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Results for “Automated phenotyping”

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PubMed2005

A detailed phenotypic study of "cone dystrophy with supernormal rod ERG".

AIMS: To characterise the detailed phenotype of "cone dystrophy with supernormal rod ERG" in a case series of 10 patients. METHODS: 10 affected patients were examined clinically and underwent colour fundus photography, with nine undergoing detailed electrophysiological testing. Five patients were assessed further with fundus autofluorescence (AF) imaging, automated photopic and dark adapted perimetry, and dark adaptometry. Detailed colour vision assessment was performed in six subjects. Blood samples were taken from four patients for DNA extraction and mutation screening of NR2E3 was undertaken. RESULTS: The onset of symptoms was in the first and second decades of life. Subjects presented with reduced central vision and marked photophobia. All individuals were myopic and colour vision testing revealed severely reduced colour discrimination predominantly along the red-green axes; tritan colour vision was relatively well preserved. Nyctalopia is a later feature of the disorder. Funduscopy and AF imaging revealed a range of macular appearances. There was electrophysiological evidence of marked macular dysfunction, reduced and delayed cone responses, and supernormal and delayed rod responses. Photopic and dark adapted perimetry revealed central scotomata with widespread peripheral sensitivity loss. No disease causing sequence variants in NR2E3 were identified. CONCLUSIONS: The largest case series to date has been described of the clinical, psychophysical and electrophysiological characteristics of this unusual cone dystrophy with supernormal rod responses. Electrophysiological data were consistent with a post-phototransduction, but pre-inner nuclear layer, site of dysfunction. While the definitive diagnosis can only be made with electrophysiological testing, several characteristics that may increase suspicion of this diagnosis are presented.

Adolescent↗

PubMed2003

Comparison of BDPhoenix and VITEK2 automated antimicrobial susceptibility test systems for extended-spectrum beta-lactamase detection in Escherichia coli and Klebsiella species clinical isolates.

The present study compares the ability to detect extended-spectrum beta-lactamases (ESBL) among a collection of 34 ESBL producing clinical isolates belonging to Escherichia coli and Klebsiella species with two new rapid susceptibility and identification instruments-VITEK2 (bioMérieux, Marcy l'Etoile, France) vs. BDPhoenix (BD Biosciences, Sparks, MD). ESBL content in these isolates was previously characterized on the basis of PCR amplification and sequencing results which were used as the reference method in our evaluation. BDPhoenix correctly determined the ESBL outcome for all strains tested (100% detection rate), whereas VITEK2 was not able to detect the ESBL status in 5 isolates (85% detection rate). Detailed analysis revealed that the discrepancies were mainly observed with 'difficult-to-detect' strains. Misidentification was either due to low oximino cephalosporin MIC in these strains or was associated with pronounced 'cefotaximase' or 'ceftazidimase' phenotypes. Klebsiella oxytoca chromosomal beta-lactamase (K1) is phenotypically quite similar to ESBL enzymes. In order to evaluate whether the K1 and ESBL enzymes could be discriminated, we expanded our analysis by 8 clinical K. oxytoca strains with K1 phenotypes. VITEK2 gave excellent identification of these strains whereas 7 out of 8 were falsely labeled ESBL-positive by the BDPhoenix system.

Anti-Bacterial Agents↗

PubMed2006

Viability and electrophysiology of neural cell structures generated by the inkjet printing method.

Complex cellular patterns and structures were created by automated and direct inkjet printing of primary embryonic hippocampal and cortical neurons. Immunostaining analysis and whole-cell patch-clamp recordings showed that embryonic hippocampal and cortical neurons maintained basic cellular properties and functions, including normal, healthy neuronal phenotypes and electrophysiological characteristics, after being printed through thermal inkjet nozzles. In addition, in this study a new method was developed to create 3D cellular structures: sheets of neural cells were layered on each other (layer-by-layer process) by alternate inkjet printing of NT2 cells and fibrin gels. These results and findings, taken together, show that inkjet printing is rapidly evolving into a digital fabrication method to build functional neural structures that may eventually find applications in neural tissue engineering.

