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In Print: May 3, 2010

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Microarray Papers of Note Published April 2010

Journal: Analytical and Bioanalytical Chemistry. 2010 Apr 28. [Epub ahead of print]
Title: Contact printing of arrayed microstructures.
Authors: Xu W, et al.

The authors of this paper developed a contact printing method, where a sacrificial layer of polyacrylic acid is used to selectively modify the upper surfaces of arrayed microstructures. The method is characterized by printing polystyrene onto microstructures to create an improved substrate for a cell-based microarray platform. Experiments measuring cell growth on arrays modified with polystyrene and fibronectin demonstrated improved growth of cells compared to that for the previously used coating method. Additionally, the use of the PAA sacrificial layer permitted the printing of functionalized polystyrene, carboxylate polystyrene nanospheres, and silica nanospheres onto the arrays, the authors reported.


Journal: Analytical Biochemistry. 2010 Apr 1;399(1):125-31.
Title: Detection of microarray-hybridized oligonucleotides with magnetic beads.
Authors: Shlyapnikov Y, et al.

The authors of this paper report two new approaches for detection of hybridization with oligonucleotide microarrays that employ magnetic beads as active labels. In the first method, streptavidin-coated magnetic beads are used to discover biotin-labeled DNA molecules hybridized with arrayed oligonucleotide probes. In the second method, biotin-labeled DNA molecules are bound first to the surface of magnetic beads and then hybridized with arrayed complementary strands on bead-array contacts. Using a low-power microscope with a dark-field illumination and a pair of complementary primers as a model hybridization system, the authors evaluated the sensitivity, speed, and cost of the new detection methods and compared their performances with detection techniques employing enzyme and fluorescent labels.


Journal: Analytical Chemistry. 2010 Apr 1;82(7):3067-72.
Title: Screening kinase inhibitors with a microarray-based fluorescent and resonance light scattering assay.
Authors: Li T, et al.

The authors report a microarray-based spectroscopic assay with two readout principles, fluorescence and resonance light scattering, for screening kinase inhibitors. In this assay, the phosphorylation and inhibition events are marked by biotinylated antiphosphoserinen/antiphosphotyrosine antibodies, and gold nanoparticles are attached to the antibodies by standard avidin-biotin chemistry followed by silver deposition for RLS signal enhancement. The avidin-conjugated fluorescein is used as a fluorescent probe. Assays for both serine kinase, the alpha-catalytic subunit of cyclic adenosine 5'-monophosphate dependent protein kinase, and tyrosine kinase, leukocyte-specific protein tyrosine kinase, have been developed, according to the authors. They tested the assay's applicability to high-throughput screening using a commercial inhibitor library of 80 kinase inhibitors, and said "satisfactory" results were obtained.


Journal: BMC Biotechnology. 2010 Apr 28;10(1):34. [Epub ahead of print]
Title: Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.
Authors: Kaplinski L, et al.

The hybridization of synthetic Streptococcus pneumoniae tmRNA on a detection microarray is slow at 34 degrees Celsius resulting in low signal intensities, the authors of this paper stated. They found that adding specific DNA helper oligonucleotides to the hybridization buffer increases the signal strength at a given temperature and makes the specific detection of S. pneumoniae tmRNA more sensitive. For instance, no loss of specificity was observed at low temperatures compared to hybridization at 42 degrees Celsius, they found.


Journal: BMC Genomics. 2010 Apr 19;11(1):251.
Title: Transcriptome sequencing and development of an expression microarray platform for the domestic ferret.
Authors: Bruder C, et al.

The ferret is an attractive animal model for the study of respiratory diseases, including influenza. The authors here present a parallel sequencing effort to produce an extensive expressed sequence tag dataset derived from a normalized ferret cDNA library made from mRNA from ferret blood, liver, lung, spleen, and brain. They produced more than 500,000 sequence reads that were assembled into 16,000 partial ferret genes. These genes were then combined with the available ferret sequences in the GenBank to develop a ferret-specific microarray platform. Using the ferret array, the authors detected tissue-specific expression patterns that were confirmed by quantitative real-time PCR assays.


Journal: BMC Genomics. 2010 Apr 28;11(1):269. [Epub ahead of print]
Title: High-throughput marker discovery in melon using a self-designed oligo microarray.
Authors: Ophir R, et al.

