Multiplex PCR for quality control of template RNA/cDNA in RT-PCR assays.
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Actins↗
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Rationale for the recommendations for harmonizing current methodology for detecting BCR-ABL transcripts in patients with chronic myeloid leukaemia.
Molecular monitoring for patients with chronic myeloid leukaemia (CML) has become an important practice in the era of imatinib therapy. For successful widespread introduction into the mainstream patient monitoring schedule, many procedural aspects of the complex real-time quantitative polymerase chain reaction (RQ-PCR) technique for measuring BCR-ABL transcripts require optimization. Recommendations for harmonizing the differing methodologies have recently been proposed. These recommendations were designed to maximize reliability of analysis for clinical decision making and proposed the adoption of an International Scale of measurement. The purpose of this review is to present the evidence and supporting data for specific recommendations. These recommendations include use of the same source of cells, either blood or marrow, for analysis; for validation of equal PCR amplification efficiencies of cDNA and standards when using a plasmid to construct standard curves and for ensuring ongoing high-level performance by undertaking a quality assurance programme. Clinicians must know the measurement reliability of an RQ-PCR assay to be able to determine the significance of a change in BCR-ABL level. An assay with poor precision limits the clinical usefulness of results. International harmonization should establish RQ-PCR measurement of BCR-ABL as the best method for monitoring treatment response for patients with CML.
Drug Monitoring↗
Microarray analysis of differentially expressed genes in rat frontal cortex under chronic risperidone treatment.
Long-term administration of antipsychotic drugs can induce differential expression of a variety of genes in the brain, which may underscore the molecular mechanism of the clinical efficacy and/or side effects of antipsychotic drugs. We used cDNA microarray analysis to screen differentially expressed genes in rat frontal cortex under 4 weeks' treatment of risperidone (1 mg/kg). Using real-time quantitative PCR, we were able to verify eight genes, whose expression were significantly upregulated in rat frontal cortex under chronic risperidone treatment when compared with control animals. These genes include receptor for activated protein kinase C, amida, cathepsin D, calpain 2, calcium-independent receptor for alpha-latrotoxin, monoamine oxidase B, polyubiquitin, and kinesin light chain. In view of the physiological function of these genes, the results of our study suggest that chronic risperidone treatment may affect the neurotransmission, synaptic plasticity, and proteolysis of brain cells. This study also demonstrates that cDNA microarray analysis is useful for uncovering genes that are regulated by chronic antipsychotic drugs treatment, which may help bring new insight into the molecular mechanism of antipsychotic drugs.
Animals↗
Limitations of the nested reverse transcriptase polymerase chain reaction on tyrosinase for the detection of malignant melanoma micrometastases in lymph nodes.
The specificity and sensitivity of the nested reverse transcriptase polymerase chain reaction (RT-PCR) on tyrosinase was studied, for the detection of micrometastases of malignant melanoma. The specificity was assessed in the blood of six healthy donors, four patients with non-melanoma cancers of which one patient was treated with granulocyte-colony stimulating factor. Lymph nodes of nine patients without malignant melanoma were tested and four cell lines of various other tumours. Six of the nine non-melanoma lymph nodes were positive in this assay. The sensitivity was tested in a spike experiment in vitro, using a melanoma cell line. The detection limit was ten melanoma cells per 10(7) peripheral blood lymphocytes.
Biomarkers, Tumor↗
Functional characterization of pro-biotic pharmaceuticals by quantitative analysis of gene expression.
Functional characterization and quality control of complex biological pharmaceuticals are currently difficult to achieve. Classical analytical methods are not suitable due to the heterogeneity of such substances. Conventional biological assays based on the detection of proteins and functional physiologic responses are highly variable in sensitivity and therefore, difficult to standardize. The quantification of expressed genes in contrast, does not require the accumulation of measurable protein and hence is a more sensitive and dynamic method for the functional characterization of complex biological substances. This report describes a standardized system based on real-time polymerase chain reaction (PCR), which allows a reliable stability monitoring and quality control of such preparations, as exemplified by three pro-biotic pharmaceuticals that contain living bacteria of Enterococcus faecalis (Symbioflor-1), Escherichia coli (Symbioflor-2) and a preparation of sterile autolysate of both species (Pro-Symbioflor). This system might be universally applicable to characterize complex biological pharmaceuticals by selecting appropriate sets of target cells and regulated genes.
Cell Line↗
Molecular detection of measles virus in primary cell cultures of otosclerotic tissue.
CONCLUSION: Primary cell cultures were established from otosclerotic/otospongiotic footplate bone particles. Although this procedure is time-consuming, the quality and quantity of RNA isolated from these cells were much higher in comparison with the direct isolation of RNA from footplate bone samples and the preparation was more suitable for the detection of measles virus (MeV) RNA. OBJECTIVE: Morphological and biochemical investigations suggest that persistent MeV infection participates in the development of otosclerotic foci. However, this hypothesis is controversial because the detection of MeV in otosclerotic foci is inconsistent since the results are dependent on the presence and stage of foci in the investigated bone particles. Unfortunately, this cannot be confirmed before investigation. To study the presence of the MeV by different techniques in otosclerotic foci, stapes footplate fragments were collected during stapedectomy from patients suffering from clinical otosclerosis. MATERIALS AND METHODS: MeV-specific RT-PCR was performed on total RNA isolated directly from four fresh frozen footplate bone fragments and from the cells of 16 primary cultures of otosclerotic tissue samples. In order to rescue persisting MeV, the primary footplate cells were cocultured with MeV permissive B95a cells. RESULTS: MeV was not detected in RNA from fresh frozen otosclerotic materials, but analysis of the RNA from 5 of the 16 primary cell cultures showed MeV-positive results. Nucleotide sequencing of a 317 bp MeV-specific RT-PCR fragment confirmed the presence of the MeV RNA genome. Here, we report the first determination of MeV sequences in total RNA isolated from primary cells cultured from otosclerotic tissue. Persisting MeV in primary footplate cells could not be recovered by coculturing with B95a cells.
