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PubMed2001

High-performance liquid chromatography multiplex detection of two single nucleotide mutations associated with hereditary hemochromatosis.

High-performance liquid chromatography (HPLC) has been applied to the multiplex detection of the two single nucleotide mutations commonly found in hereditary hemochromatosis (HH). HH is associated with a major G to A transition at position 845 (mutation Cys282Tyr) and a minor C to G transition at position 187 (mutation His63Asp) in the cDNA of the HFE gene. Two detection assays were developed based on HPLC analysis of restriction fragment length polymorphism (RFLP) or single nucleotide extension (SNE) products following multiplex PCR amplification. RFLP genotypes the two sites as dsDNA fragments of different lengths generated by restriction enzymes Rsa I/Bcl I. SNE extends primers 5'-adjacent to the sites of interest with a dideoxynucleotide triphosphate (ddNTP) to generate extended ssDNA. The identity of the added ddNTP reveals the identity of the original possible mutation site(s). Application of these methods with HPLC analysis provides simple and reliable genotyping for HH and can be applied to other single nucleotide polymorphism studies.

Chromatography, High Pressure Liquid↗
PubMed2001

Sequenced allelic ladders and population genetics of a new STR multiplex system.

The advent of PCR technology and use of short tandem repeat (STR) loci improves throughput and reduces costs whilst a high level of discrimination can be achieved. A new system, comprising seven STRs, was developed to compliment the existing systems. This paper describes the preparation of allelic ladders of the most commonly observed alleles of a new STR multiplex system (third generation; TGM multiplex); all alleles have been sequenced. Meioses studies estimated a mutation rate of 0-0.4% across loci. Statistical independence was investigated by employing exact tests; chi(2)-tests and excess homozygosity tests. The results demonstrated that the allele proportions do not differ from those expected and that there was no consequential dependence between loci. The discriminating power of the system was examined using 295 Caucasian, 140 Afro-Caribbean and 212 Asian unrelated samples, and was found to be approximately 1 in 50 million, 1 in 85 million and 1 in 20 million for each of these groups, respectively.

Alleles↗
PubMed2002

High resolution Y chromosome typing: 19 STRs amplified in three multiplex reactions.

Nineteen Y-specific short tandem repeat (STR) loci have been amplified in 768 samples from the Iberian Peninsula in order to evaluate their usefulness in forensic casework. Two previously published multiplex reactions by Thomas et al. [Hum. Genet. 6 (1999) 577] (MS1, modified here: DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393) and by Ayub et al. [Nucl. Acids Res. 28 (2000) e8] (CTS: DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439) plus a novel one reported here (EBF: DYS385, DYS389, DYS460, DYS461, DYS462 and amelogenin) have been used. DYS385, DYS439 and DYS391 were the most informative loci with allele diversities of 0.7997, 0.6683 and 0.5940, respectively. A total of 635 different haplotypes were observed, of which 573 (90.24%) were found in single individuals. The overall haplotype diversity was 0.9988 and that obtained by each multiplex system was 0.9812 for EBF, 0.9292 for MS1 and 0.9089 for CTS.

Base Sequence↗
PubMed1997

Multiplex amplification of STR loci with gender alleles using infrared fluorescence detection.

The analysis of short tandem repeat (STR) polymorphisms has proven extremely useful for gene mapping, paternity testing, and forensic analysis. Several commercial products are currently available for performing amplification and analysis of STRs. We have adapted Promega Geneprint Systems for use with a high sensitivity infrared (IR) fluorescent automated DNA sequencer. IR-labeled amplification products are generated by including a small quantity of IR-labeled dATP in the reaction. Several Geneprint STR loci can be multiplexed together with the amelogenin sex identification locus in a single amplification reaction. We have successfully amplified up to five Geneprint STR loci together with the amelogenin locus thus improving the throughput of analysis. Purified genomic DNA as well as simulated forensic samples have been utilized for these multiplex amplifications.

Alleles↗
PubMed2000

Portuguese population and paternity investigation studies with a multiplex PCR--the AmpFlSTR Profiler Plus.

