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In Print: Feb 2, 2010


Microarray Papers of Note Published January 2010

Journal: Analytical Biochemistry. 2010 Jan 1;396(1):30-5.

Title: Quantitative label-free screening for antibodies using scattering biophotonic microarray imaging.

Authors: Olkhov R, et al.

This paper described a biophotonic array based on gold nanoparticles functionalized with antigen proteins that can be used to determine the concentrations of the respective antibodies in solution. Four proteins — fibrinogen, bovine serum albumin, transferrin, and C-reactive protein — were used to construct a test array with the assay repeated a number of times. The antibody-antigen association and dissociation rate constants were determined for the antibody assays from a series of calibration experiments. The label-free determination of the unknown antibody concentrations was performed using two related kinetic analyses to assess the sensitivity of the assay.

Journal: Applied Microbiology and Biotechnology. 2010 Jan 29. [Epub ahead of print]

Title: Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing.

Authors: Borneman A, et al.

Oenococcus oeni, a bacterium used during winemaking, is an industrial bacterium species where large numbers of strains show significant differences in commercially important industrial phenotypes. To better understand these phenotypic differences, the authors of this paper mapped the genomic content of 10 wine strains of O. oeni using array-based comparative genome hybridization. These strains composed a genomically diverse group where large sections of the reference genome were often absent from individual strains. To place the aCGH results in context, whole-genome sequence was obtained for one of these strains and compared with two previously sequenced, unrelated strains. The authors concluded that the genome of O. oeni is likely to be much larger than that which is present in any single strain and it is these strain-specific regions that are likely to be responsible for differences in industrial phenotypes.

Journal: Biosensors and Bioelectronics. 2010 Jan 4. [Epub ahead of print]

Title: Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.

Authors: Ozkumur E, et al.

The authors propose a method for the direct detection of DNA hybridization on microarrays. Optical interferometry is used for label-free sensing of biomolecular accumulation on glass surfaces, enabling dynamic detection of interactions. Capabilities of the method are demonstrated by high-throughput sensing of solid-phase hybridization of oligonucleotides. For example, the hybridization of surface immobilized probes with 20 base pair-long target oligonucleotides was detected by comparing the label-free microarray images taken before and after hybridization, according to the authors. Through dynamic data acquisition during denaturation by washing the sample with low ionic concentration buffer, melting of duplexes with a single-nucleotide mismatch was distinguished from perfectly matching duplexes with a high confidence interval.

Journal: Biostatistics. 2010 Jan;11(1):164-75. Epub 2009 Oct 15.

Title: PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.

Authors: Greenman C, et al.

Algorithms used to extract genotypes and copy number variation function optimally for diploid genomes usually associated with inherited disease, the authors of this paper state. However, cancer genomes are aneuploid in nature, which leads to systematic errors when using these techniques. The authors therefore created a preprocessing transformation and hidden Markov model algorithm for use in cancer studies. The algorithm produces genotype classification, specification of regions of loss of heterozygosity, and absolute allelic copy number segmentation.

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Journal: Biotechnology and Bioengineering. 2010 Jan 12. [Epub ahead of print]

Title: Three-dimensional cell culture microarray for high-throughput studies of stem cell fate.

Authors: Fernandes T, et al.

The authors developed a three-dimensional cellular microarray platform to track stem cell fate and quantify specific stem cell markers. This platform consists of a miniaturized 3D cell culture array on a functionalized glass slide for spatially addressable high-throughput screening. A microarray spotter was used to deposit cells onto a modified glass surface to yield an array consisting of cells encapsulated in alginate gel spots. A method based on an immunofluorescence technique scaled down to function on a cellular microarray was also used to quantify specific cell marker protein levels in situ. The authors' results revealed that this platform is suitable for studying the expansion of mouse embryonic stem cells as they retain their pluripotent and undifferentiated state.

Journal: BMC Bioinformatics. 2010 Jan 25;11(1):49.

Title: M3G: maximum margin microarray gridding.

Author: Bariamis D, et al.