Melon, among other crops, is still lagging in genomic resources, limiting the ability to discover new markers in a high-throughput fashion, according to the authors of this paper. Using a custom-designed oligonucleotide microarray based on a partial EST collection of melon, they discovered 6,184 putative single feature polymorphisms between the parents of their mapping population. Validation by sequencing of 245 SFPs from the two parents showed a sensitivity of around 79 percent, the authors reported. Most SFPs contained single-nucleotide polymorphisms. Testing the SFPs on another mapping population of melon confirmed that many of them are conserved and could be used in future breeding programs.

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Journal: European Journal of Pediatrics. 2010 Apr;169(4):421-5.
Title: Rapid diagnosis of herpetic encephalitis in children by PCR-microarray technology for simultaneous detection of seven human herpes viruses.
Authors: Shi J, et al.

The authors of this paper evaluated a PCR and microarray technology platform that can be used to simultaneously detect seven human herpes viruses for the diagnosis of herpetic encephalitis in children. In this study, the authors amplified herpes simplex virus type 1 and type 2; varicella-zoster virus; Epstein-Barr virus; cytomegalovirus; and human herpes virus 6 by multiplex PCR, and genotyped the viruses using array technology. Nearly 300 cerebrospinal fluid specimens from children with clinical suspicion of viral encephalitis were screened using the platform. The results were compared with those of TaqMan PCR kits of common herpes virus to establish concordance. The authors concluded that their PCR-microarray technology platform should be a preferred method for diagnosis of herpetic encephalitis in children.


Journal: Human Reproduction. 2010 Apr;25(4):1066-75.
Title: Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-h protocol.
Authors: Johnson D, et al.

The authors of this paper developed a method for pre-implantation genetic screening, called 'parental support,' that uses microarray measurements from parental DNA to clean single-cell microarray measurements on embryonic cells and compute confidence in each copy number call. The method also distinguishes mitotic and meiotic copy errors and determines parental source of aneuploidy. The authors validated the method on 459 single cells where the known karyotype indicated that per-cell false-positive and false-negative rates were roughly equivalent to metaphase karyotype. The majority of the cells were run in parallel with a clinical commercial PGS service. The authors concluded that the computed confidences were conservative and roughly concordant in terms of accuracy.


Journal: Journal of Clinical Microbiology. 2010 Apr 26. [Epub ahead of print]
Title: A simple PCR-based DNA microarray system to identify human pathogenic fungi in skin.
Authors: Sato T, et al.

The authors developed a system to identify 26 clinically important fungi using a combination of PCR amplification and DNA microarray, in which PCR-amplified DNA was hybridized to a microarray fabricated with species-specific probes sets using inkjet technology. The array reliably identified all 26 reference strains, and was applied subsequently to onychomycosis, taking advantage of tissue accessibility from skin. The array detected fungal DNA and identified pathogens in 92 percent of 106 microscopy-confirmed onychomycosis specimens. In contrast, culture was successful for only 34 percent, they reported.


Journal: Journal of Clinical Oncology. 2010 Apr 20. [Epub ahead of print]
Title: Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia study group.
Authors: Haferlach T, et al.

The Microarray Innovations in Leukemia study assessed the clinical utility of gene expression profiling as a single test to subtype leukemias into conventional categories of myeloid and lymphoid malignancies. The investigation was performed in 11 laboratories across three continents and included 3,334 patients. An exploratory retrospective stage I study was designed for biomarker discovery and generated whole-genome expression profiles from 2,143 patients with leukemias and myelodysplastic syndromes. The gene expression profiling-based diagnostic accuracy was further validated in a prospective second study stage of an independent cohort of 1,191 patients. The authors determined that gene-expression profiling is a "robust" technology for the diagnosis of hematologic malignancies with high accuracy.


Journal: Molecular Biotechnology. 2010 Apr 30. [Epub ahead of print]
Title: Power of deep sequencing and Agilent microarray for gene expression profiling study.
Authors: Feng L, et al.

To compare the quality of gene expression data generated by microarrays and high-throughput sequencers, the authors of this paper examined the gene expression profiles of an in vitro cell model with both platforms. In this study, 17,362 and 15,938 genes were detected by microarray and digital gene expression, respectively, with 13,221 overlapping genes. The dynamic range of the microarray was fixed with four orders of magnitude, while that of DGE was extendable. The authors found the consistency of the two platforms to be high, especially for abundant genes. It was more difficult for the microarray to distinguish the expression variation of less abundant genes. According to the authors, though microarrays might be eventually replaced by DGE or transcriptome sequencing in the near future, microarrays are still "stable, practical, and feasible."

