SEARCH · Search PubMed

Results for “Multiplex”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,027 records · Page 57Linked to original sources

PubMed2006

Sarcoglycanopathies: a multiplex molecular analysis for the most common mutations.

Sarcoglycanopathies (SGpathies) are highly frequent among severely affected limb-girdle muscular dystrophy patients. On the basis of the findings of 5 common mutations in the 4 sarcoglycan (SG) genes in the Brazilian population, we standardized a multiplex polymerase chain reaction-single-strand conformation polymorphism methodology for their concomitant analysis in DNA samples. The test was able to confirm the diagnosis in about 63% of new patients with a suspected SGpathy and was particularly important in patients in advanced stages of the disease, when obtaining a muscle biopsy for analysis may be very difficult. As common mutations have been described in several countries, this multiplex analysis could be useful for the diagnosis of SGpathies if established according to the most prevalent mutations in each population. Besides, even though the disorder studied is rare, the technique could be broadly applicable to other genes and disorders.

Adolescent↗

PubMedDate not supplied

Technical validation of a multiplex platform to detect thirty mutations in eight genetic diseases prevalent in individuals of Ashkenazi Jewish descent.

PURPOSE: This study determines the analytic accuracy of a Luminex bead-based commercial analyte-specific reagent for the simultaneous analysis of 30 mutations prevalent in Ashkenazi Jews at eight genetic disease loci. METHODS: DNA from 20 samples with known abnormal genotypes were run a total of 109 times. DNA from 820 patients with unknown genotypes submitted for Ashkenazi Jewish testing panels were analyzed using our current laboratory techniques. The 820 samples were then stripped of identifiers, coded, and reanalyzed using the Tm Biosciences (Toronto, Canada) Ashkenazi Jewish panel analyte-specific reagent in a blinded fashion. For the controls, comparisons were made with their known genotypes. For the patient samples, the results of the Tm assay were compared with the results of our current assay. For 24 of the 30 mutations, we had genomic DNA controls or detected patients' samples heterozygous for these mutations. RESULTS: There were no discrepant results in the control or patient samples. In the patient samples, 19,680 genotyping reactions were performed without error in both our laboratory-developed single-disease assays and the Tm multiplex assay. Including the controls, 22,296 genotypes were determined without error. CONCLUSION: The Tm Biosciences Ashkenazi Jewish analyte-specific reagent is capable of performing accurate analyses of 24 different mutations in eight different genes in a single multiplex reaction and can be used with confidence in the clinical molecular genetics laboratory.

DNA Mutational Analysis↗

PubMed2005

Multiplex PCR for identification of Campylobacter coli and Campylobacter jejuni from pure cultures and directly on stool samples.

A multiplex-PCR method, specifically designed for application in routine diagnostic laboratories, was developed for the detection of Campylobacter coli and Campylobacter jejuni. Primers were directed towards the following loci: the hippuricase gene (hipO) characteristic of C. jejuni, a sequence partly covering an aspartokinase gene characteristic of C. coli, and a universal 16S rDNA gene sequence serving as an internal positive control for the PCR. The method was tested on 47 C. coli strains and 88 C. jejuni strains, and found to be almost 100% in concordance with biochemical analyses (all except for one C. coli strain), regardless of whether the DNA was prepared from colonies by a simple boiling procedure or by DNeasy Tissue Kit. Pure cultures of C. coli and C. jejuni were identified at 10-100 cells per PCR. When the multiplex-PCR method was used on spiked human stool samples, both strains were identified at 10(5) cells per ml stool. This sensitivity limit was the same whether the DNA was purified by the method of KingFisher mL or QIAamp DNA Stool Kit. When the same spiked stools were grown on modified charcoal cefoperazone deoxycholate agar (mCCDA) plates before PCR, the sensitivity was 100 cells per ml stool, indicating that culturing of campylobacters on mCCDA plates is superior to direct DNA extraction at least when fresh stool samples are analysed by PCR.

