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In Print: May 5, 2009

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Journal: The Analyst. 2009 Apr;134(4):800-4.
Title: Magnetic bead-based DNA hybridization assay with chemiluminescence and chemiluminescent imaging detection.
Authors: H Li; Z He

Abstract: This paper describes chemiluminescence and CL-imaging methods developed for a magnetic bead-based DNA hybridization assay. The assay relies on the high sensitivity and long stable light signal of the CL system in which horseradish peroxidase catalyzes the luminol-H(2)O(2) reaction with para-iodophenol as the enhancer. In the described protocol, a sandwich DNA hybridization is performed by mixing the target DNA with the magnetic bead-captured DNA and the biotinylated reporter DNA, followed through the biotin-streptavidin reaction with conjugated HRP, and then the conjugated HRP is determined by the CL system. The authors claim the proposed CL protocol is suitable for the detection of sequence-specific DNA related to the avian influenza A H1N1 virus at levels as low as 10 amol, and the CL imaging detection has a similar sensitivity.


Journal: Analytical Biochemistry. 2009 Apr 15;387(2):150-61.
Title: Peptide microarrays for detailed, high-throughput substrate identification, kinetic characterization, and inhibition studies on protein kinase A.
Authors: R Hilhorst; L Houkes; A van den Berg; R Ruijtenbeek

Abstract: This paper discusses a microarray-based mix-and-measure, nonradioactive multiplex method with real-time detection used for substrate identification, assay development, assay optimization, and kinetic characterization of protein kinase A. The peptide arrays in the study included either up to 140 serine/threonine-containing peptides or a concentration series of a smaller number of peptides. According to the authors, data quality was high, variation in assay conditions and reagent consumption was reduced, and assay development was accelerated because phosphorylation kinetics was monitored simultaneously on four, 12, or 96 arrays. Ultimately, the authors showed that the technology can monitor kinase activity in a multiplex setting such as a cell or tissue lysate and allow fast identification of peptide substrates for serine/threonine kinases that are still uncharacterized.


Journal: Applied Environmental Microbiology. 2009 Apr 10. [Epub ahead of print]
Title: High-throughput quantitative analysis of human intestinal microbiota with phylogenetic microarray.
Authors: O Paliy; H Kenche; F Abernathy; S Michail

Abstract: The aim of this study was to develop a custom microarray to identify hundreds of intestinal bacterial species. The authors used the Entrez nucleotide database to compile a dataset of bacterial 16S rDNA sequences isolated from human intestinal and fecal samples. The identified sequences were clustered into separate phylo-species groups. Representative sequences from each phylo-species were used to develop a microbiota microarray based on the Affymetrix GeneChip platform. The designed microbiota array contains probes to 775 different bacterial phylo-species. Using the developed microarray, fecal samples from two healthy children and two healthy adults were analyzed for bacterial presence. Between 227 and 232 species were detected in fecal samples from children, whereas 191 to 208 species were found in adult stools. The array revealed putative differences between gut microbiota of healthy children and adults.


Journal: Bioinformatics. 2009 Apr 1;25(7):861-7.
Title: A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs, and analysis methods.
Authors: H Bengtsson; A Ray; P Spellman; T Speed

Abstract: The expansion of whole-genome copy number studies has created a demand for increased precision and resolution of CN estimates, according to the authors. In response, they propose in this paper a single-sample multi-source normalization that brings full-resolution CN estimates to the same scale across sources. The normalized CNs are such that for any underlying CN level, their mean level is the same regardless of the source, which make them better suited for being combined across sources. Such existing segmentation methods may be used to identify aberrant regions, the authors write. The authors use microarray-based CN estimates from the Cancer Genome Atlas project to illustrate and validate the method. They conclude that it is possible to combine CNs from multiple sources such that the resolution becomes effectively larger, and argue that when multiple platforms are combined, they also enhance the genome coverage by complementing each other in different regions.

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Journal: BMC Genomics. 2009 Apr 8;10(1):153. [Epub ahead of print]
Title: Learning from microarray interlaboratory studies: measures of precision for gene expression.
Authors: D Duewer; W Jones; L Reid; M Salit

Abstract: This collaborative study aimed to estimate a variety of gene-expression measurement precision metrics: repeatability, several flavors of intermediate precision, and reproducibility. Beginning with three 2004 Expression Analysis Pilot Proficiency Test collaborative studies, each with 13 to 16 participants, triplicate microarray measurements on each of two reference RNA pools were provided. The authors evaluated the metrological precision figures of merit for individual microarray signal measurement, building from calculations appropriate to single measurement processes, such as technical replicate expression values for individual probes on a microarray, to the estimation and display of precision functions representing all of the probes in a given platform. The authors conclude that with only modest extensions of International Standard Organization metrics, the established metrological framework can be used to characterize the measurement performance of microarray and other highly-multiplexed systems.