The authors of this paper discuss M3G, a method for automatic gridding of cDNA microarray images based on the maximization of the margin between the rows and the columns of the spots. Initially, the microarray image rotation is estimated and then a pre-processing algorithm is applied for a rough spot detection. In order to diminish the effect of artifacts, only a subset of the detected spots is selected by matching the distribution of the spot sizes to the normal distribution, according to the authors. Then, a set of grid lines is placed on the image in order to separate each pair of consecutive rows and columns of the selected spots. The optimal positioning of the lines is determined by maximizing the margin between these rows and columns by using a maximum margin linear classifier, effectively facilitating the localization of the spots.

Journal: BMC Genomics. 2010 Jan 5;11(1):7.

Title: Decoding pooled RNAi screens by means of barcode tiling arrays.

Authors: Boettcher M, et al.

The authors describe a method to decode pooled RNAi screens called barcode tiling array analysis, and demonstrate how the approach can be used to quantify the abundance of individual shRNAs from a pool. To do this, they synthesized DNA microarrays with six overlapping long tiling probes complementary to each molecular barcode sequence associated with every shRNA expression construct. By analyzing dilution series of expression constructs, they showed how the approach allows quantification of shRNA abundance from a pool and how it clearly outperforms the commonly used analysis via the shRNA's half hairpin sequences. They also demonstrated how barcode tiling arrays can be used to predict anti-proliferative effects of individual shRNAs from pooled negative selection screens.

Journal: BMC Genomics. 2010 Jan 7;11(1):15.

Title: Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments.

Authors: Celton M, et al.

In this study, the authors evaluated 12 different methods for imputing missing microarray expression values, and their influence on the quality of gene clustering. They used several datasets, both kinetic and non-kinetic experiments from yeast and human, in their evaluation. They found that an EM_array algorithm approach is an efficient method for restoring the missing expression gene values, with a lower estimation error level. Still, the presence of missing values even at a low rate is a major factor of gene cluster instability, they noted.

Journal: European Journal of Dermatology. 2010 Jan-Feb;20(1):54-61.

Title: Allergen microarrays: a novel tool for high-resolution IgE profiling in adults with atopic dermatitis.

Authors: Ott H, et al.

The authors of this study aimed to evaluate the use of allergen microarrays in the diagnostic workup of adults with atopic dermatitis and to compare this approach with a conventional method of specific IgE measurement. In sera of 40 atopic adults, sIgE levels detected by microarray analysis were correlated with the results of an established fluorescence enzyme immunoassay. In an additional 20 patients with AD, individual sIgE recognition patterns were established by microarray analysis and evaluated with regard to clinical features of AD. The allergen microarray and FEIA results were significantly correlated, especially if recombinant allergens were employed, according to the authors.

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Journal: Glycobiology. 2010 Jan;20(1):13-23.

Title: Analysis of differential expression of glycosyltransferases in healing corneas by glycogene microarrays.

Authors: Saravanan C, et al.

In this study, a glycogene microarray was used to identify the differentially expressed glycosylation-related genes in healing mouse corneas. Of approximately 2,000 glycogenes on the array, the expression of 11 glycosytransferase and glycosidase enzymes was found to be upregulated and that of 19 was downregulated more than 1.5-fold in healing corneas compared with the normal, uninjured corneas. Results of glycogene microarray data were confirmed by qRT-PCR and lectin blot analyses.

Journal: Journal of Microbiology Methods. 2010 Jan 14. [Epub ahead of print]

Title: Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD).

Authors: Curran T, et al.

An array was constructed with DNA PCR product probes targeting species-specific functional genes of nine clinically significant respiratory pathogens. The microarray was compared with real-time PCR from 14 sputum specimens from COPD patients. All of the samples positive for bacterial species in real-time PCR were also positive for the same bacterial species using the microarray. This study shows that a microarray using PCR probes is a potentially useful method to monitor the populations of bacteria in respiratory specimens and can be tailored to specific clinical needs such as respiratory infections of particular patient populations, including patients with cystic fibrosis and bronchiectasis, according to the authors.

Journal: Journal of Virological Methods. 2010 Jan;163(1):17-24.

Title: A low density oligonucleotide microarray for the detection of viral and atypical bacterial respiratory pathogens.

Authors: Cannon G, et al.

The authors of this paper developed a PCR-based, low-density oligonucleotide microarray for the detection of 16 viral and two atypical bacterial pathogens associated with acute respiratory tract infections. The performance of the array-based analysis exhibited comparable sensitivities and specificities to multiplex real-time reverse transcription polymerase chain reactions, confirming the potential diagnostic utility of the method. The authors argue that their study demonstrates that microarray technology provides a viable alternative to conventional serological-based approaches and multiplex PCR for pathogen identification in acute respiratory tract infections.