A Portuguese Caucasian population of 146 unrelated individuals was studied. DNA samples were amplified by multiplex PCR for D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 using the AmpFlSTR Profiler Plus PCR Amplification Kit (Perkin-Elmer). All loci met Hardy-Weinberg expectations. Forensic statistical parameters were according to those obtained by other authors. Statistical differences were observed concerning three loci when comparing the Portuguese Caucasian population and an Italian Caucasian population, although these differences mainly concern the less frequent alleles. Eighty-three paternity investigation cases were analysed. Exclusions in between three and nine loci were observed in all the 23 exclusion cases obtained. Most of the non-exclusion cases had probability of paternity > 99.9%. Two cases with an isolated genetic incompatibility between the alleged father and the child were detected, which may indicate probable mutation cases. These results demonstrate that the AmpFlSTR Profiler Plus is a suitable multiplex for paternity investigation in the Portuguese population.

Alleles↗
PubMed2006

Fluorescent multiplex amplification of three X-STR loci.

This study was carried out to evaluate the value of three X-STR loci (DXS6803, DXS981and DXS6809) in forensic application and thereby investigate their polymorphism. The primer for each locus was labeled with fluorochrome 6-FAM. A fluorescent multiplex PCR for simultaneously amplifying three X-STR loci was set up. The PCR products that were obtained were analyzed using capillary electrophoresis and ABI PRISM 3100 Genetic Analyzer, with GENESCAN Analysis Software. When 340 male and 195 female individuals of Han population in China were tested, 13, 12, and 11 alleles were observed for DXS6803, DXS981 and DXS6809, respectively. One hundred and eighty three haplotypes were detected in the male individuals. The haplotype diversity reached 0.9926. The results show that the three loci of the multiplex system provide significant information on polymorphism for forensic identification and paternity testing, particularly for complicated paternity deficient cases.

Chromosomes, Human, X↗
PubMed1984

Arthrogryposis multiplex congenita in an infant with posterior agenesis of the corpus callosum.

A term male infant with arthrogryposis multiplex congenita and agenesis of the corpus callosum is described. Physical examination revealed multiplex dysmorphic features and fixed joints. A muscle biopsy showed type II fibers to be more than 12% smaller than type I fibers, consistent with the diagnosis of fiber type disproportion. The CT scan disclosed absence of the posterior corpus callosum and moderate atrophy of the cerebellar hemispheres. The pathogenetic mechanism for the muscle (and thus joint) abnormalities of this infant is discussed with respect to a central etiology.

Abnormalities, Multiple↗
PubMed2001

Multi-channel magnetic resonance spectroscopy through time domain multiplexing.

Time domain multiplexing (TDM) is presented as a viable approach to increasing the sensitivity and efficiency of magnetic resonance spectroscopic (MRS) experiments through multi-channel signal acquisition. By switching very rapidly between coils of a receive phased array, TDM receiver extensions allow the acquisition of multiple, independent spectra through a single channel magnetic resonance console. A TDM receiver extension designed for imaging and spectroscopy is described, and the impact of this hardware extension on the processing and quantitation of MRS data is addressed. The primary complication involves the use of fixed bandwidth RF band-pass filters that can not be adjusted to match the spectral width of the desired MRS experiment.MRS sequences whose bandwidths are narrower than the bandwidth provided by TDM band-pass filters can be acquired through TDM with minimal loss of SNR as long as two constraints are met. The first constraint requires that the entire bandwidth of the band-pass filters be sampled at or more rapidly than the Nyquist rate associated with their bandwidth, to prevent extra noise from aliasing into the final spectrum. The second requirement is that spectral resolution be held constant to that of the desired experiment. Results from a two-channel multiplexed MRS experiment, conducted according to these guidelines, illustrate that TDM can be used to allow acquisition of multi-channel MRS experiments through single channel console systems with a minimal loss in SNR.

Equipment Design↗
PubMed2003

Description of a multiplex Bordetella pertussis and Bordetella parapertussis LightCycler PCR assay with inhibition control.

