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In Print: Dec 1, 2009


Microarray Papers of Note Published in November 2009

Journal: American Journal of Human Genetics. 2009 Nov 25 [Epub ahead of print]

Title: Genomic dissection of population substructure of Han Chinese and its implication in association studies.

Authors: Xu S, et al.

In this study, the authors examined population substructures in a diverse set of over 1,700 Han Chinese samples collected from 26 regions across China, each genotyped at about 160,000 SNPs. Their results showed that the Han Chinese population is intricately substructured, with the main observed clusters corresponding roughly to northern Han, central Han, and southern Han. These signals indicated that significant differences among Han Chinese subpopulations should be carefully explained in case they are also detected in association studies, especially when sample sources are diverse.

Journal: Analytical and Bioanalytical Chemistry. 2009 Nov;395(6):1623-30.

Title: Development of a multichannel flow-through chemiluminescence microarray chip for parallel calibration and detection of pathogenic bacteria.

Authors: Karsunke X, et al.

The authors developed a multichannel flow-through chemiluminescence microarray chip for parallel detection of pathogenic bacteria. The disposable chip, made of acrylonitrile-butadiene-styrene copolymer, was devised as a support for a multiplexed sandwich immunoassay. Calibration and measurement was possible in one experiment, because the developed chip contains six parallel flow-through microchannels. Polyclonal antibodies against the pathogenic bacteria Escherichia coli O157:H7, Salmonella typhimurium, and Legionella pneumophila were immobilized on the chip by microcontact printing in order to use them as specific receptors. Detection of the captured bacteria was carried out by use of specific detection antibodies labeled with biotin and horseradish peroxidase-streptavidine conjugates. The enzyme HRP generates chemiluminescence after adding luminol and hydrogen peroxide. This signal was observed by use of a sensitive CCD camera. The overall assay time for measurement and calibration is 18 minutes.

Journal: Analytical Chemistry. 2009 Nov 1;81(21):9183-7.

Title: Microarray-based multiplexed scanometric immunoassay for protein cancer markers using gold nanoparticle probes.

Authors: Kim D, et al.

The authors report the use of electroless gold deposition as a light-scattering signal enhancer in a multiplexed, microarray-based scanometric immunoassay using gold nanoparticle probes. The use of gold development resulted in greater signal enhancement than the typical silver development, and multiple rounds of metal development were found to increase the resulting signal compared to one round of development, according to the authors. Using these conditions, the assay was capable of detecting approximately 9,000 copies of prostate-specific antigen in buffer and in 10 percent serum.

Journal: Antimicrobial Agents and Chemotherapy. 2009 Nov 2. [Epub ahead of print]

Title: Screening and quantification of the expression of antibiotic resistance genes in Acinetobacter baumannii with a microarray.

Authors: Coyne S, et al.

An oligonucleotide-based DNA microarray was developed to evaluate expression of genes for efflux pumps in Acinetobacter baumannii and to detect acquired antibiotic resistance determinants. The microarray contained probes for 205 genes including those for 47 efflux systems, 55 resistance determinants, and 35 housekeeping genes. The microarray was validated by comparative analysis of mutants overexpressing or deleted for the pumps relative to the parental strain. The performance of the microarray was also evaluated using in vitro single step mutants obtained on various antibiotics.

Journal: Bioinformatics. 2009 Nov 20. [Epub ahead of print]

Title: Joint estimation of DNA copy number from multiple platforms.

Authors: Zhang N, et al.

The authors propose a method called multi-platform circular binary segmentation, which pools statistical evidence across platforms during copy number detection, and does not require pre-standardization of different data sources. It involves a weighted sum of t-statistics, which arises naturally from the generalized log-likelihood ratio of a multi-platform model. The authors compared the integrated analysis of Affymetrix and Illumina SNP array data with Agilent and fosmid clone end sequencing results on eight HapMap samples to achieve improved spatial resolution and detection power using MPCBS. They also applied the new method to analyze multi-platform data for tumor samples.

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Journal: BMC Bioinformatics. 2009 Nov 19;10(1):380. [Epub ahead of print]

Title: An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

Authors: Allemeersch J, et al.

