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Results for “Automated phenotyping”

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PubMed2006

Development and implementation of multiplexed cell-based imaging assays.

Fluorescence microscopy, image analysis, and automated screening technologies are some of the most powerful tools enabling cell biologists to investigate complex signaling pathways and compound or siRNA effects on cellular function in individual cells. Researchers can now use multiple fluorescent probes to quantify effects on intracellular molecular events, measure phenotypic changes, and provide contextual information about cellular pathways not discernible by traditional single-parameter, end point experiments. This chapter focuses on fluorescent labeling techniques and methods for designing image-based assays, multiplexed readouts, and image analysis routines. Case studies are presented describing the use of cell-based imaging assays for monitoring cell proliferation, cell cycle stage, and apoptosis.

Animals↗

PubMed2001

Infantile demyelinating neuropathy associated with a de novo point mutation on Ser72 in PMP22 and basal lamina onion bulbs in skin biopsy.

Codon 72 has been designated as a hot spot for distinct missense mutations in the peripheral myelin protein 22 (PMP22) gene. Ser72Leu substitution was associated with Dejerine-Sottas syndrome (DSS) in four patients and with congenital hypomyelination neuropathy (CHN) in one patient. Our objective was to report one other DSS patient with Ser72Leu substitution in PMP22 and to concurrently illustrate how less invasive procedures such as skin biopsy could provide a rapid and reliable alternative to conventional sural nerve biopsy for the characterization of histophenotypic features. A skin biopsy was carried out in a 2 4/12-year-old girl with muscle atrophy, hypotonia and weakness, as well as generalized areflexia and absent sensory and motor nerve responses. Standard electron microscope techniques were used. PMP22 was screened by automated direct nucleotide sequencing analysis. Morphological examination revealed basal lamina onion bulbs surrounding a de- or hypomyelinated axon in all nerve bundles. Mutation analysis demonstrated a missense point mutation in codon 72 of the PMP22 gene leading to a Ser72Leu substitution. Further genotype-phenotype correlations will have to determine whether morphologically distinct phenotypes can be correlated with specific mutations. For this purpose, cutaneous nerve bundles could serve as an alternative tool to help identify and classify subtypes in this heterogeneous syndrome.

Amino Acid Substitution↗

PubMed2004

Accurate detection of aneuploidies in array CGH and gene expression microarray data.

MOTIVATION: Chromosomal copy number changes (aneuploidies) are common in cell populations that undergo multiple cell divisions including yeast strains, cell lines and tumor cells. Identification of aneuploidies is critical in evolutionary studies, where changes in copy number serve an adaptive purpose, as well as in cancer studies, where amplifications and deletions of chromosomal regions have been identified as a major pathogenetic mechanism. Aneuploidies can be studied on whole-genome level using array CGH (a microarray-based method that measures the DNA content), but their presence also affects gene expression. In gene expression microarray analysis, identification of copy number changes is especially important in preventing aberrant biological conclusions based on spurious gene expression correlation or masked phenotypes that arise due to aneuploidies. Previously suggested approaches for aneuploidy detection from microarray data mostly focus on array CGH, address only whole-chromosome or whole-arm copy number changes, and rely on thresholds or other heuristics, making them unsuitable for fully automated general application to gene expression datasets. There is a need for a general and robust method for identification of aneuploidies of any size from both array CGH and gene expression microarray data. RESULTS: We present ChARM (Chromosomal Aberration Region Miner), a robust and accurate expectation-maximization based method for identification of segmental aneuploidies (partial chromosome changes) from gene expression and array CGH microarray data. Systematic evaluation of the algorithm on synthetic and biological data shows that the method is robust to noise, aneuploidal segment size and P-value cutoff. Using our approach, we identify known chromosomal changes and predict novel potential segmental aneuploidies in commonly used yeast deletion strains and in breast cancer. ChARM can be routinely used to identify aneuploidies in array CGH datasets and to screen gene expression data for aneuploidies or array biases. Our methodology is sensitive enough to detect statistically significant and biologically relevant aneuploidies even when expression or DNA content changes are subtle as in mixed populations of cells. AVAILABILITY: Code available by request from the authors and on Web supplement at http://function.cs.princeton.edu/ChARM/

Algorithms↗

PubMed2005

Shewanella algae and Shewanella putrefaciens: clinical and microbiological characteristics.

