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In Print: Feb 8, 2011


Microarray Papers of Note Published December 2010 — January 2011

Journal: Acta Biomaterialia. 2010 Dec;6(12):4614-21.

Title: A matrix micropatterning platform for cell localization and stem cell fate determination.

Authors: Huang N, et al.

Using a microscale direct writing technique, the authors characterized the generation of multicomponent extracellular matrix microarrays for cellular micropatterning, localization, and stem cell fate determination. They claim that MDW is a versatile approach to print ECMs of diverse geometries and compositions onto surfaces, and is amenable to the generation of multicomponent ECM arrays for stem cell fate determination.

Journal: Biosensors and Bioelectronics. 2011 Jan 15;26(5):1839-46.

Title: Polysaccharide microarrays with a CMOS based signal detection unit.

Authors: Baader J, et al.

The authors developed a procedure to create polysaccharide microarrays that can be used to analyze antibodies using an integrated, complementary metal-oxide-semiconductor-based electric signal readout process. In this study, the arrays were used to measure IgG antibody concentrations in human blood sera using either chemiluminescence- or fluorescence-based detection.

Journal: BMC Genomics. 2011 Jan 6;12:11.

Title: The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis.

Authors: Fang X, et al.

The gene SOX2 is implicated in maintaining the "stemness" of embryonic and adult stem cells. The authors of this study used ChIP-seq, arrays, and RNA-seq to characterize SOX2 response in LN229 GBM cells. They claimed the insights gained serve as a useful resource for the research community.

Journal: BMC Medical Genomics. 2011 Jan 27;4(1):16.

Title: The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.

Authors: Przybytkowski E, et al.

The authors performed array comparative genomic hybridization on whole genome amplified and non-amplified genomic DNA from MCF-7 breast cancer cells, using 244K and 1M Agilent arrays. Their ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 megabase in genomic length.

Journal: BMC Research Notes. 2010 Dec 28;3:349.

Title: Exploring the use of internal and external controls for assessing microarray technical performance.

Authors: Lippa K, et al.

The authors compared several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. They support the use of spike-in controls as general tools for performance assessment across time, experimenters, and array batches, and suggest that spike-in controls have potential for comparison of microarray data generated across species using different technologies.

Journal: Genes, Chromosomes, and Cancer. 2011 Jan 13. [Epub ahead of print]

Title: Evaluation of TP53 mutations with the AmpliChip p53 research test in chronic lymphocytic leukemia: correlation with clinical outcome and gene expression profiling.

Authors: Chiaretti S, et al.

The authors evaluated the impact of TP53 mutations on clinical outcome by analyzing 98 untreated chronic lymphocytic leukemia using the AmpliChip p53 Research Test and direct sequencing and performed microarrays analysis on TP53 mutated and/or deleted cases. The AmpliChip p53 Research Test detected 17 mutations in 14 patients, and a significant association between TP53 mutations and del(17p) was recorded.

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Journal: Genes to Cells. 2011 Jan;16(1):1-11.

Title: Lectin microarray analysis of pluripotent and multipotent stem cells.

Authors: Toyoda M, et al.

The authors used a lectin microarray to categorize murine somatic stem cells into groups according to differentiation potency. They then classified human embryonic stem cells and induced pluripotent stem cells by the same approach. The authors believe the approach can be used for quality control in cell-based therapy and regenerative medicine.

Journal: Human Mutation. 2011 Jan;32(1):91-7.

Title: High-resolution genomic arrays identify CNVs that phenocopy the chromosome 22q11.2 deletion syndrome.

Authors: Busse T, et al.

The authors analyzed DNA from eight patients with 22q11 deletion syndrome by high-density SNP arrays and identified potentially pathogenic copy number variants in four of eight patients. They argue that their findings support a recent consensus statement advocating chromosomal microarray analysis as a first-line diagnostic approach for patients with multiple congenital anomalies.

Journal: International Journal of Food Microbiology. 2011 Jan 13. [Epub ahead of print]

Title: Development of a DNA microarray for detection and identification of Legionella pneumophila and ten other pathogens in drinking water.

Authors: Zhou G, et al.

The authors developed an oligonucleotide-based microarray using the sequences of 16S-23S rDNA internal transcribed spacer regions and the gyrase subunit B gene, which are found in most waterborne pathogenic agents. The new diagnostic contains 26 specific probes and can simultaneously detect Aeromonas hydrophila, Klebsiella pneumonia, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella spp., Shigella spp., Staphylococcus aureus, Vibrio choleraeo, Vibrio parahaemolyticus, Yersinia enterocolitica, and Leptospira interrogans.

Journal: Journal of the American Chemical Society. 2011 Jan 19. [Epub ahead of print]

Title: A peptide aldehyde microarray for high-throughput profiling of cellular events.

Authors: Wu H, et al.