While culture for Bordetella species is highly specific, sensitivity is extremely variable due to patient age, immunization status, antibiotic treatment, and specimen transport conditions. We evaluated a real-time multiplex PCR assay as an alternative to culture for the detection and differentiation of Bordetella pertussis and Bordetella parapertussis. The PCR conditions allowed the simultaneous detection of one B. pertussis organism and five B. parapertussis organisms per reaction. An inhibition control was incorporated into the assay. Of 163 total samples evaluated, 37 of 38 samples positive by either culture or direct fluorescent antibody testing (DFA) were also positive by PCR (97% sensitivity). Of 125 culture- or DFA-negative samples, 101 were also negative by PCR (81% specificity). The described multiplex assay is a rapid, sensitive, contamination-limiting, real-time PCR assay that controls for inhibition. The assay performs well using liquid or swab samples and from dried material on slides.

Adult↗
PubMed1999

Detection of ileS-2 gene encoding mupirocin resistance in methicillin-resistant Staphylococcus aureus by multiplex PCR.

The presence of the ileS-2 gene, responsible for mupirocin resistance, in clinical isolates of methicillin-resistant Staphylococcus aureus was determined by multiplex polymerase chain reaction. Three pairs of primers were used, which yielded specific fragments of femA (encoding a unique feature of S. aureus), mecA (encoding resistance to methicillin) and ileS-2 genes. The multiplex polymerase chain reaction system is an easy and time-saving technique that, together with a rapid method for DNA extraction by boiling, may be incorporated as a routine analysis in clinical diagnostic laboratories.

Anti-Bacterial Agents↗
PubMed2001

Asymmetric arthrogryposis multiplex congenita with focal pachygyria.

A male infant with predominantly right-sided arthrogryposis multiplex congenita is presented. His posture in the lower extremities was asymmetric, and left thoracic scoliosis was present. This patient also manifested focal pachygyria dominantly affecting the contralateral cerebral hemisphere and hypoplasia of the corpus callosum, brainstem, and cerebellar vermis. Generalized tonic seizures began at 2 months of age, and an electroencephalogram revealed epileptic discharge. Biopsy of the right biceps revealed a nonspecific change. A direct causal relationship between neuronal migration disorders and arthrogryposis multiplex congenita has not been established, but considering the abnormal neuronal migration along the entire neural axis in focal pachygyria, the predominantly right-sided arthrogryposis in this patient was speculated to be closely related to the pachygyria of the frontal and temporal lobes dominantly affected in the left cerebral hemisphere.

Arthrogryposis↗
PubMed2000

Mitochondrial complex I deficiency in a female with multiplex arthrogryposis congenita.

A 10-year-old female with arthrogryposis multiplex congenita is presented. Clinical, neurophysiologic, and histologic findings suggested a mild myopathy. The analysis of enzymatic activity in the homogenate and of mitochondrial function in saponin-permeabilized fibers from the muscle biopsy revealed an approximately twofold-decreased specific activity of the NADH:CoQ oxidoreductase (complex I of the mitochondrial respiratory chain) that was compensated for by an increased number of mitochondria. The complex I deficiency was also detected in cultivated skin fibroblasts of the patient. The observed defect of mitochondrial oxidative phosphorylation in arthrogryposis multiplex congenita may be of pathogenetic relevance.

Arthrogryposis↗
PubMedDate not supplied

Multiplex PCR using real time DNA amplification for the rapid detection and quantitation of HTLV I or II.