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Journal: Nature. 2010 Apr 1;464(7289):713-20.
Title: Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.
Authors: Craddock N, et al.

The authors of this project undertook a genome-wide study of association between copy number variants and eight common human diseases. Using a purpose-designed array, they typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50 percent of all common CNVs larger than 500 base pairs. The authors identified several biological artifacts that led to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease: IRGM for Crohn's disease; HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes; and TSPAN8 for type 2 diabetes, though in each case the locus had previously been identified in SNP-based studies. The authors concluded that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.


Journal: Nature Biotechnology. 2010 Apr;28(4):322-4.
Title: A global map of human gene expression.
Authors: Lukk M, et al.

The authors of this correspondence constructed a global gene-expression map by integrating microarray data from 5,372 human samples representing 369 different cell and tissue types, disease states and cell lines. These data have been compiled in an online resource that allows the user to search for a gene of interest and find the conditions in which it is over- or underexpressed, or, conversely, to find which genes are over- or underexpressed in a particular condition.


Journal: Nature Genetics. 2010 Apr 4 [Epub ahead of print]
Title: Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.
Authors: Park H, et al.

The authors of the paper developed and applied a new method to combine high-resolution array comparative genomic hybridization data with whole-genome DNA sequencing data resulting in a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome and two Asian genomes were then used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. The authors discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. They believe the common Asian CNVs will be a useful resource for subsequent genetic studies in these populations.


Journal: Nature Methods. 2010 Apr;7(4):287-9.
Title: Cell type-specific gene expression differences in complex tissues.
Authors: Shen-Orr S, et al.

The authors describe a method called cell type-specific significance analysis of microarrays, or csSAM, for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. To test the method, they validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejections, which revealed hundreds of differentially expressed genes that were otherwise undetectable.


Journal: Nucleic Acids Research. 2010 Apr 1;38(7):2168-76.
Title: Estimating the proportion of microarray probes expressed in an RNA sample.
Authors: Shi W, et al.

According to the authors of this paper, a fundamental question in microarray analysis is the estimation of the number of expressed probes in different RNA samples. Negative control probes available in the latest microarray platforms, such as Illumina whole-genome expression BeadChips, provide an opportunity to estimate the number of expressed probes without setting a threshold. In this study, an algorithm was proposed to estimate the number of expressed probes in an RNA sample by using negative controls to measure background noise. The performance of the algorithm was demonstrated by comparing different generations of Illumina BeadChips, comparing the set of probes targeting well-characterized RefSeq NM transcripts with other probes on the array, and comparing pure samples with heterogenous samples.


Journal: Pathology & Oncology Research. 2010 Apr 23. [Epub ahead of print]
Title: Nuclear grading versus Gleason grading in small samples containing prostate cancer: a tissue microarray study.
Authors: Wittschieber D, et al.

In this study, the authors sought to determine whether nuclear grading in very small samples of prostate cancer would provide additional prognostic information as compared to Gleason grading. A tissue microarray was constructed composed of a total number of 3,261 prostate cancers. Blinded for all clinical and pathological data, the TMA spots containing cancer were graded with two systems: first, for nuclear features according to a modified Fuhrman grading system, and second, by using a simplified Gleason system. The results were compared with tumor stage, tumor grade, and follow-up data. Though nuclear grading could be performed on the TMA spots, no correlation was found with tumor stage, grade, or PSA recurrence after prostatectomy. Still, Gleason grading provided "significant" prognostic information. The authors determined that the Fuhrman grading of prostate cancer does not appear to be of any prognostic importance.


Journal: PLoS One. 2010 Apr 16;5(4):e10174.
Title: A protein allergen microarray detects specific IgE to pollen surface, cytoplasmic, and commercial allergen extracts.
Authors: Vigh-Conrad K, et al.

The authors of this paper sought to develop a high-throughput assay to measure allergen-specific IgE in sera and to explore the relative allergenicity of different pollen fractions. To do this, they generated a protein microarray containing surface, cytoplasmic, and commercial extracts from 22 pollen species, commercial extracts from nine non-pollen allergens, and five recombinant allergenic proteins. Pollen surface and cytoplasmic fractions were prepared by extraction into organic solvents and aqueous buffers, respectively. Arrays were incubated with serum from 176 individuals and bound IgE was detected by indirect immunofluorescence, providing a high-throughput measurement of IgE. They concluded that the allergen microarray is a reproducible method to measure allergen-specific IgE in small amounts of sera.

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