Amidohydrolases↗

PubMed2025

HyperCas12a enables multiplexed CRISPRi screens.

Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We further show that the system can be used in cultured primary immune cells and to drive differentiation of induced pluripotent stem cells. We also developed new approaches to use the dCas12a platform for simultaneous activation and repression from a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, we demonstrate that the dHyperLbCas12a effectors are highly effective for multiple modalities of high-throughput screens, namely proliferation screens and screens to dissect the independent and combinatorial contributions of CREs on gene expression. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.

Journal Article↗

PubMed2000

A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension.

A rapid, high throughput readout for single-nucleotide polymorphism (SNP) analysis was developed employing single base chain extension and cytometric analysis of an array of fluorescent microspheres. An array of fluorescent microspheres was coupled with uniquely identifying sequences, termed complementary ZipCodes (cZipCodes), which allowed for multiplexing possibilities. For a given assay, querying a polymorphic base involved extending an oligonucleotide containing both a ZipCode and a SNP-specific sequence with a DNA polymerase and a pair of fluoresceinated dideoxynucleotides. To capture the reaction products for analysis, the ZipCode portion of the oligonucleotide was hybridized with its cZipCodes on the microsphere. Flow cytometry was used for microsphere decoding and SNP typing by detecting the fluorescein label captured on the microspheres. In addition to multiplexing capability, the ZipCode system allows multiple sets of SNPs to be analyzed by a limited set of cZipCode-attached microspheres. A standard set of non-cross reactive ZipCodes was established experimentally and the accuracy of the system was validated by comparison with genotypes determined by other technologies. From a total of 58 SNPs, 55 SNPs were successfully analyzed in the first pass using this assay format and all 181 genotypes across the 55 SNPs were correct. These data demonstrate that the microsphere-based single base chain extension (SBCE) method is a sensitive and reliable assay. It can be readily adapted to an automated, high-throughput genotyping system. [Primer sequences used in this study are available as online supplementary materials at www.genome.org.]

DNA, Complementary↗

PubMed1995

Nonradioactive multiplex PCR screening strategy for the simultaneous detection of multiple low-density lipoprotein receptor gene mutations.

We have developed a rapid, nonradioactive screening test enabling the simultaneous analysis of three low-density lipoprotein receptor (LDLR) gene mutations (D154N, D206E, and V408M), which together account for familial hypercholesterolemia (FH) in approximately 90% of the South African Afrikaner population. The assay is designed so that FH patients, negative for these founder-related mutations (found in descendants of European settlers), subsequently can be screened for unknown mutations in the mutation-rich exon 4 of the LDLR gene. Our screening assay consists of two steps: (1) multiplex allele-specific PCR amplification of exons 4 and 9, and (2) simultaneous analysis of single- and double-strand conformational polymorphisms in exon 4 by vertical electrophoresis on low cross-linked polyacrylamide gels. The simplicity, specificity, and versatility of the multiplex assay makes it an ideal system for routine screening of FH mutations in large population samples.

Base Sequence↗

PubMed1996

Chromosome-specific panels of tri- and tetranucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics.

A set of 391 microsatellite markers (Weber set 6), 85% of which consist of tri- and tetranucleotide repeat markers, were used to design chromosome-specific panels that allowed for a high degree of multiplexing with respect to the fragment size range and fluorophore (FAM, HEX, TET). This marker set has an average coverage of 10.5 cM, with the largest gap being 28.1 cM. The markers were divided into 49 panels, with a maximum degree of multiplexing of 15 markers per panel. The utility of the markers for analysis of DNA from blood, hair, and formalin-fixed archival tissue biopsies was evaluated with respect to amplification efficiency, product yield, and degree of preferential amplification of the shorter allele in heterozygotes. The amplification efficiency was inversely related to repeat length and amplicon length. Based on the analysis of DNA from formalin-fixed biopsies, 51 markers suitable for loss of heterozygosity (LOH) studies were identified. The utility of the marker set for genome scanning, LOH, and forensic analyses is discussed.