Journal: BMC Genomics. 2009 Apr 16;10(1):161. [Epub ahead of print]
Title: Estimating accuracy of RNA-Seq and microarrays with proteomics.
Authors: X Fu; N Fu; S Guo; Z Yan; Y Xu; H Hu; C Menzel; W Chen; Y Li; R Zeng; P Khaitovich

Abstract: In this study, the authors evaluated the relative accuracy of microarrays and transcriptome sequencing, RNA-seq, using a third methodology: proteomics. The authors found that RNA-seq provides a better estimate of absolute expression levels, and is the "technique of choice for studies that require accurate estimation of absolute transcript levels."


Journal: Cancer Research. 2009 Apr 1;69(7):2950-5.
Title: Associations between selected biomarkers and prognosis in a population-based pancreatic cancer tissue microarray.
Authors: M Takikita; S Altekruse; C Lynch; M Goodman; B Hernandez; M Green; W Cozen; M Cockburn; M Sibug Saber; M Topor; C Zeruto; B Abedi-Ardekani; M Reichman; S Hewitt

Abstract: Tissues from US Surveillance, Epidemiology, and End Results registries were used to build a tissue microarray of 161 pancreatic tumors, including 113 resections and 48 biopsies. Proportional hazard models were adjusted for age, race, sex, stage, time-period of diagnosis, and treatment. Associations were examined between over a dozen markers and survival time from diagnosis. After adjusting for covariates, borderline statistically significant associations were seen between expression of each of the three mucins surveyed and shorter survival time. The tissue microarray is available for evaluating other biomarkers and the authors claim that issue-based surveillance can be used to monitor tumor histology in populations and facilitate applied research.


Journal: Genetics in Medicine. 2009 Apr 10. [Epub ahead of print]
Title: Impact of genotype-first diagnosis: the detection of microdeletion and microduplication syndromes with cancer predisposition by aCGH.
Authors: S Adams; J Coppinger; S Saitta; Y Stroud; M Kandamurugu; Z Fan; B Ballif; L Shaffer; B Bejjani

Abstract: Using microarray-based comparative genomic hybridization, the authors tested 18,437 individuals with indications such as developmental disabilities and congenital anomalies. They identified 34 individuals with DNA copy number gains or losses that encompassed gene regions associated with recognized genetic conditions with an increased risk for cancer. Three of the 34 individuals had a previously abnormal cytogenetic study, which microarray-based comparative genomic hybridization confirmed and further characterized. Seven of the 34 individuals either had the correct disease specified in the clinical indication for study or had clinical features highly indicative of that syndrome. The remaining 24 patients had indications for study that were not specific to the diagnosed syndrome, such as developmental delay or dysmorphic features. The authors conclude that microarray-based comparative genomic hybridization has led to the opportunity to optimize medical management and outcome.


Journal: Genetics in Medicine. 2009 Apr;11(4):232-40.
Title: Targeted comparative genomic hybridization array for the detection of single- and multiexon gene deletions and duplications.
Authors: M Tayeh; E Chin; V Miller; L Bean; B Coffee; M Hegde

Abstract: The authors developed a high-resolution comparative genomic hybridization array to detect single- and multiexon deletions and duplications in a large set of genes on a single microarray, using the Roche NimbleGen 385K array with an exon-centric design. They conclude that the comparative genomic hybridization arrays can be adopted readily by clinical molecular diagnostic laboratories as an approach for the detection of single- and multi-exon deletions or duplications, particularly in cases where direct sequencing fails to identify a mutation.

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Journal: Genomics. 2009 Apr;93(4):343-9.
Title: Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms.
Authors: C McHale; L Zhang; Q Lan; G Li; A Hubbard; M Forrest; R Vermeulen; J Chen; M Shen; S Rappaport; S Yin; M Smith; N Rothman

Abstract: The authors used two microarray platforms to identify global gene-expression changes associated with well-characterized occupational benzene exposure in the peripheral blood mononuclear cells of a population of shoe-factory workers. Differential expression of 2,692 genes on the Affymetrix platform, and 1,828 genes on the Illumina platform, was found and the concordance was 50 percent, with similar expression ratios among the concordant genes. The authors conclude that the two-platform approach allows for changes in the PBMC transcriptome of benzene-exposed individuals to be identified.


Journal: Nucleic Acids Research. 2009 Apr;37(6):1726-39.
Title: An evaluation of custom microarray applications: the oligonucleotide design challenge.
Authors: S Lemoine; F Combes; S Le Crom

Abstract: The increase in feature resolution and the availability of multipack formats from microarray providers has opened the way to various custom genomic applications. However, oligonucleotide design and selection remains a bottleneck of the microarray workflow, the authors claim. In this paper, they review the oligonucleotide design field to help users make their choice. Specifically, they conducted a comparative evaluation of the available design tools based on a set of criteria including: ease of installation, user-friendly access, the number of parameters, and settings available. In a second step, they submitted two real cases to a selection of programs. Finally, the authors used a set of tests for the in silico benchmark of the oligo sets obtained from each type of software. The authors conclude that oligo design software must be selected according to the goal of the scientist, depending on factors such as the organism used, the number of probes required, and their localization on the target sequence.