A multiplex 'real-time' polymerase chain reaction (PCR) has been established as a general technique for the quantitation of proviral human T-lymphotrophic virus types 1 and 2 (HTLV-I/II). The technology utilizes fluorescence to measure amplification products from the tax gene of Human T-cell lymphotropic virus type 1 or the 5' long terminal repeat of Human T-cell lymphotropic virus type 2. The quantitative amplification of the standard was linear across four orders of magnitude with nearly identical amplification efficiencies for monoplex or the biplex format from 1.4 copes/assay (60 copies proviral DNA/0.5 micrograms human DNA) to 6000 copies/assay (240000 proviral copies/0.5 micrograms human DNA). The human beta-globin gene was used to normalize for human DNA input to determine the proviral DNA load. Three hundred fifty-six specimens received by Specialty Laboratories for HTLV I/II detection provided identical results in the detection of HTLV I/II proviral DNA. No additional positive specimens were identified with the biplex assay format. The coefficient of variation for the proviral DNA load was less than 30% for HTLV I or II quantitation (n=5). For spiked specimens, two groups of five separate 0.25 ml blood specimens (20 total) were spiked, respectively, with 0, 9.6, 48, 240 and 1200 copies of HTLV I or HTLV II DNA standards. The specimens were amplified with the HTLV I/II multiplex format. Twenty of twenty expected negative HTLV I or HTLV II specimens were negative (100% specificity) and 14/16 specimens spiked with 48 copies or more HTLV I were detected (87.5% sensitivity). Thirteen of sixteen HTLV II spiked specimens (>48 copies of HTLV II standard per 10 assays) were detected (81.2%). The real-time detection provides accurate and reliable results in a single amplification for both HTLV (I or II) targets with a more rapid turnaround time and a decrease in material required for results.

DNA, Viral↗
PubMed2001

Schizophrenia spectrum disorders: an autosomal-wide scan in multiplex pedigrees.

Genome-wide linkage studies, examining the relationship between the schizophrenia syndrome(s) and possible susceptibility regions within the human genome have identified multiple regions within which linkage to the syndrome may be explored. No regions have been found to provide supportive evidence for linkage in all cohorts. These findings are consistent with the schizophrenia syndrome being genetically heterogeneous, with genetic susceptibility arising from multiple sites which are differentially distributed in from pedigree to pedigree. The authors present data from an autosomal-wide scan of 30 multiplex pedigrees, each with a mean of 4.1 members affected with a schizophrenia spectrum disorder with respect to regions of interest for linkage with the schizophrenia spectrum disease(s). Partial, though not significant replications of susceptibility sites at D1S518 (P=0.029) described by Shaw et al. (1998: Shaw, S.H., Kelly, M., Smith, A.B., Shields, G., Hopkins, P.J., Loftus, J., Laval, S.H., Vita, A., DeHert, M., Cardon, L.R., Crow, T.J., Sherrington, R., DeLisi, L.E., 1998. A Genome-wide search for schizophrenia susceptibility genes. Am. J. Med. Genet. (Neuropsychiatric Genet.) 81, 364-376.), and at D5S426 (P=0.015) described by : Silverman, J.M., Greenberg, D.A., Altstiel, L.D., Siever, L.J., Mohs, R.C., Smith, C.J., Zhou, G., Hollander, T.Y., Yang, X.-P., Kedache, M., Li, G., Zaccario, M.L., Davis, K.L., 1996. Evidence of a locus for schizophrenia and related disorders on the short arm of chromosome 5 in a large pedigree. Am. J. Med. Genet. 67, 162-171.) were documented using multipoint non-parametric (NPL) statistics. Two additional novel regions worthy of further investigation were identified at D1S1150 (P=0.004) and at D20S171 (P=0.009). Previously reported genomic regions of interest for the schizophrenias are reviewed in the context of the same/flanking markers utilized with the present cohort of pedigrees. The data further suggests that only a fraction of pedigrees multiplex for schizophrenia link at any single susceptibility region.

Chromosomes, Human↗
PubMed2003

Schizophrenia spectrum disorders and eye tracking dysfunction in singleton and multiplex schizophrenia families.

One line of research which is helping to unravel the genetic susceptibility to schizophrenia (SZ) is the analysis of eye tracking dysfunction (ETD), a quantifiable phenotypic marker. To investigate if such a biological marker is also present in singleton schizophrenia families, we examined eye tracking in members of singleton families (N=53) and compared it to members of multiplex (N=76) and nonpsychiatric families (N=71) using high resolution infrared oculography. The prevalence of ETD defined by gain values (eye/target velocity) and saccadic frequencies during smooth pursuit at 15 degrees /s did not differ between multiplex and singleton families in either the schizophrenic index patients or their relatives, but was significantly different from nonpsychotic families. ETD rate was higher in those relatives with compared to those without a diagnosis of a schizophrenia spectrum disorder. In relatives with a spectrum disorder, ETD appeared to be associated with traits for "sensitivity" and "suspiciousness". In the group of relatives from singleton families without a schizophrenia spectrum disorder, we still found a higher prevalence of ETD than in nonpsychotic families. Our results suggest that eye tracking dysfunction is a very sensitive biological marker for the vulnerability to schizophrenia, even in those cases where no psychopathological symptoms or signs are obvious. ETD in schizophrenia is suggested to serve as a neurophysiological type model, indicating a perception deficit.