The occurrence of the two Shewanella species found in clinical specimens, Shewanella algae and Shewanella putrefaciens, correlates with the temperature and salinity of seawater. This means that Shewanella infections occur in warm climates or during especially warm summers in temperate climates. The infections described most commonly involve ears, skin and soft tissue, with or without bacteraemia. Primary bacteraemia with a fulminant course is also seen in immunocompromised patients. Important differential characteristics between the two species include the ability of S. algae to produce mucoid colonies with beta-haemolysis on sheep blood agar, to grow at 42 degrees C and in NaCl 6% w/v, and to reduce nitrite, and an inability to produce acid from maltose, all of which are in contrast to the characteristics of S. putrefaciens. Automated identification systems fail to differentiate between S. algae and S. putrefaciens, as S. algae is not included in the databases of these systems. Presumably for this reason, most Shewanella infections reported during recent years have been attributed to S. putrefaciens. However, when extensive phenotypic characterisation is performed, most human infections are seen to be caused by S. algae. As the two species seem to have different pathogenic potential for humans, correct identification is important, and this is possible in routine clinical microbiology laboratories.

Animals↗

PubMed2003

Four additional CLCN5 exons encode a widely expressed novel long CLC-5 isoform but fail to explain Dent's phenotype in patients without mutations in the short variant.

BACKGROUND: Dent's disease is caused by mutations in the CLCN5 gene coding for the chloride channel CLC-5. However, sequencing of CLCN5 exonic regions in some patients presenting with low-molecular-weight proteinuria and hypercalciuria - the hallmarks of Dent's disease - failed to identify causative mutations. AIM: Given the observation that some species harbour a CLCN5 mRNA encoding an extended CLC-5 aminoterminus compared with the so far known human form, we worked on the presumption that an orthologous (longer) CLCN5 transcript is also present in humans and that our patients may have mutations herein. METHODS: Extensive databank mining, reverse transcription polymerase chain reaction (RT-PCR) and automated sequencing were used in the search for novel CLCN5 transcripts. The human CLCN5 gene was investigated in 7 patients out of five families by direct automated sequencing of PCR-amplified DNA products. RESULTS: Two new human CLCN5 transcripts expressed in kidney and various other tissues could be identified. These arise from a novel site of transcription initiation, alternative splicing and the use of four additional CLCN5 exons. If being translated, both these mRNAs would lead to an enlarged CLC-5 protein consisting of 816 amino acids by adding 70 aminoterminal residues to the so far known 746-amino-acid-long isoform. Sequence analysis of the henceforward 17 CLCN5 exons revealed no mutation in the patients with a phenotype resembling Dent's disease. CONCLUSIONS: Despite the identification of further targets to explain Dent's disease, the molecular defect in our patients remains to be elucidated. Hence, their phenotype may be explained by mutations that affect so far unknown regulating elements of the CLCN5 gene or another gene(s), probably encoding CLC-5 accessory protein(s).

Adult↗

PubMed2004

Quantitative analysis of highly parallel transfection in cell microarrays.

As more genomes are sequenced, we are facing the challenge of rapidly unraveling the functions of genes. To that end, cell microarrays have recently been described that transfect thousands of nucleic acids in parallel and can be used to analyze the phenotypic consequences of such perturbations. As many parameters can influence the efficacy of transfection in such a format, we describe some important features in manufacturing cell microarrays that may improve reliability and efficiency of both plasmid DNA and siRNA transfection. We have also developed image analysis software that allows automatic detection of cell clusters, quantification of transfection efficiency and levels of expression/extinction of genes. Along with cell microarrays, this bioinformatic tool should expedite functional exploration of the human genome.

Automation↗

PubMed1998

Different ocular abnormalities in individuals of a three-generation family caused by a new nonsense mutation in the PST domain of the PAX6 gene. Mutations in brief no. 189. Online.