Animals↗

PubMed2002

Asaia sp., an unusual spoilage organism of fruit-flavored bottled water.

A gram-negative bacillus was isolated from a batch of fruit-flavored bottled water, which had spoiled as a result of bacterial overgrowth (>10(6) CFU/ml). The spoilage organism was extremely difficult to identify phenotypically and was poorly identified as Pasturella sp. (78.7% identification profile) employing the API 20NE identification scheme, which gave the profile 5040000. Molecular identification through PCR amplification of a partial region of the 16S rRNA gene followed by direct automated sequencing of the PCR amplicon allowed identification of the organism. Due to the sequence identity (100%) between the spoilage organism and a reference strain in GenBank, the spoilage isolate was considered to be an Asaia sp., a recently described genus and member of the acetic acid bacteria. This is the first report of Asaia sp. causing spoilage of a foodstuff and highlights the benefits of molecular identification techniques based on 16S rRNA gene sequences in the identification of unusual spoilage organisms.

Acetobacteraceae↗

PubMed1986

Evaluation of laboratory tests for detection of methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis.

Few studies evaluating susceptibility testing of methicillin-resistant staphylococci have included isolates of Staphylococcus epidermidis, a known pathogen in many types of serious infections. We tested 175 S. epidermidis and 95 Staphylococcus aureus isolates to determine the most sensitive procedures for detecting methicillin-resistant staphylococci. Reference procedures included agar dilution with methicillin and 4% NaCl in the agar and broth microdilution with methicillin and 2% NaCl in cation-supplemented Mueller-Hinton broth. After 24 h of incubation, the results from both methods correlated well and were within 1 log2 dilution for all isolates tested. Only one-half of all resistant isolates (92 of 183) were detected at 18 h by using the standard disk diffusion technique with 5-micrograms methicillin disks, and even fewer were detected with 10-micrograms methicillin disks and newly recommended zone-size criteria. However, the standard disk diffusion method with 4% NaCl in the agar increased the sensitivity and specificity for identification of the proper phenotype to greater than 92%. The spread plate and new spot techniques, both using agar with 4% NaCl, were also sensitive methods. Of 47 S. epidermidis isolates tested against oxacillin, 6 (13%) were oxacillin susceptible but methicillin resistant. Two automated systems, the Automicrobic system (Vitek Systems) and MicroScan (American MicroScan), as well as two broth screening systems available from Remel and Austin Biological Laboratories, failed to detect several resistant isolates, depending on the species.

Culture Media↗

PubMed2001

Molecular markers for diagnosis, staging, and prognosis of bladder cancer.

Conventional histopathologic evaluation of bladder cancer, encompassing tumor grade and stage, is inadequate to accurately predict the behavior of most bladder tumors. Intense research efforts are under way to identify and characterize various bladder cancers and their true biological potential more effectively. The need to predict which superficial tumors will recur or progress--and which invasive tumors will metastasize--has led to the identification of a variety of potential prognostic markers for patients with bladder cancer. The molecular changes that occur in transitional cell carcinoma of the bladder are numerous and can be categorized into (1) chromosomal alterations, leading to carcinogenesis; (2) loss of cell-cycle regulation, accounting for cellular proliferation; and (3) growth control events such as angiogenesis, resulting in metastasis. It is becoming apparent that the accumulation of genetic and molecular changes ultimately determines a tumor's phenotype and subsequent clinical behavior. The potential clinical application of new diagnostic techniques (ie, loss-of-heterozygosity analysis to identify tumor suppressor genes) and older, well-established, techniques (ie, immunohistochemistry) combined with improvements in the use of automated and standardized systems are areas of active investigation.

Biomarkers, Tumor↗

PubMed2004

Evaluation of phenotypic methods for methicillin resistance characterization in coagulase-negative staphylococci (CNS).