Adult↗
PubMed2002

Multiplex PCR-based detection and identification of the most common Salmonella second-phase flagellar antigens.

Most Salmonella serotypes alternatively express phase 1 or phase 2 flagellar antigens encoded by fliC and fljB genes respectively. Flagellar phase reversal to identify both flagellar antigens is not necessary at the genetic level. Variable internal regions of the fljB genes encoding H:1,w, H:e,n,x and H:e,n,z15 antigens have been sequenced and the specific sites for each antigen determined in selected Salmonella serotypes. These results, together with flagellar H1 complex variable internal sequences previously published, have been used to design a multiplex-PCR to identify H:1,2, H:1,5, H:1,6, H:1,7, H:1,w, H:e,n,x and H:e,n,z15 second-phase antigens. These antigens are part of the most common Salmonella serotypes possessing second-phase flagellar antigens. This multiplex-PCR includes 10 primers. A total of 140 Salmonella strains associated with 49 different serotypes were tested. Each strain generated one second-phase-specific antigen fragment, ranging between 50 and 400 bps. Twenty-five strains associated with 17 serotypes, with no second-phase antigen or with an antigen different from those tested in this work, did not generate any fragments. The method is quick, specific and reproducible and is independent of the phase expressed by the bacteria when tested.

Antigens, Bacterial↗
PubMed1999

Development of a simple multiplex polymerase chain reaction for the simultaneous detection of factor V Leiden and prothrombin 20210A mutations.

BACKGROUND: The demand for thrombophilia testing at the molecular level is increasing, and consequently, the work load of the routine molecular laboratory is also increasing. Efforts to lighten the work load, economize on time, and strive for reduced costs while still maintaining quality assurance are thus necessary. METHODS AND RESULTS: A multiplex polymerase chain reaction (PCR) for the detection of factor V Leiden and prothrombin 20210A mutations was designed that enables the use of the same inexpensive restriction enzyme, controls for the digestion, and produces easily interpretable results. CONCLUSION: The use of this new multiplex PCR and digestion analysis enabled us to simultaneously perform a routine screen for factor V Leiden and prothrombin 20210A mutations.

3' Untranslated Regions↗
PubMed2002

A rapid, single-step multiplex reverse transcription-PCR assay for the detection of human H1N1, H3N2, and B influenza viruses.

BACKGROUND: Influenza is a viral respiratory pathogen responsible for frequent seasonal epidemics. There are currently three major human influenza viruses in global circulation, H1N1, H3N2 and B. OBJECTIVES: A one-step multiplex reverse transcription (RT)-polymerase chain reaction (PCR) assay targeting the HA1 segment of the human hemagglutinin gene was developed as a rapid surveillance method. STUDY DESIGN: A researcher-blind study was performed using 112 randomly selected, culture-positive clinical samples collected through the Department of Defense (Global Emerging Infectious Surveillance (DOD-GEIS) influenza network during the 2000-2001 influenza season. Three subtype specific primer sets capable of producing PCR products with base-pair lengths of 585, 402 and 290 corresponding to influenza H1, H3, and B subtypes, respectively, were utilized together in a one step, one tube, reaction. RESULTS: Multiplex primers were able to simultaneously type, and subtype 100% (112/112) of positive cultures. CONCLUSIONS: The results confirm that this assay is a highly sensitive and timely surveillance tool for rapid detection and simultaneous subtyping of clinical influenza specimens isolated worldwide.

Hemagglutinin Glycoproteins, Influenza Virus↗