Adult↗
Contrast normalization of oligonucleotide arrays.
Affymetrix high-density oligonucleotide array is a tool that has the capacity to simultaneously measure the abundance of thousands of mRNA sequences in biological samples. In order to allow direct array-to-array comparisons, normalization is a necessity. When deciding on an appropriate normalization procedure there are a couple questions that need to be addressed, e.g., on which level should the normalization be performed: On the level of feature intensities or on the level of expression indexes? Should all features/expression indexes be used or can we choose a subset of features likely to be unregulated? Another question is how to actually perform the normalization: normalize using the overall mean intensity or use a smooth normalization curve? Most of the currently used normalization methods are linear; e.g., the normalization method implemented in the Affymetrix software GeneChip is based on the overall mean intensity. However, along with alternative methods of summarizing feature intensities into an expression index, nonlinear methods have recently started to appear. For many of these alternative methods, the natural choice is to normalize on the level of feature intensities, either using all feature intensities or only perfect match intensities. In this report, a nonlinear normalization procedure aimed for normalizing feature intensities is proposed.
Algorithms↗
Selecting signature oligonucleotides to identify organisms using DNA arrays.
MOTIVATION: DNA arrays are a very useful tool to quickly identify biological agents present in some given sample, e.g. to identify viruses causing disease, for quality control in the food industry, or to determine bacteria contaminating drinking water. The selection of specific oligos to attach to the array surface is a relevant problem in the experiment design process. Given a set S of genomic sequences (the target sequences), the task is to find at least one oligonucleotide, called probe, for each sequence in S. This probe will be attached to the array surface, and must be chosen in a way that it will not hybridize to any other sequence but the intended target. Furthermore, all probes on the array must hybridize to their intended targets under the same reaction conditions, most importantly at the temperature T at which the experiment is conducted. RESULTS: We present an efficient algorithm for the probe design problem. Melting temperatures are calculated for all possible probe-target interactions using an extended nearest-neighbor model, allowing for both non-Watson-Crick base-pairing and unpaired bases within a duplex. To compute temperatures efficiently, a combination of suffix trees and dynamic programming based alignment algorithms is introduced. Additional filtering steps during preprocessing increase the speed of the computation. The practicability of the algorithms is demonstrated by two case studies: The identification of HIV-1 subtypes, and of 28S rDNA sequences from >or=400 organisms.
Algorithms↗
Robust estimators for expression analysis.
MOTIVATION: We consider the problem of estimating values associated with gene expression from oligonucleotide arrays. Such estimates should linearly track concentration, yield non-negative results, have statistical guarantees of robustness against outliers, and allow estimates of significance and variance. RESULTS: A hierarchy of simple models is used to design robust estimators meeting these goals for both stand alone and comparative experiments. This algorithm has been validated against an extensive panel of known spike experiments, and shows comparable performance to existing standards.
Algorithms↗
Multiple sequence alignment using partial order graphs.
MOTIVATION: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts. RESULTS: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism. AVAILABILITY: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.
Algorithms↗
Reconstruction of DNA sequencing by hybridization.
MOTIVATION: It is widely recognized that the hybridization process is prone to errors and that the future of DNA sequencing by hybridization is predicated on the ability to successfully cope with such errors. However, the occurrence of hybridization errors results in the computational difficulty of the reconstruction of DNA sequencing by hybridization. The reconstruction problem of DNA sequencing by hybridization with errors is a strongly NP-hard problem. So far the problem has not been solved well. RESULTS: In this paper, a new approach is presented to solve the reconstruction problem of DNA sequencing by hybridization, which realizes the computational part of the SBH experiment. The proposed algorithm accepts both the negative and positive errors. The computational experiments show that the algorithm behaves satisfactorily, especially for the case with k-tuple repetitions and positive errors.
Algorithms↗
Non-linear normalization and background correction in one-channel cDNA microarray studies.
MOTIVATION: Data from one-channel cDNA microarray studies may exhibit poor reproducibility due to spatial heterogeneity, non-linear array-to-array variation and problems in correcting for background. Uncorrected, these phenomena can give rise to misleading conclusions. RESULTS: Spatial heterogeneity may be corrected using two-dimensional loess smoothing (Colantuoni et al., 2002). Non-linear between-array variation may be corrected using an iterative application of one-dimensional loess smoothing. A method for background correction using a smoothing function rather than simple subtraction is described. These techniques promote within-array spatial uniformity and between-array reproducibility. Their application is illustrated using data from a study of the effects of an insulin sensitizer, rosiglitazone, on gene expression in white adipose tissue in diabetic db/db mice. They may also be useful with data from two-channel cDNA microarrays and from oligonucleotide arrays. AVAILABILITY: R functions for the methods described are available on request from the author.
Adipose Tissue↗
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.
Acetic Acid↗
An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression.
The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12-14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.
Analysis of Variance↗
WormBase: a cross-species database for comparative genomics.
WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.
Animals↗
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
Amino Acid Sequence↗
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.
Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/).
Databases, Nucleic Acid↗
IntAct--open source resource for molecular interaction data.
IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.
DNA↗