PAX6 is a candidate gene for familial aniridia. We have carried out a mutational analysis of the PAX6 gene in a three-generation family from Germany, containing 5 individuals affected with ocular abnormalities. In all affected individuals, a heterozygous mutation was detected in the PAX6 gene, exchanging tyrosine 369 by a stop codon. The mutation is located in the 3' moiety of the PST domain, at the C terminus of the PAX6 protein. In the affected family members, the same heterozygous mutation leads to distinct phenotypes of varying severity. Most notably, no aniridia was observed in one of the family members carrying the mutation, although other ocular abnormalities (underdeveloped iris and cataracts) were present. We discuss the possibility that small C terminal truncations of the PAX6 protein might lead to less severe or more divergent phenotypes than trancations at internal positions.

Aniridia↗

PubMed2005

Entrez Gene: gene-centered information at NCBI.

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.

Databases, Genetic↗

PubMed2000

Low frequency of replication errors in primary nervous system tumours.

OBJECTIVES: Automated DNA technology was used to analyze the incidence of microsatellite instability (MIN) among the most frequent types of adult primary CNS tumours and to determine its relation with clinicopathological characteristics. METHODS: Fifty six gliomas, 32 meningiomas and 11 schwannomas were screened for size changes at eight microsatellite loci using fluorescent polymerase chain reaction (PCR) followed by fragment analysis in an automated sequencer. A tumour was considered as MIN+ when a different electrophoretic pattern between constitutional and tumour DNA was evidenced in one or more microsatellite markers and as replication error positive (RER+) when at least 25% of the markers analyzed (2/8) showed instability. The MIN phenotype was correlated with relevant clinical and pathological parameters. RESULTS: Globally, instability was found in 19/767 analyses (2.47%), with a higher rate among tetranuceotide than dinucleotide repeats (chi(2) test, p=0.018). Ten gliomas (17.9%), two meningiomas (6.3%), and two schwannomas (18.2%) were MIN+, whereas one glioma (1.8%), two meningiomas (6.3%), and one schwannoma (9.1%) were classified as RER+. A possible association between microsatellite instability and a shorter duration of clinical course was found in meningiomas. The MIN+ phenotype was more frequent in spinal than intracranial schwannomas (Fisher's exact test, p=0.018). No other significant association with clinical or histological features was detected. CONCLUSIONS: Although microsatellite instability can be demonstrated at a low rate in some primary CNS tumours, a true replication error phenotype (revealed by widespread microsatellite instability at numerous loci) is uncommon and unlikely to play an important part in the pathogenesis of these neoplasms. This form of instability was more frequent in tetranucleotide than in dinucleotide repeats. To our knowledge, this is the first report of MIN in schwannomas, where it was associated with the spinal localisation of the tumour.

Adult↗

PubMed2001

Mutations in the CRB1 gene cause Leber congenital amaurosis.

OBJECTIVES: To test the hypothesis that mutations in the CRB1 gene cause Leber congenital amaurosis (LCA) and, if so, to describe the ocular phenotype of patients with LCA who harbor CRB1 sequence variations. PATIENTS: One hundred ninety probands with a clinical diagnosis of LCA were selected from a cohort of 233 probands ascertained in 5 different countries. The remaining 43 probands (18%) were excluded because they harbored sequence variations in previously identified LCA genes. METHODS: One hundred ninety unrelated individuals with LCA were screened for coding sequence mutations in the CRB1 gene with single-strand conformation polymorphism analysis followed by automated DNA sequencing. RESULTS: Twenty-one of the 190 probands (9% of the total cohort of 233) and 2 (1.4%) of 140 controls harbored amino acid-altering sequence variations in the CRB1 gene (P =.003). CONCLUSIONS: In our cohort of patients with LCA, coding sequence variations were observed in the CRB1 gene more frequently than in any of the other 5 known LCA-associated genes. Likely disease-causing sequence variations have now been identified in 64 (28%) of 233 subjects in this cohort. CLINICAL RELEVANCE: Molecular diagnosis can confirm and clarify the diagnosis in an increasing fraction of patients with LCA. As genotype data accumulate, clinical phenotypes associated with specific mutations may be established. This will facilitate the counseling of patients regarding their visual prognosis and the likelihood of associated systemic anomalies.

Adolescent↗

PubMed2003

Analysis of GSTP1-1 polymorphism using real-time polymerase chain reaction.