Chromosomes↗

PubMed2000

Limits for interchannel frequency separation in a soliton wavelength-division multiplexing system.

We identify the required interchannel frequency separation of the input field for a soliton wavelength-division multiplexing (WDM) system. It is found that the critical frequency separation above which WDM with solitons is feasible increases with the number of transmission channels. Moreover, it is shown that a combination of time- and wavelength-division multiplexing yields the largest transmission capacity. Finally, the structure of the soliton spectra which correspond to the frequency separation smaller than the critical frequency is discussed.

Journal Article↗

PubMed2005

Simple acoustic multiplexer.

Simple structures enabling the multiplexing of acoustic waves are presented. Such structures are constructed out of two monomode acoustic wires and two masses bound together, and to the wires by springs. We show analytically that these simple structures can transfer with selectivity and in one direction one acoustic wavelength from one wire to the other, leaving neighbor acoustic wavelengths unaffected. We give closed-form relations enabling to obtain the values of the relevant physical parameters for this multiplexing phenomena to happen at a chosen wavelength. Finally, we illustrate this general theory by an application.

Journal Article↗

PubMed1992

Adaptive control of multiplexed closed-circuit anesthesia.

This paper describes the design of an adaptive closed-circuit anesthesia controller based on a multiplexed mass spectrometer system. The controller deals with measurement deterioration caused by measurement delay and rise time through a long catheter as well as long sampling times due to the multiplexed measurements. Measurement data are extrapolated between sampling periods to increase the estimation convergence rate. A multiple-step-ahead predictive control algorithm is used to calculate intermediate control inputs between sampling intervals. Simulations are used to validate the designed controller.

Algorithms↗

PubMed2004

Multiplexed analysis of polymorphisms in the HLA gene complex using bead array chips.

A novel custom bead array technology is introduced, and it is applied to multiplexed analysis of highly polymorphic human leukocyte antigen (HLA) genetic loci. Our technology combines the construction of probe libraries on color-encoded microparticles (beads) with semiconductor chip processing to produce custom-designed high-density bead array chips in large quantities. Using this novel assay format, two modes of parallel molecular typing of the HLA complex were implemented, namely direct hybridization, illustrated here for class II HLA-DR, and a novel format of on-chip polymerase-mediated primer elongation, illustrated here for class I HLA-A, HLA-B, and HLA-DR using patient and reference cell-line DNA samples. Hybridization-mediated multiplexed analysis of polymorphism method was validated with 142 samples, resulting in 100% concordance with sequence-specific oligonucleotide typing results and a concomitant average of 40% less allele ambiguity. In addition, elongation and hybridization reactions were combined to identify multiple polymorphisms on the same phase of DNA for allele identification.

HLA Antigens↗

PubMed1991

Eruptive steatocystoma multiplex on the scalp.

We report a 71-year-old Japanese woman who noticed approximately 120 small yellowish cysts on the scalp from nine months before her first visit. An incision made into the cysts discharged oily yellow material. Biopsy of a lesion disclosed that the cysts had typical features of steatocystoma multiplex histologically. This case was a unique eruptive variety of steatocystoma multiplex on the scalp.

Age Factors↗

PubMed1998

Pachyonychia congenita associated with steatocystoma multiplex.

We present an unique case of pachyonychia congenita associated with steatocystoma multiplex. A 33-year-old Japanese man had thickening and gray-brown dicoloration of all nails and a large number of nodules or tumors over his entire skin. No palmar and plantar hyperkeratosis, leukokeratosis of the mucous membranes, or follicular keratosis were observed. Histology of these tumors revealed the typical features of steatocystoma multiplex.

Adult↗

PubMed1996

Detection and identification of Yersinia pestis by polymerase chain reaction (PCR) using multiplex primers.