The authors developed a microarray with a focused positional-scanning library of enzyme inhibitors. The peptide aldehyde-based small-molecule microarray specifically targeted cysteine proteases, enabling large-scale functional assessment of this subgroup of proteases, within fluorescently labeled samples, including pure proteins, cellular lysates, and infected samples.

Journal: Journal of Clinical Microbiology. 2011 Jan 26. [Epub ahead of print]

Title: Utility of a panviral microarray for detection of swine respiratory viruses in clinical samples.

Authors: Nicholson T, et al>.

The authors used the Virochip, a panviral DNA microarray that is capable of detecting all known viruses, to positively detect swine viruses in both cell culture derived samples and clinical swine samples. They determined the array can detect pathogenic viruses frequently found in swine in a variety of solid and liquid specimens, such as turbinate tissue homogenate and lung lavage, as well as antemortem samples, such as serum.

Journal: Journal of Clinical Pathology. 2011 Jan;64(1):88-90.

Title: High-density tissue microarrays from prostate needle biopsies.

Authors: McCarthy F, et al.

Formalin-fixed prostate biopsies are frequently the only tissue collected at the time of prostate cancer diagnosis. The authors describe a system of biopsy-tissue microarray construction, where the arrays contain up to 104 cores each and allow a multiplex analysis of biomarkers in the context of clinical trials.

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Journal: Journal of Proteome Research. 2011 Jan 7;10(1):85-96.

Title: Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer.

Authors: Anderson K, et al.

To detect the presence of autoantibodies, the authors used protein microarrays expressing 4,988 candidate tumor antigens with sera from patients with early-stage breast cancer, where bound IgG was measured. Twenty-eight antigens were identified as biomarkers for the early detection of breast cancer.

Journal: Lab on a Chip. 2010 Dec 21;10(24):3413-21.

Title: Sorted cell microarrays as platforms for high-content informational bioassays.

Authors: Anglin E, et al.

The authors report on surface-engineered microarrays that provide in situ cell sorting, localization, and immobilization of various subsets of human primary lymphocytes, followed by an on-chip bioassay for ionizing-radiation-induced cytogenetic damage. To demonstrate the platform, the users also integrated the cytokinesis-block micronucleus cytome assay with the microarray platform for analysis of the chromosome damage profile of specific subsets of human peripheral lymphocytes.

Journal: Molecular and Cellular Probes. 2010 Dec;24(6):387-95.

Title: An integrated bioinformatics approach to the characterization of influenza A/H5N1 viral sequences by microarray data: Implication for monitoring H5N1 emerging strains and designing appropriate influenza vaccines.

Authors: Kaewpongsri S, et al.

Seeking to characterize influenza A/H5N1 viral sequences, the authors of this paper implemented a bioinformatics approach that identified viral sequences from discovery of a sequence signature. Eight highly pathogenic H5N1 viral isolates were collected from different areas of Thailand between 2003 and 2006, and were used for analysis of H5N1 genotypic testing with a semiconductor-based oligonucleotide microarray. All H5N1 samples and H1N1, H4N8 negative controls were correctly subtyped using the method.

Journal: Methods in Molecular Biology. 2011;706:107-18.

Title: Reverse transfected cell microarrays in infectious disease research.

Authors: Konrad A, et al.

The authors describe a reverse-transfected cell microarray and demonstrate its application for the systematic analyses of single and combination effects of genes encoded by the human herpesvirus-8 on the NF-kappaB signal transduction pathway. They claim the RTCM provides an approach to investigate combination effects of viral genes on cellular functions.

Journal: Methods in Molecular Biology. 2011;703:247-63.

Title: RIP-Chip analysis: RNA-binding protein immunoprecipitation-microarray (ChIP) profiling.

Authors: Jain R, et al.

The authors have developed a high-throughput platform for the global analysis of subsets of mRNAs bound to RNA-binding proteins, called RNA-binding protein immunoprecipitation-microarray profiling. They claim the tool has revealed information about mRNP networks in the cell and the regulation of gene expression.

Journal: Nature Genetics. 2011 Jan;43(1):60-5.

Title: Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3.

Authors: Purdue M, et al.

The researchers conducted a two-stage genome-wide association study of renal cell carcinoma in 3,772 affected individuals and 8,505 controls of European background from 11 studies using a variety of Illumina BeadChips. They followed up 6 SNPs in 3 replication studies of 2,198 cases and 4,918 controls using TaqMan genotyping assays. Two loci on the regions of 2p21 and 11q13.3 were associated with RCC susceptibility below genome-wide significance.

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Journal: Nature Methods. 2011 Jan;8(1):85-90.

Title: Shotgun glycomics: a microarray strategy for functional glycomics.

Authors: Song X, et al.

The authors of this paper developed an approach called shotgun glycomics that relies on printing glycosphingolipids onto arrays. They then interrogated the arrays with cholera toxin antibodies and sera from individuals with Lyme disease to identify biologically relevant GSLs that were subsequently characterized by mass spectrometry.