Journal: Journal of Virological Methods. 2010 Jan;163(1):57-67.

Title: Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets.

Authors: Grover V, et al.

A microarray system is described for an unbiased detection of plant viruses using both short and long oligonucleotide probes. The assay involves amplification of target nucleic acid using random primers followed by in vitro transcription whose cRNA product is labeled chemically, fragmented and used as target for hybridization. Initial optimization tests with turnip-vein clearing virus and cauliflower mosaic virus showed increased hybridization efficiency with shorter cDNA targets and longer probes, according to the authors. The system was then validated in pure and mixed samples by detection of three tymovirus species: asclepias asymptomatic virus, kennedya yellow mosaic virus, and turnip yellow mosaic virus. The method could detect sequence variants with about 75 percent or higher sequence identity, according to the paper, indicating the possible use of the approach for virus discovery.

Journal: Mutation Research. 2010 Jan 18. [Epub ahead of print]

Title: Genome-wide analysis of chromosomal alterations in patients with esophageal squamous cell carcinoma exposed to tobacco and betel quid from high-risk area in India.

Authors: Chattopadhyay I, et al.

In this study, Affymetrix 10K SNP arrays were used to evaluate genomic alterations in 20 pairs of matched germ-line and tumor DNA obtained from patients with esophageal squamous cell carcinoma from a high-risk area of India where tobacco, betel quid, and alcohol use are widespread. Twenty-two amplified regions and 16 deleted regions identified across chromosomal arms were biologically relevant. These unique copy number alteration profiles should be taken into consideration when developing biomarkers for the early detection of ESCC in high-risk areas of India in association with tobacco and betel quid use.

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Journal: Nature Biotechnology. 2010 Jan;28(1):25-7.

Title: High-density resequencing DNA microarrays in public health emergencies.

Authors: Berthet N, et al.

The authors describe the use of random non-PCR–based nucleic acid amplification and high-density resequencing DNA microarrays to rapidly identify reassorted influenza A virus strains of swine origin. To do so, they designed a PathogenID microarray with a total of 126 viral sequences from a whole range of viruses. The array was engineered to detect and describe four genes in order to type and subtype influenza viruses from a large diversity of natural and permanent hosts — humans, birds, horses and pigs — with a minimum of sequences tiled on the array. The authors believe the array can be used to monitor changes in influenza virus strains during public outbreaks.

Journal: PLoS One. 2010 Jan 21;5(1):e8820.

Title: ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

Authors: Akkers R, et al.

The authors report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. A whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5' ends of genes. These regions represent promoters as shown by binding of TBP, a key transcription initiation factor, the authors state in the paper. Both designs can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos.

Journal: PLoS Biology. 2010 Jan 26. [Epub ahead of print]

Title: Rare variants create synthetic genome-wide associations.

Authors: Dickson S, et al.

Genome-wide association studies have now identified at least 2,000 common variants that appear associated with common diseases or related traits, the authors of this paper state. It is generally thought that the associated markers reflect the effect of a nearby common causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites. The authors propose as an alternative explanation that variants much less common than the associated one may create synthetic associations by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are a possibility, they have never been systematically explored as a possible explanation for GWAS findings, according to the authors. In the paper, they used computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. They claim that it is "inevitable" that these associations account for many of the signals reported in GWAS. The authors also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations.

Journal: Proceedings of the National Academy of Sciences. 2010 Jan 8. [Epub ahead of print]

Title: Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.

Authors: Gresham D, et al.

By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, the authors of this paper studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions. They found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature and the temperature at which the hybridization reaction is performed. This relationship can be exploited through the design of microarrays containing probes of equal by varying the length of probes. The authors also demonstrated the use of such a microarray.

Journal: Science. 2010 Jan 1;327(5961):78-81.

Title: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

Authors: Drmanac R, et al.

The authors describe a genome-sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe-anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. In this project, the authors sequenced three human genomes with the platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The cost of $4,400 for sequencing consumables and scalability of the platform enables complete human genome sequencing for the detection of rare variants in large-scale genetic studies, according to the authors.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.