For researchers who use a two-channel microarray of genomic DNA probes for array comparative genomic hybridization, the basic setup consists of hybridizing a patient against a normal reference sample. According to the authors, two disadvantages of this setup are the use of half of the resources to measure a reference sample, and the possibility that deviating signals are caused by benign copy number variation in the normal reference instead of a patient aberration. In this study, the authors applied an experimental loop design that compares three patients in three hybridizations. More specifically, they developed and compared two statistical methods — linear models of log ratios and mixed models of absolute measurements. In an analysis of 27 patients, they observed that the linear models of the log ratios performed better than the mixed models of the absolute intensities.

Journal: BMC Bioinformatics. 2009 Nov 26;10(1):389. [Epub ahead of print]

Title: A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

Authors: Sontrop H, et al.

Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide, according to the authors. The estimated expression values also vary depending on the selected preprocessing scheme. The authors of this paper performed a comprehensive sensitivity analysis of microarray breast cancer classification under these two types of feature variability. They used data from six preprocessing methods, using a compendium consisting of eight different datasets, involving 1,131 hybridizations, containing data from both one- and two-color array technology. The authors additionally performed a joint study on performance, concordance, and stability. In the stability analysis, they tested classifiers for their noise tolerance by using perturbed expression profiles that are based on uncertainty information directly related to the preprocessing methods. The results indicated that signature composition is strongly influenced by feature variability, even if the array platform and the stratification of patient samples are identical. They also argue that there is a high level of discordance between individual class assignments for signatures constructed on data coming from different preprocessing schemes, even if the actual signature composition is identical.

Journal: BMC Biotechnology. 2009 Nov 25;9(1):97. [Epub ahead of print]

Title: A rapid and inexpensive labeling method for microarray gene expression analysis.

Authors: Ouellet M, et al.

The authors describe a new method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the Roche NimbleGen microarray platform with the NimbleGen-recommended double-stranded cDNA protocol and the indirect aminoallyl-based labeling method. As part of the study, two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. The new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and increased the authors' ability to find statistically significant differentially expressed genes.

Journal: BMC Genomics. 2009 Nov 24;10(1):555. [Epub ahead of print]

Title: Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species.

Authors: Bellin D, et al.

The authors developed a method based on Roche 454 Life Sciences-based sequencing of 3' cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence is not available. They evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera as if no other sequence information was available for this species. The microarray designed on the berries' transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proved to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes in the same samples, according to the authors.

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Journal: Breast Cancer Research and Treatment. 2009 Nov 26. [Epub ahead of print]

Title: High-throughput resequencing in the diagnosis of BRCA1/2 mutations using oligonucleotide resequencing microarrays.

Authors: Schroeder C, et al.

The authors present an oligonucleotide resequencing microarray that covers the complete coding sequence of both the BRCA1 and BRCA2 genes. In total, 36 previously characterized DNAs were resequenced. Of the 36 samples, all 11 patients with single-nucleotide mutations and, due to a special mutational design, eight patients with heterozygous deletions were detected correctly. In total, 47 different single-nucleotide variants were found during the study. A software tool called SeqC reduced the number of ambiguous calls with the help of a statistical module comparing the acquired data to an online database. SeqC improved the average call rate to 99 percent and reduced time and effort for manual analysis. In total, 945 kilobases were screened and the overall turnaround time for each patient took approximately three days, including analysis.

Journal: Chromosome Research. 2009 Nov 26. [Epub ahead of print]

Title: Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas.

Authors: Thomas R, et al.

This paper describes the construction of a genomic microarray platform for detection of recurrent copy number aberrations in feline tumors through cytogenetic assignment of 210 large-insert DNA clones selected at intervals of approximately 15 megabases from the feline genome sequence assembly. Microarray-based profiling of 19 injection-site associated sarcomas and 27 non-ISAS cases identified an extensive range of genomic imbalances that were recurrent throughout the combined panel of 46 sarcomas, according to the authors. Deletions of two specific regions were significantly associated with the non-ISAS phenotype. Further characterization of these regions may permit molecular distinction between ISAS and non-ISAS, as a tool for predicting tumor behavior and prognosis, as well as refining means for therapeutic intervention, the authors stated.