Journal: Nucleic Acids Research. 2011 Jan 1;39(2):e10.

Title: A novel method for the genome-wide high resolution analysis of DNA damage.

Authors: Teng Y, et al.

DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome's integrity. This paper describes a new development based on microarray technology that uses ultraviolet light induced DNA damage as a paradigm to determine the position and frequency of DNA damage and its subsequent repair throughout the entire yeast genome.

Journal: Organic & Biomolecular Chemistry. 2010 Dec 7;8(23):5313-23.

Title: Discovery of a quorum sensing modulator pharmacophore by 3D small-molecule microarray screening.

Authors: Marsden D, et al.

The authors describe the use of a 3D, microarray-assisted screening platform to assay thousands of compounds. In this proof-of-principle study, the platform was exploited to screen a number of quorum sensing analogs.

Journal: Pathology International. 2011 Jan;61(1):1-6.

Title: Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays.

Authors: Khoo S, et al.

The authors report an assay using Agilent 4x44K microarrays for acquiring genome-wide gene expression profiles from blood spots on Guthrie cards. Due to the small amount of RNA obtained from each sample, the authors made some modifications, such as concentrating and amplifying the RNA and using a different labeling procedure. Approximately 9,000 expressed genes were detected after normalization of data, an increment of 260 percent in detection power compared with previously reported cDNA microarrays made in-house with standard procedures, the authors claimed.

Journal: PLoS Genetics. 2010 Dec 16;6(12):e1001249.

Title: Functional comparison of innate immune signaling pathways in primates.

Authors: Gilad Y,et al.

A team of University of Chicago researchers used multi-species microarrays to look at the expression of roughly 18,100 genes in human, chimpanzee, and rhesus macaque monocytes in reaction to immune challenges. Though the researchers discovered species-specific patterns, their results suggest that genes involved in general immune responses share similar patterns in all three primates.

Journal: PLoS One. 2010 Dec 7;5(12):e15004.

Title: Aptamer-based multiplexed proteomic technology for biomarker discovery.

Authors: Gold L, et al.

The authors present an aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes. The technology translates a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. The assay described in the paper measures 813 proteins with low limits of detection. The authors applied the assay to a clinical study of chronic kidney disease and identified two well-known CKD biomarkers as well as an additional 58 potential CKD biomarkers.

Journal: Prenatal Diagnostics. 2010 Dec;30(12-13):1170-7.

Title: Molecular diagnosis of Down syndrome using quantitative APEX-2 microarrays.

Authors: Oitmaa E, et al.

The authors developed the trisomy 21 arrayed primer extension-2 assay to discriminate between trisomy and euploid DNA samples by comparing the signal intensities of allelic fractions of SNPs after APEX reaction. Analysis of the T21 APEX-2 assay results revealed that 90 SNPs were sufficient for reliable discrimination between T21 and euploid DNA samples using 134 clinical samples from cultured or uncultured fetal cells.

Journal:Proceedings of the National Academy of Sciences.2011 Jan 18. [Epub ahead of print]

Title: Genetic structure and domestication history of the grape.

Authors: Myles S,et al.

To explore the effects of domestication on grape genetic diversity and gain insights into the relationships between existing grape cultivars, the team used a Vitis9KSNP array to genotype 950 accessions belonging to the domesticated V. vinifera subspecies vinifera and 59 accessions from the wild subspecies sylvestris.

Journal: Proceedings of the National Academy of Sciences. 2011 Jan 25;108(4):1591-6.

Title: A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations.

Authors: Yan X,et al.

By comparing the gene expression patterns in glioblastoma multiforme cells that are positive or negative for expression of CD133 — a transmembrane protein that has been used to identify putative cancer stem cell populations in other cancers — the team found a CD133-related gene expression profile resembling that of human embryonic stem cells.

Journal: Science. 2011 Jan 28;331(6016):435-9.

Title: The genetic landscape of the childhood cancer medulloblastoma.

Authors: Parsons D, et al.

Researchers from the US, Brazil, and Canada used a combination of whole-exome sequencing and microarray analyses to identify mutations and copy number changes in nearly two dozen pediatric brain tumors. As in adult forms of the disease, they found that a subset of these tumors contain mutations in Hedgehog or Wnt signaling pathways.

Journal: Science. 2011 Jan 14;331(6014):214-7.

Title: Genomic signatures predict migration and spawning failure in wild Canadian salmon.

Authors: Miller K,et al.

In an effort to get a clearer understanding of wild sockeye salmon death during and after their spawning migration, the researchers used a salmonid 16K cDNA microarray to measure gene expression patterns in gill tissue biopsies from salmon sampled along their migratory route, both in the ocean and at sites along the Fraser River in British Columbia. They also measured gene expression at spawning sites using a salmonid 32K cDNA array.

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.