Coagulase-negative staphylococci (CNS) are the major cause of nosocomial infections. Methicillin-resistant strains are particularly important because they narrow therapeutic options. Detecting methicillin resistance among CNS has been a challenge for years. The objective of this study was to determine the accuracy of an agar screening test (0.6 and 4 microg oxacillin ml(-1)), disc diffusion and the automated MicroScan system to characterize methicillin resistance among CNS. One hundred and seventy five strains were analysed: 41.1 % Staphylococcus epidermidis and 59.9 % other species; 69.1 % were mecA-positive. The results showed that the methods have optimal correlation with the detection of mecA gene for S. epidermidis, Staphylococcus hominis and Staphylococcus haemolyticus. However, accuracy of the tests is impaired when less common species are analysed. The only 100 % accurate test was agar screening with 4 microg oxacillin ml(-1).

Anti-Bacterial Agents↗

PubMed2004

A novel mtDNA point mutation in tRNA(Val) is associated with hypertrophic cardiomyopathy and MELAS.

BACKGROUND: Pathological mutations of mitochondrial (mt) DNA may cause specific diseases such as cardiomyopathies or hearing loss, or syndromes such as mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episode (MELAS) syndrome. We describe a novel mtDNA mutation in a patient with severe hypertrophic cardiomyopathy associated with MELAS. The familial phenotype included 1) hypertrophic cardiomyopathy and MELAS, 2) clinically mild cardiac hypertrophy, and 3) deafness. METHODS: The proband and her first degree relatives underwent echo and electrocardiograms, and biochemical tests. Magnetic resonance imaging of the brain was performed in the proband. mtDNA was fully analyzed by sequencing. DNA purification, polymerase chain reaction and direct automated sequencing were performed following standard procedures. Heteroplasmy of the novel mutation was quantified by densitometric analysis. RESULTS: A novel G1644A transition affecting the tRNA(Val) was identified in the proband and maternal relatives. The mutation has been interpreted as pathological because the G at the 1644 position is a highly conserved base, is heteroplasmic with higher levels of mutant DNA in the proband than in the relatives, is located in the unique tRNA(Val), is very close to a mutation described as causative of MELAS, and finally has not been found in 100 healthy controls. CONCLUSIONS: Although it is rare for patients with MELAS to be referred to cardiological evaluation because of coexisting cardiomyopathy, cardiologists should be aware of this association as well as of the non cardiac signs that may address the diagnosis to mtDNA defect-related disease in families with a variable phenotype.

Adult↗

PubMed2001

Flow cytometry: an 'old' tool for novel applications in medical genetics.

Flow cytometry was originally established as an automated method for measuring optical or fluorescence characteristics of cells or particles in suspension. In the meantime, flow cytometers have become user-friendlier, less expensive instruments with an increasing importance in clinical diagnostics. Besides the classical fields of application, such as immunophenotyping blood cells or analyzing the cell cycle status by measuring the DNA content, novel flow cytometric methods have been developed to identify and to quantify disease-related gene sequences. Here we give an overview of current and future applications, including the detection of viral sequences via microsphere-based PCR assays and the analysis of single nucleotide polymorphisms, reflecting individual phenotypic traits. Furthermore, flow cytometry allows the quantification of gene expression changes as well as the isolation of differentially expressed gene sequences. Flow cytometry is also convenient for multiplex analyses, e.g. when hybridizing DNA samples to a mixture of various microsphere populations each coated with different DNA probes. Last but not least, the use of magnetic beads in combination with flow cytometers coupled with automated devices enables molecular diagnostics on a large scale. Overall, this review demonstrates flow cytometry as a rapid, sensitive, and reproducible tool applicable to a wide range of medical genetic approaches.

DNA↗

PubMed2002

Novel NCCT gene mutations as a cause of Gitelman's syndrome and a systematic review of mutant and polymorphic NCCT alleles.

