpha (4.2) chromosomes, and it is suitable for large-scale population screening and for rapid molecular genotyping in clinics.

Asian People↗
PubMed2005

Multiplexed serum measurement of IgG, IgA, IgM, and IgE antibody responses to therapeutic biologicals.

Analytical methods characterizing the immunogenicity of therapeutic proteins are useful for monitoring, characterizing and predicting reactions to biopharmaceuticals. A multiplexed assay capable of isotyping the specific IgG, IgA, IgM and IgE (IgGAME) antibody responses against a biotherapeutic was demonstrated in a hyper-immunized cynomolgus monkey, over a 15-month period. The quantitative range of the antibody measurements was determined to be 15 ng/ml to 50 ng/ml in 10% serum. By the use of any biotinylated or fluorescently tagged therapeutic as a detector, this multiplexed isotyping assay can be broadly applied to human and non-human primate IgG, IgA, IgM and IgE immunogenicity studies.

Animals↗
PubMedDate not supplied

[Validation of a multiplex PCR for detection of Shiga toxin-producing Escherichia coli].

Shiga toxin-producing Escherichia coli (STEC) cause non-bloody or bloody diarrhea, hemorrhagic colitis and hemolytic uremic syndrome (HUS) in humans. The aim of the present study was to validate a multiplex PCR for the STEC diagnosis based on the detection of stx1, stx2 and rfbO157 genes. The multiplex PCR validation was carried out in two independent laboratories in a parallel way. Work range, selectivity and robustness were established. The PCR performance was evaluated using different concentrations of two STEC strains harboring different target genes. The work range depended on the strain analyzed, the maximum and the minimum values were 6.6 x 10(7) and 1.0 x 10(4) CFU/50 microl. The detection limit was 1.0 x 10(4) CFU/50 microl and the cut limit 1.0 x 10(5) CFU/50 ml. A good robustness was observed when different variables were introduced. Inclusivity, exclusivity, positive predictivity, negative predictivity and analytical accuracy were of 100%. Interference was not shown when different concentrations of STEC strains, carrying different genes, were used. The validated technique is an appropriate alternative for detection and confirmation of STEC O157 and non-O157 strains from bacterial cultures.

Cell Fractionation↗
PubMed2005

A comparison of fluorescent in situ hybridization and multiplex short tandem repeat polymerase chain reaction for quantifying chimerism after stem cell transplantation.

BACKGROUND AND OBJECTIVES: Despite the great utility of chimerism analysis after allogeneic stem cell transplantation, a gold standard method for its quantification has not yet been defined. The objective of the present investigation was to compare the sensitivity (detection limit) and the quantification accuracy of fluorescent in situ hybridization with specific probes for the sex chromosomes (XY-FISH) and multiplex short tandem repeat polymerase chain reaction (STR-PCR) revealed by capillary electrophoresis for the quantification of chimerism after stem cell transplantation. DESIGN AND METHODS: A first experiment was performed on two sets of artificial cell mixtures from two sex-mismatched healthy donors mixed in different proportions (% male: 100, 75, 50, 25, 10, 5, 3, 1, 0.1, 0). In a second experiment, 58 samples obtained from 10 selected patients with different clinical courses and chimerism evolution after sex-mismatched stem cell transplantation, which had been studied by XY-FISH, were retrospectively analyzed by STR-PCR. In a third experiment, 60 unselected prospective samples belonging to 15 patients (5 of whom had also been included in the retrospective study) were analyzed by both XY-FISH and STR-PCR. RESULTS: Both techniques showed high quantification accuracy and were highly reproducible. The sensitivity of both approaches reached 1% under standard conditions. Moreover, the use of long injection times for the capillary electrophoresis (30 and 50s vs. the standard 10s) resulted in an increase of sensitivity of the STR-PCR assay up to 0.1%, which has interesting clinical implications. INTERPRETATION AND CONCLUSIONS: Considering the high sensitivity and quantification accuracy of multiplex STR-PCR and the fact that this assay is sex-independent and can be applied to virtually all patients, STR-PCR could be considered as the method of choice for chimerism quantification after stem cell transplantation when high sensitivity is not a requirement.

Adolescent↗
PubMed2005

[Detection of fetal short tandem repeat genotype in maternal plasma by multiplex fluorescent polymerase chain reaction].

OBJECTIVE: To study the feasibility of using free fetal DNA in maternal plasma for non-invasive prenatal diagnosis. METHODS: Maternal DNA extracted from plasma samples of 10 pregnant women at early pregnancy, medium pregnancy and late pregnancy and their husband's DNA isolated from whole blood samples were used to detect genotype by multiplex fluorescent PCR at nine different polymorphic short tandem repeat(STR) loci. RESULTS: Fetus-specific alleles were found in maternal plasma samples studied. By the application of these polymorphic short repeat sequences, every pregnant women/husband pair was informative in at least three of nine loci. Paternally inherited fetal alleles were detected in 23 of 30 plasma samples. They are 6/10 cases in early pregnancy, 8/10 cases in middle pregnancy and 9/10 cases in late pregnancy respectively. CONCLUSION: Fluorescent multiplex PCR can be used for amplification of male and female fetal STRs in maternal plasma to obtain genetic information, which may have implication for non-invasive prenatal diagnosis of certain hereditary diseases independent of the fetal sex.

Adult↗
PubMed2005

[Application of the multiplex PCR and PCR-RFLP method in the identification of the Bacillus anthracis].

The aim of this study was to apply the multiplex PCR and PCR-RFLP method for the identification of the B. anthracis strains and to distinguish those bacteria from other members of the Bacillus cereus group. The multiplex PCR method enables to detect the virulence factors, i.e. the toxin and the capsule in B. anthracis strains. To do that, the authors have used 5 primer pairs specific for the fragments of lef, cya, pag genes which are present in the pXO1 plasmid and encode the toxin, the cap gene, which is present in the pXO2 plasmid and encodes the capsule, and the Ba813 chromosomal sequence. Among the four B. anthracis strains examined, three contained two plasmids and the Ba813 chromosomal sequence, while the fourth one contained the pXO1 plasmid only, together and the Ba813 chromosomal sequence. Other bacterial species, belonging to the B. cereus group, were also examined: 6 strains of B. cereus, 4 strains of B. thuringiensis and one strain of B. mycoides. The presence of Ba813 chromosomal sequence has been detected in two B. cereus strains. Neither plasmids nor Ba813 chromosomal sequence have been discovered in other B. cereus, B. thuringiensis and B. mycoides strains. The results of the survey indicate that the Ba813 chromosomal sequence does not occur solely in B. anthracis strains. The PCR-RFLP method with the use of SG-749f and SG-749r primers enabled to demonstrate the presence of DNA sequence (SG-749) in B. anthracis, B. cereus, B. thuringiensis and B. mycoides strains. Restriction analysis with enzyme AluI of the SG-749 sequence, has shown the presence of two DNA fragments at the size of about 90 and 660 bp in all B. anthracis strains. The restriction profile obtained was characteristic for B. anthracis strains and it did not occur in other investigated bacterial species belonging to the B. cereus group. It was not observed even in such B. cereus strains in which the presence of Ba813 sequence was discovered and it enabled to differentiate between B. anthracis strains and other closely related species of the B. cereus group.

Bacillus anthracis↗