Journal: Clinical Chemistry. 2009 Nov 12. [Epub ahead of print]

Title: DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model.

Author: Chou L, et al.

In this study, the authors investigated a process for enriching DNA samples by using a customized high-density oligonucleotide microarray to enrich a targeted 280-kb region of the neurofibromin 1 gene. The captured DNA was sequenced with the Roche 454 GS FLX system. Two NF1 samples, CN1 and CN2, with known genotypes were tested with this protocol. The authors found that targeted microarray capture may also capture sequences from non-targeted regions in the genome. The capture specificity estimated for the targeted NF1 region was approximately 60 percent. The de novo Alu insertion was partially detected in sample CN1 by additional de novo assembly with 50 percent base-match stringency, and the single-base deletion in sample CN2 was successfully detected by reference mapping. Interferences by pseudogene sequences were removed by means of dual-mode reference-mapping analysis, which reduced the risk of generating false-positive data.

Journal: Clinical Chemistry. 2009 Nov;55(11):1995-2003.

Title: A high-sensitivity, medium-density, and target amplification-free planar waveguide microarray system for gene expression analysis of formalin-fixed and paraffin-embedded tissue.

Authors: Schwers S, et al.

The authors developed an approach for measuring mRNA abundances in formalin-fixed, paraffin-embedded tissue samples. The approach involves automated RNA extractions, direct hybridization of extracted RNA to immobilized capture probes, antibody-mediated labeling, and readout with an instrument applying the principle of planar waveguides. A 14-gene multiplex assay conducted with RNA isolated from 20 FFPE blocks was successfully correlated to an analysis of the same with reverse-transcription quantitative real-time PCR, according to the authors

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Journal: Genome Research. 2009 Nov 6. [Epub ahead of print]

Title: Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis.

Authors: Stambuk B, et al.

Using microarray-based comparative genome hybridization, the authors identified gene copy number variations common to five industrially important fuel ethanol Saccharomyces cerevisiae strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. These strains have significant amplifications of the telomeric SNO and SNZ genes, which are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin), according to the authors. They show that increased copy number of these genes confers the ability to grow more efficiently under the repressing effects of thiamin, especially in media lacking pyridoxine and with high sugar concentrations. These genetic changes have likely been adaptive and selected for in the industrial environment, and may be required for the efficient utilization of biomass-derived sugars from other renewable feedstocks, they state.

Journal: Journal of Agricultural and Food Chemistry. 2009 Nov 25;57(22):10964-71.

Title: Administration of tomato and paprika beverages modifies hepatic glucose and lipid metabolism in mice: a DNA microarray analysis.

Authors: Aizawa K, et al.

To examine whether the expression of hepatic genes, including biomarkers, is affected by the ingestion of tomato or paprika, the authors of this study fed mice tomato beverage (TB), paprika beverage (PB), or water (control) ad libitum for 6 weeks. The body weights in the TB and PB groups were significantly lower than those in the control group and administration of PB significantly increased the plasma high-density lipoprotein-cholesterol level, the authors found. Hepatic gene expression was also investigated using DNA microarrays. The authors found that ingestion of TB or PB up-regulated the expression of 687 and 1,045 genes and down-regulated the expression of 841 and 653 genes, respectively. These changes in gene expression suggest that TB ingestion promotes glycogen accumulation and stimulates some specific steps in fatty acid oxidation, according to the authors. PB ingestion, meantime, promoted the entire glucose and fatty acid metabolic pathways to improve lipid profiles. The authors believe their results provide genetic information about a variety of biochemical processes by which vegetables can contribute to good health.

Journal: Journal of the American Chemical Society. 2009 Nov 25;131(46):16660-2.

Title: Small molecule-based binding environments: combinatorial construction of microarrays for multiplexed affinity screening.

Authors: Roska R, et al.