BACKGROUND: Gitelman's syndrome (GS) is characterized by hypokalemic metabolic alkalosis, hypomagnesemia and hypocalciuria and these phenotypic features have been shown to be attributable to mutations in the gene encoding the thiazide-sensitive Na/Cl cotransporter (NCCT). Until now, 55 different mutations have been reported and most of the families affected with GS exhibit autosomal recessive inheritance. METHODS: All 26 exons of the human NCCT gene were investigated in 2 German NCCT-deficient patients and their families. Mutation detection was performed by either direct automated sequencing of polymerase chain reaction (PCR)-amplified DNA products or by sequence analysis of cloned PCR products. RESULTS: In a 47-year-old German GS female a novel non-conservative missense mutation (S314F) and a complex deletion/insertion in the NCCT gene were found to be associated with the disorder. A further novel non-conservative substitution (S402F) together with a frequently observed R209W exchange were found in a 19-year-old German GS female. CONCLUSIONS: The observation of a compound heterozygote state in both females affected and the absence of a GS phenotype in their relatives carrying a single mutant allele is consistent with an autosomal recessive pattern of inheritance.

Adult↗

PubMed2004

PAX6 gene variations associated with aniridia in south India.

BACKGROUND: Mutations in the transcription factor gene PAX6 have been shown to be the cause of the aniridia phenotype. The purpose of this study was to analyze patients with aniridia to uncover PAX6 gene mutations in south Indian population. METHODS: Total genomic DNA was isolated from peripheral blood of twenty-eight members of six clinically diagnosed aniridia families and 60 normal healthy controls. The coding exons of the human PAX6 gene were amplified by PCR and allele specific variations were detected by single strand conformation polymorphism (SSCP) followed by automated sequencing. RESULTS: The sequencing results revealed novel PAX6 mutations in three patients with sporadic aniridia: c.715ins5, [c.1201delA; c.1239A>G] and c.901delA. Two previously reported nonsense mutations were also found: c.482C>A, c.830G>A. A neutral polymorphism was detected (IVS9-12C>T) at the boundary of intron 9 and exon 10. The two nonsense mutations found in the coding region of human PAX6 gene are reported for the first time in the south Indian population. CONCLUSION: The genetic analysis confirms that haploinsuffiency of the PAX6 gene causes the classic aniridia phenotype. Most of the point mutations detected in our study results in stop codons. Here we add three novel PAX6 gene mutations in south Indian population to the existing spectrum of mutations, which is not a well-studied ethnic group. Our study supports the hypothesis that a mutation in the PAX6 gene correlates with expression of aniridia.

Adolescent↗

PubMed2002

UV-visible spectrophotometric approach to blood typing II: phenotyping of subtype A2 and weak D and whole blood analysis.

BACKGROUND: A recently introduced quantitative blood typing approach uses antibody-induced changes in the UV-visible spectra of blood. Changes in the blood spectra's slope, caused by RBC agglutination, are translated into a numerical agglutination index (AI). Comparing the AI value against an established threshold yields a "yes and/or no" output from which to determine the phenotype. The efficacy and flexibility of this approach with whole blood use and the ability to analyze weak D, A2, and A2B were examined. STUDY DESIGN AND METHODS: Two hundred randomly selected blood bank donor samples were coded and forward typed directly from whole blood by using the spectrophotometric analysis. Reverse grouping on plasma from each sample was carried out with a new modified procedure by using higher ratios of plasma to RBCs. Results were compared to typing by an FDA-cleared automated typing system. Twenty-seven weak D samples, 15 A2 and 12 A2B, were similarly analyzed from whole blood. PEG improved detection of weak D, A2 and A2B subtypes. RESULTS: All two hundred coded samples were accurately typed, yielding identical results to the blood bank analysis in both forward and reverse grouping. All the weak D samples and A2 and A2B samples were clearly identified, having AIs above the type threshold indicator value. CONCLUSION: Spectrophotometric blood typing successfully phenotyped ABO and D in 200 whole blood samples. Reverse grouping of plasma was equally successful. The same method can identify weak D and A2 and A2B subtypes.

ABO Blood-Group System↗

PubMed2006

Accuracy and biological variation of human serum paraoxonase 1 activity and polymorphism (Q192R) by kinetic enzyme assay.