Journal: Pathology International. 2009 Apr;59(4):218-28.
Title: Copy number estimation algorithms and fluorescence in situ hybridization to describe copy number alterations in human tumors.
Authors: M Suzuki; K Nagura; H Igarashi; H Tao; Y Midorikawa; Y Kitayama; H Sugimura

Abstract: Platforms of high-resolution genetic analysis of human tumors have become popular, and several copy number estimation algorithms have been applied to the data generated by SNP microarrays. Although comparisons have been made between several different platforms or methodologies, there has never been a robust comparison of different copy number estimation algorithms, and the validity of the estimations in comparison with multiple fluorescence in situ hybridization data in tumors has rarely been addressed, the authors write. In this study, a dataset that the Affymetrix 250K Nsp array generated in two cancer cases was used to compare the two algorithms for estimating copy number alterations: the genotyping microarray-based copy number variation analysis algorithm and the copy number analyzer for the Affymetrix GeneChip mapping algorithm. The authors found "considerable differences" between the estimations by these two algorithms, and though both yielded "highly-consistent data with fluorescence in situ hybridization results, the latter was "more stringent" for detecting loss.


Journal: PLoS Genetics. 2009 Apr;5(4):e1000449.
Title: Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions.
Authors: G Freckleton; S Lippman; J Broach; S Tavazoie

Abstract: The authors developed a strategy for microarray-based profiling of phage-display selection that allows a survey of an organism's proteome for sequence-specific interactions with putative DNA regulatory elements. The application of the strategy to a variety of known yeast transcription-factor binding sites successfully identified the cognate TF from the background of a complex whole-proteome library, the authors write. They argue that MaPS technology should enable "rapid and proteome-scale" studies of bimolecular interactions within transcriptional networks.

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Journal: Proceedings of the National Academy of Sciences. 2009 Apr 2. [Epub ahead of print]
Title: High-throughput, high-accuracy array-based resequencing.
Authors: J Zheng; M Moorhead; L Weng; F Siddiqui; V Carlton; J Ireland; L Lee; J Peterson; J Wilkins; S Lin; Z Kan; S Seshagiri; R Davis; M Faham

Abstract: To identify rare alleles missed by genome-wide association studies, the authors developed a high-throughput, high-accuracy resequencing technology based on the Affymetrix platform. The authors' pipeline consists of target amplification from genomic DNA, followed by allele enrichment to generate pools of purified variant or nonvariant) DNA and ends with interrogation of purified DNA on resequencing arrays. The authors used this pipeline to resequence approximately 5 Mb of DNA on three arrays corresponding to the exons of 1,500 genes in 473 samples. In total, more than 2,350 Mb were sequenced. In the context of this large-scale study, they obtained a false positive rate of approximately 1 in 500,000 base pairs and a false negative rate of approximately 10 percent. BioArray News spoke with co-author Malek Faham about the new method in March (see BAN 3/31/2009).


Journal: Proteomics. 2009 Apr;9(8):2098-107.
Title: Detection of allergen-specific immunoglobulins by microarrays coupled to microfluidics.
Authors: M Cretich; G Di Carlo; C Giudici; S Pokoj; I Lauer; S Scheurer; M Chiari

Abstract: The authors report an improved microarray coupled to microfluidics for the detection of allergen-specific immunoglobulin E. The signal intensity for IgE detection in serum has been improved by using glass slides coated with a novel poly[DMA-co-NAS] brush copolymer that is able to immobilize allergens in their native conformation and by carrying out the incubation step in dynamic conditions. The assay was performed in a microcell using a software-controlled fluidic processor, to bring assay reagents on the surface of the array. Microfluidics turns the binding between serum immunoglobulins and immobilized allergens from a diffusion-limited to a kinetic-limited process by ensuring a mixing of serum samples on the surface of the microarray. As a result of this, the binding of high affinity IgE antibodies is enhanced whereas that of low affinity IgG antibodies, which are present at higher concentration, is impaired, the authors state.


Journal: Veterinary Parasitology. 2009 Apr 6;161(1-2):76-87.
Title: Sequential microarray to identify timing of molecular responses to Haemonchus contortus infection in sheep.
Authors: A Rowe; C Gondro; D Emery; N Sangster

Abstract: Anthelmintics are currently the most common method of worm control, and the emergence of worms with multiple-drug resistance and issues of residues in the food chain make alternative parasite control measures a priority, according to the paper's abstract. To develop methods for controlling Haemonchus contortus such as genetic selection of resistant sheep, a trial was undertaken using sheep surgically implanted with abomasal fistulas to enable sequential biopsy of the abomasal mucosa during trickle infection with two strains of H. contortus. Microarray results from biopsies taken on the same day in different groups were combined and compared between different biopsy dates to observe differential gene transcription over time. The microarray data were validated in silico by comparison with data from other gene-transcription studies and with phenotypic data such as the response by gammadelta T cells and immunoglobulins to H. contortus. As the trial progressed, the immunoglobulin genes surveyed in the study became strongly upregulated, the authors reported.

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