BACKGROUND: Glutathione transferases (GSTs) play an important role in the protection of cells from the products of oxidative stress as well as from several environmental carcinogens. The GSTP1-1 gene class is significantly overexpressed in many human tumors. Four allelic variants have been described for the GSTP1-1 gene (*A, *B, *C, *D) leading to different amino acid substitutions in position 105 and 114 of the protein sequence. The proteins encoded by the different alleles show different abilities to metabolize carcinogens and anticancer agents, suggesting an association between GSTP1 polymorphism and the risk for a variety of cancers as well as between said polymorphism and varying responses to cancer treatments. METHODS: The GSTP1-1 polymorphism was determined using a real-time polymerase chain reaction (PCR) and fluorescence resonance energy transfer with a Light-Cycler Instrument. ARMS was used in the case of *A/*C or *B/*D heterozygosity. We used this method to determine the GSTP1-1 polymorphism in 250 free-living Italian subjects of both sexes. RESULTS: Among 250 subjects representative of an Italian population, we observed the following allelic frequencies: f(A)=0.710, f(B)=0.236, f(C)=0.054 and f(D)=0. The observed phenotypes are in Hardy-Weinberg equilibrium (chi(2)=0.71, df=4, P=0.95). CONCLUSIONS: We have extended and improved a method of GSTP1-1 complete genotyping. This method provides the ability to genotype 30 samples in 2 h and it represents a fast, reliable and automated methodology to determine GSTP1-1 polymorphism in order to perform large-scale population studies.

Adult↗

PubMed2003

Large-scale genotyping of complex DNA.

Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals. Public efforts have so far identified over two million common human SNPs; however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation. Our method amplifies highly reproducible fractions of the genome across multiple DNA samples and calls genotypes at >99% accuracy. We rapidly genotyped 14,548 SNPs in three different human populations and identified a subset of them with significant allele frequency differences between groups. We also determined the ancestral allele for 8,386 SNPs by genotyping chimpanzee and gorilla DNA. WGSA is highly scaleable and enables the creation of ultrahigh density SNP maps for use in genetic studies.

Algorithms↗

PubMed2006

Entrez Gene: gene-centered information at NCBI.

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to contribute gene-specific information or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is provided via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programing utilities (E-Utilities), and for bulk transfer by ftp.

Databases, Genetic↗

PubMed1990

Km(3) identification by enzyme-linked immunosorbent assay (ELISA) as an internal control for Km(1) activity determined by inhibition in dried bloodstains.

A stability study comparing the identification of kappa marker Km(1), using the classical inhibition of agglutination, and the identification of Km(3), using an automated enzyme-linked immunosorbent assay (ELISA) technique, was done. Preliminary tests were performed to establish the specificity and sensitivity of the methods. Based on the results, the quantities of stain required to detect each marker were determined. Blood samples from 24 staff donors of known phenotype were aged at room temperature and at 37 degrees C in the dried stain and liquid forms. In addition, 192 stains from cases 1 to 7 months old and 76 staff-donor stains from 1 1/2 to 10 years old were tested in dried stain form. The known sensitivity of the ELISA technique was exploited by deliverately testing a decreased quantity of antigen. As control stains were aged beyond the detectable limits of sensitivity, results consistently showed an almost simultaneous success or failure to detect Km(1) and Km(3). This indicates that the interpretive criteria established for ELISA are sufficiently demanding to eliminate the danger of reporting false Km(-1) results but true Km(3) results.

Blood Stains↗

PubMed2002

[Interpretive reading of the antibiogram: Intellectual exercise or clinical need?].

Clinical categorisation of susceptibility testing results according to criteria established by different committees is daily performed in clinical microbiology laboratories. By this process clinicians can predict the therapeutic success of antimicrobial treatment in patients infected with susceptible microorganisms. In addition, microbiology laboratories that include a suitable number of antimicrobial agents in susceptibility tests can perform interpretive reading of the antibiogram. With this approach, resistance phenotypes are recognized and allow microbiologist: a) detection of mechanisms of resistance, including low levels of expression; b) modification of clinical classifications that are inconsistent with the inferred resistance mechanism; and c) inference of susceptibility values for antimicrobials that are not included in the antibiogram. In the laboratory, this approach facilitates quality control and validation of susceptibility results. Moreover, it increases the value of the results obtained because new mechanisms of resistance can be characterized and the epidemiology of resistance can be established. From the clinical point of view, this approach contributes to improving the adequacy of treatment (since it is useful for predicting therapeutic failure with the use of antimicrobials in patients with infections due to resistant microorganisms) and to controlling and defining antimicrobial policies. Despite the growing complexity of resistance mechanisms, which makes interpretative reading of the antibiogram difficult, this process should be incorporated into routine practice in microbiology laboratories. Interpretive reading of antibiograms is clinically necessary and not simply a intellectual exercise.