BACKGROUND: Paraoxonase 1 (PON1) phenotype is a better predictor of atherosclerosis risk than are PON1 genetic polymorphisms alone. Larger studies are required to determine the role of PON1 and there is a need for standardized PON1 assays between laboratories. METHODS: We have adapted 5 enzyme kinetic assays for high-throughput automated analysis of PON1 activity. Using different substrates and reaction conditions, we measured PON1 activity and used activity ratios to identify the PON1 Q192R genetic polymorphisms and assessed the accuracy of the genotype assignments in 79 adult study participants by comparing them with genotypes determined by AlwI restriction enzyme digestion of a 176-bp PCR amplification product from genomic DNA. Imprecision was determined using pooled serum and purified enzyme preparations. Biological variability was estimated by analysis of serial samples from 17 individuals. Variability parameters were compared with total cholesterol as a point of reference to a recognized biomarker of coronary heart disease risk. RESULTS: Salt stimulation and inhibition ratios were 97.4% and 94.7% correct in assigning Q192R genotype, respectively. Analytical imprecision (CV) was 1.0%-3.0% for phenylacetate and paraoxon substrate assays and 3.0%-8.0% for the para-nitrophenylacetate substrate assays. Combination of the 2 ratios into a double ratio resulted in 100% correct genotype classification. CONCLUSION: The described methods for measurement of PON1 activity and accurate genotype assignment are rapid and have potential to facilitate the efficient investigation of PON1 status in clinical and epidemiological studies.

Adult↗

PubMed1998

The interferon-gamma gene as a positional and functional candidate gene for inflammatory bowel disease.

Epidemiological and genome-wide linkage analyses have provided firm evidence for a genetic component in the pathogenesis of inflammatory bowel disease. The linkage regions on chromosomes 12 and 16 have been replicated in several independent samples. These represent the best positional evidence in the search for inflammatory bowel disease susceptibility genes. While systematic association and physical mapping studies in these regions are under way, the direct analysis of immunologically relevant genes as positional and functional candidates may provide a shortcut in this process. The interferon-gamma gene resides in the chromosome 12 linkage region near the marker D12S83. Interferon-gamma is an important proinflammatory cytokine in the interleukin-12 cascade and has been implicated in the pathogenesis of mucosal inflammation. We tested this gene for evidence of linkage and association in 133 German multiplex families and 506 single patients with their parents. An intragenic, highly informative CA-repeat marker in intron 1 of the gene was typed using fluorescence-labeled polymerase chain reaction and analysis on an automated sequencer. In the nonparametric linkage analysis using GENEHUNTER, a nonsignificant maximum LOD score of 0.67 was obtained. The transmission disequilibrium test for association was negative (P > or = 0.22) for Crohn's disease, ulcerative colitis, and the combined inflammatory bowel disease phenotype. In summary, the findings make interferon-gamma a very unlikely candidate for the major susceptibility gene in the chromosome 12 linkage interval. Future efforts can concentrate on other transcripts in the region.

Base Sequence↗

PubMed1996

Molecular genetic defect underlying alpha-L-iduronidase pseudodeficiency.

Mucopolysaccharidosis type I (i.e., Hurler, Hurler-Scheie, and Scheie syndromes) and type II (i.e., Hunter syndrome) are lysosomal storage disorders resulting from alpha-L-iduronidase (IDUA) deficiency and iduronate-2-sulfatase (IDS) deficiency, respectively. The a priori probability that both disorders would occur in a single individual is approximately 1 in 5 billion. Nevertheless, such a proband was referred for whom clinical findings (i.e., a male with characteristic facies, dysostosis multiplex, and mental retardation) and biochemical tests indicated these concomitant diagnoses. In repeated studies, leukocyte 4 methylumbelliferyl-alpha-L-iduronidase activities in this kindred were as follows: <1.0 nmol/mg protein/h in the proband and proband's clinically normal sister; 45.3 in mother; and 45.7 in father (normal range 65.0-140). Leukocyte L-O-(alpha-iduronate-2-sulfate)-(1->4)-D-O-2,5-anhydro[1-3H]mannitol-6- sulfate activities were as follows: 0.0 U/mg protein/h in the proband; 5.7 in his sister; 4.9 in mother; and 15.0 in father (normal range 11.0-18.4). Multiple techniques, including automated sequencing of the entire IDS and IDUA coding regions, were employed to unravel the molecular genetic basis of these intriguing observations. The common IDS mutation R468W was identified in the proband, his mother, and his sister, thus explaining their biochemical phenotypes. Additionally, the proband, his sister, and his father were found to be heterozygous for a common IDUA mutation, W402X. Notably, a new IDUA mutation A300T was also identified in the proband, his sister, and his mother, accounting for reduced IDUA activity in these individuals; the asymptomatic sister, whose cells demonstrated normal glycosaminoglycan metabolism, is thus a compound heterozygote for W402X and the new allele. This A300T mutation is the first IDUA pseudodeficiency gene to be elucidated at the molecular level.