This paper describes the construction of a combinatorial artificial receptor array and the application of the array to differentiation of proteins based on their binding patterns. Microarrays displaying 5,035 unique binding environments were prepared using a library of 19 small-molecule building blocks. Each building block was equipped with a carboxylic acid handle, allowing mixtures of the building blocks to be spotted onto the surface of an amine functionalized glass slide for covalent immobilization as subunits of the binding environments. The microarray surface was then used as the receptor synthesis platform. Four fluorescently labeled proteins — ubiquitin, myoglobin, alpha-1-acid glycoprotein, and lysozyme — were incubated with the arrays to demonstrate the reproducibility of binding and the level of differentiation that can be achieved.

Journal: Journal of Neuroscience Research. 2009 Nov 23. [Epub ahead of print]

Title: Genome wide profiling of altered gene expression in the neocortex of Alzheimer's disease.

Authors: Tan M, et al.

In this study, the authors investigated genome-wide gene alterations in the temporal cortex of a well-characterized cohort of Alzheimer's disease patients using an internally developed microarray platform, and compared some of the transcript changes with immunoblotting. Of the 5,485 genes found to be significantly altered in AD, they identified consistent patterns of changes that show that the AD transcriptome in the neocortex is characterized by changes indicative of synaptic dysfunction, perturbed neurotransmission, and activation of neuroinflammation. The authors also highlighted several genes of potential pathogenic significance that have not been well studied in AD.

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Journal: Journal of Virology Methods. 2009 Nov 13. [Epub ahead of print]

Title: A diagnostic oligonucleotide microarray for simultaneous detection of grapevine viruses.

Authors: Engel E, et al.

The authors designed a 70-mer oligonucleotide microarray to detect known grapevine viruses as well as new viruses by cross-hybridization to highly conserved probes. The array contains 570 unique probes designed against highly conserved and species-specific regions of 44 plant viral genomes. In addition, probes designed against plant housekeeping genes are also included. By using a random-primed RT-PCR amplification strategy of grapevine double stranded RNA-enriched samples, viral agents were detected in single and mixed infections. The microarray accuracy to detect 10 grapevine viruses was compared with RT-PCR, yielding consistent results. Genomic libraries containing complete viral genomes were also used as part of the validation process. Three Closteroviridae members were detected for the first time in Chilean grapevines using the microarray, according to the authors.

Journal: Nucleic Acids Research. 2009 Nov 23. [Epub ahead of print]

Title: H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.

Authors: Yamasaki C, et al.

The authors discuss H-InvDB, a comprehensive annotation resource of human genes and transcripts that consists of two main views and six sub-databases. The latest release of H-InvDB provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB also provides several new annotation features, such as mapping of microarray probes, new gene models, and relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides data-mining resources including a navigation search, an H-InvDB enrichment analysis tool, and web service application programming interfaces.

Journal: PLoS Genetics. 2009 Nov 13 [Epub ahead of print]

Title: Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer

Authors: Lando M, et al.

The authors performed integrative analysis of gene dosage, expression, and ontology data to discover driver genes in the carcinogenesis and chemoradioresistance of cervical cancers. Gene dosage and expression profiles of 102 locally advanced cervical cancers were generated by microarray techniques. Fifty-two of these patients were also analyzed with Illumina expression arrays to confirm the gene expression results. An independent cohort of 41 patients was used for validation of gene expressions associated with clinical outcome. Statistical analysis identified 29 recurrent gains and losses and three losses associated with poor outcome after chemoradiotherapy. The intratumor heterogeneity, assessed from the gene dosage profiles, was low for these alterations, showing that they had emerged prior to many other alterations and probably were early events in carcinogenesis. Integration of the alterations with gene expression and Gene Ontology data identified genes that were regulated by the alterations and revealed five biological processes that were significantly overrepresented among the affected genes: apoptosis, metabolism, macromolecule localization, translation, and transcription. Four genes correlated with outcome at both the gene dosage and expression level and were satisfactorily validated in the independent cohort. These integrated analyses yielded 57 candidate drivers of 24 genetic events, including novel loci responsible for chemoradioresistance.

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