A PCR method for detection of Yersinia pestis-virulence determinants by the use of multiplex primers was developed. Four pairs of oligonucleotide primers were designed from each gene of three kinds of virulent plasmids and a chromosomal DNA; 60-Md plasmid-located gene (caf1)encoding Y.pestis-specific capsular antigen fraction 1, a Y.pestis-specific region of a yopM gene encoded on 42-Md virulent plasmid, a plasminogen activator gene (pla) encoded on Y.pestis-specific 7-Md plasmid and an invasin protein gene (inv) encoded on chromosomal DNA. This multiplex-primer system was specific for the detection of Y.pestis among pathogenic Yersinia species and other enterobacteriaceae having antigens common to Y.pestis. Since this method is simple and safe, it will be useful to identify and confirm Y.pestis in cases of emergency and for the surveillance of epidemics.

Adhesins, Bacterial↗

PubMed1991

Hypermetabolism in arthrogryposis multiplex congenita.

Two patients who developed hypermetabolic reactions during anaesthesia and surgery and who were suffering from arthrogryposis multiplex congenita are reported and it is proposed that the reaction is distinct from malignant hyperthermia and independent of the anaesthetic agents used. The implications for anaesthetists involved in the management of patients with arthrogryposis multiplex congenita are discussed.

Anesthesia, General↗

PubMed1997

Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing.

Six multiplexes developed for semiautomated fluorescence genotyping were evaluated for parentage testing. These multiplexes contained primer pairs for the amplification of 22 microsatellites on 17 bovine autosomes. Exclusion probabilities were determined from genotypes of 1022 Holstein cattle and 311 beef cattle belonging to five breeds. Two cases were considered: case 1, genotypes are known for an alleged parent and an offspring but genotypes of a confirmed parent are unknown; and case 2, genotypes are known for an alleged parent, a confirmed parent and an offspring. If the alleged parent is not the true parent, then the 22 markers will exclude the alleged parent with a probability of > 0.9986 for case 1 and with a probability of > 0.99999 for case 2. On the basis of these exclusion probabilities, the probability that an alleged parent will be falsely included as a parent is in the range of 1/716 to 1/2845 for case 1 and 1/1.2 million to 1/159753 for case 2. In addition to these results, a rapid and efficient non-organic method for extraction of DNA from semen is described.

Animals↗

PubMed1992

Successful treatment of steatocystoma multiplex by simple surgery.

Steatocystoma multiplex is usually a minor cosmetic problem but rarely can be extremely disfiguring. Unfortunately, the very patients who would benefit most from treatment are usually regarded as having too may cysts for surgery. We report a case of extensive steatocystoma multiplex which was treated by a simple surgical technique under general anaesthetic.

Arm↗

PubMed1994

Multiplex analysis of two intragenic microsatellite repeat polymorphisms in the genetic diagnosis of haemophilia A.

Use of molecular genetic studies for carrier detection and prenatal diagnosis of haemophilia A will be informative in approximately 75% of kindreds with a prior history of the disorder if previously reported bi-allelic intragenic polymorphisms are used. In this study we report the use of two multi-allelic, microsatellite repeat polymorphisms within the factor VIII gene in genetic testing for this disease. These two, dinucleotide repeat, polymorphisms have been analysed using a multiplex polymerase chain reaction (PCR) protocol, and results can be available within 3 d of receipt of samples. At the intron 13 polymorphic locus we have confirmed the original observation of eight alleles, whilst at the intron 22 locus, in contrast to a preliminary report of this polymorphism, we have seen five alleles. We have analysed 32 families (174 subjects) with the two microsatellite repeat markers and have found that using these two polymorphisms alone, 81% of families are informative for linkage analysis. The intron 13 repeat was informative in 22/31 families tested (71%) and the intron 22 polymorphism was informative in 12/17 families (71%). We have also found that in 11/32 families tested (34%) the microsatellite repeats were the only informative intragenic markers. In view of these observations, we believe that the most effective strategy for initiating haemophilia A genetic testing is to combine the multiplex PCR analysis of the intron 13 and 22 dinucleotide repeats with the PCR analysis of the intron 18 BclI marker. In our population this protocol provided informative results in approximately 88% of families and results can be available within 3 d of receiving the samples for testing.

Alleles↗