Base Sequence↗

PubMed1996

Mean cell haemoglobin concentration in subjects with haemoglobin C, D, E and S traits.

The Bayer H1 automated blood counter was used to assess the MCHC values of 40 nonanaemic patients with HbC trait, 21 with HbD trait, 23 with HbE trait and 69 with HbS trait. These were compared with values from controls with a normal Hb phenotype. Values were significantly higher in those with HbC, D and S traits and approached significance in those with HbE trait. In 45%, of subjects with HbC trait the MCHC value was > or = 35 g/dl. Such values may prove a useful marker for this abnormality. In a further 12 patients with HbC, D, E or S traits and coexisting iron deficiency anaemia, MCHC values were usually higher and the percentage of hypochromic cells (red cells with CHC <28 g/dl, directly measured by the H1) usually lower than values derived from controls with a normal Hb phenotype and iron deficiency anaemia of similar degree. In individuals with HbC, D, E or S traits, the MCHC and proportion of hypochromic cells are less sensitive indicators of iron lack than in subjects with a normal Hb phenotype.

Adolescent↗

PubMed2005

Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics.

The clinical relevance of Campylobacter concisus in gastrointestinal disease has not been determined definitively. This study investigated the phenotypic and genotypic characteristics of 39 C. concisus isolates from Danish patients with diarrhoea, three isolates from healthy individuals and the type strain. A cytolethal distending toxin (CDT)-like effect on Vero cells was observed in 35 (90%) isolates from patients with diarrhoea, in all three isolates from healthy individuals and in the type strain. Analysis of SDS-PAGE protein profiles and PCR amplification of 23S rDNA assigned the isolates into two distinct, but discordant groups. Automated ribotyping (RiboPrinting) identified 34 distinct patterns among the 43 isolates, but cluster analysis did not separate isolates from patients with diarrhoea from isolates from healthy patients. Random amplified polymorphic DNA (RAPD) analysis with three primers identified 37 unique profiles, but requires further evaluation. The isolates obtained from healthy carriers were distinguished by cluster analysis from the isolates obtained from patients with diarrhoea. All the isolates were susceptible to 11 antimicrobial agents tested. Overall, there was considerable variability between the C. concisus isolates, but there were no clear phenotypic or genotypic differences between isolates from patients with diarrhoea and isolates from healthy carriers. Further evidence is needed to support the possible role of C. concisus as a human enteric pathogen.

Animals↗

PubMed2004

A global approach combining proteome analysis and phenotypic screening with RNA interference yields novel apoptosis regulators.

Global approaches like proteome or transcriptome analyses have been performed extensively to identify candidate genes or proteins involved in biological and pathological processes. Here we describe the identification of proteins implicated in the regulation of apoptosis using proteome analysis and the functional validation of targets by RNA interference. A high-throughput platform for the validation of synthetic small interfering RNAs (siRNAs) by quantitative real-time PCR was established. Genes of the identified factors were silenced by automated siRNA transfection, and their role in apoptotic signaling was investigated. Using this strategy, nine new modulators of apoptosis were identified. A subsequent detailed study demonstrated that hepatoma-derived growth factor (HDGF) is required for TNFalpha-induced release of pro-apoptotic factors from mitochondria. The strategy described here may be used for hypothesis-free, global gene function analysis.

Apoptosis↗