Algorithms↗

PubMedDate not supplied

Autosomal dominant cone-rod dystrophy with R838H and R838C mutations in the GUCY2D gene in Japanese patients.

PURPOSE: To describe the clinical phenotypes of two Japanese families with autosomal dominant cone-rod dystrophy (CORD) caused by an R838H or R838C mutation. METHODS: Complete ophthalmological examinations were performed on three affected individuals from two Japanese families with autosomal dominant CORD. One family had an R838H mutation, and the other family had an R838C mutation in the GUCY2D gene. The tests included best-corrected visual acuity, slit-lamp and fundus examinations, fundus photography, electroretinography, Goldmann kinetic perimetry, and automated light- and dark-adapted static perimetry. RESULTS: The three patients showed essentially normal fundus or little pigmentary change in the maculae by indirect ophthalmoscopy, and only fluorescein angiography revealed clear atrophy of the retinal pigmented epithelium around the fovea. Central or paracentral scotoma was detected by the Goldmann kinetic visual field test. Electroretinography as well as light-adapted and dark-adapted two-color perimetry showed more severe impairment of cone than of rod function. The clinical features in our patients resembled those in Caucasian families with R838H or R838C mutations. CONCLUSIONS: The R838H and R838C mutations in GUCY2D cause CORD in the Japanese population. These mutations can cause a similar clinical phenotype in other races.

Adult↗

PubMed2005

Further evidence of genetic heterogeneity in familial exudative vitreoretinopathy; exclusion of EVR1, EVR3, and EVR4 in a large autosomal dominant pedigree.

BACKGROUND/AIMS: Familial exudative vitreoretinopathy (FEVR) is an inherited blinding condition characterised by abnormal development of the retinal vasculature. The aim of this study was to perform linkage analysis in a large family affected with FEVR to determine whether the mutation involved was in one of the three known autosomal dominant FEVR loci or in another as yet unidentified gene. METHODS: Genomic DNA samples from family members were polymerase chain reaction (PCR) amplified with fluorescently tagged microsatellite markers spanning the EVR1/EVR4 locus (11q13-14) and the EVR3 locus (11p12-13). The resulting PCR products were resolved using an automated DNA sequencer and the alleles sized. These data were used to construct haplotypes across each locus and linkage analysis was performed to prove or exclude linkage. RESULTS: The clinical evaluation in this family suggested features typical of FEVR, with deficient peripheral retinal vascularisation being the common phenotype in all affected individuals. However, linkage analysis proved that this family has a form of FEVR genetically distinct from the EVR1, EVR3 and EVR4 loci. CONCLUSION: The exclusion of linkage in this family to any of the known FEVR loci proves the existence of a fourth locus for autosomal dominant FEVR and shows that this rare disorder is far more heterogeneous than previously thought.

Adult↗

PubMed1998

Macrophage scavenger receptor confers an adherent phenotype to cells in culture.

Several cell lines have become widely used in biotechnology, pharmaceutical and academic laboratories because of their desirable characteristics. Among these, the human embryonic kidney cell line HEK293 is one of the most versatile and powerful for expression of recombinant proteins, permitting the establishment of stable cell lines in just three weeks. Unfortunately, HEK293 cells adhere weakly to tissue culture grade plastic. Therefore, without cumbersome and sometimes expensive modifications to equipment, these cells are not suitable for use in a number of extremely important applications, including robot-based, high-throughput drug screening formats, growth and expansion in roller bottles and expression cloning experiments. We have cloned and transfected the human Class A macrophage scavenger receptor into 293EBNA cells (293EM) and found that expression of this receptor confers a sufficiently adherent property to the cells as to render them usable with automated equipment. In addition, the 293EM cells are now able to adhere to the surface of roller bottles and to untreated glass substrates, allowing growth of these cells in formats for which they are not normally well suited.

Cell Adhesion↗