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In Print: Mar 16, 2010


Microarray Papers of Note Published February 2010

Journal: BMC Bioinformatics. 2010 Feb 24;11(1):105.

Title: Free energy estimation of short DNA duplex hybridizations.

Authors: Tulpan D, et al.

The authors of this study present a quantitative comparison of the similarities and differences among four published DNA/DNA duplex free energy calculation methods and an extended nearest neighbor model for perfect matches based on triplet interactions. They concluded that no statistically significant differences exist among free energy approximations obtained with four publicly available and widely used programs, when benchmarked against a collection of 695 pairs of short oligos collected and curated by the authors of this work based on 29 publications.

Journal: BMC Genomics. 2010 Feb 24;11(1):134.

Title: Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles.

Authors: Kitchen R, et al.

The authors exploited the design of the Illumina BeadChip platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridizations of universal human reference RNA and duplicate hybridizations of primary breast tumor samples from a clinical study. They detected a clear batch-specific bias in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalization techniques. However, when mean-centering or empirical Bayes batch-correction methods were applied to the data, inter-batch variation in the UHRR and clinical samples were reduced. The authors suggest that other researchers take such variation into account in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.

Journal: BMC Genomics. 2010 Feb 26;11(1):142. [Epub ahead of print]

Title: TobEA: an atlas of tobacco gene expression from seed to senescence.

Authors: Edwards K, et al.

The authors of this paper designed an Affymetrix-manufactured tobacco expression microarray from a set of over 40,000 unigenes and used it to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas, or TobEA. According to the authors, TobEA provides a snapshot of transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. The authors believe that TobEA can be used to identify gene targets for both fundamental and applied scientific applications in tobacco.

Journal: Journal of the American Medical Association. 2010 Feb 10;303(6):535-43.

Title: Age- and sex-specific genomic profiles in non-small cell lung cancer.

Authors: Mostertz W, et al.

The authors of this paper identified age- and sex-specific gene expression profiles corresponding to higher or lower risk of cancer recurrence in non-small cell lung cancer patients. The researchers focused on combining gene expression profiles with other clinically relevant data — specifically a patient's age and sex — to find pathways involved in cancer recurrence risk in these subgroups. To do this, the team combined gene expression data for 787 NSCLC tumors from four previously published studies. Most of the data was generated using the Affymetrix Human Genome U133A GeneChip, though the researchers used Chip Comparer to convert U95A GeneChip data to U133A data for 125 samples before analyzing the results. When they looked at the gene expression patterns in four patient groups — one containing individuals younger than 70 years old, another containing those who were 70 years old or older, a group of male patients, and a group of female patients — they found distinct gene expression signatures within these sub-groups.

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Journal: Journal of Microbiology Methods. 2010 Feb 19. [Epub ahead of print]

Title: Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis.

Authors: Salonen A, et al.

The authors compared four widely used methods for fecal DNA extraction, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal, and human DNA was first quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the human intestinal tract chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects. A comparative analysis of mechanical and enzymatic methods showed that despite their similarity, mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria.

Journal: Journal of Pathology. 2010 Feb;220(3):338-47.

Title: Prognostic relevance of DNA copy number changes in colorectal cancer.

Authors: Poulogiannis G, et al.

In a study of 109 colorectal cancers, the authors of this paper identified DNA copy number aberrations using a comparative genomic hybridization array covering the entire genome at an average interval of less than 1 megabase. Four patterns were revealed by unsupervised clustering analysis, one of them associated with significantly better prognosis than the others. This group contained tumors with short, dispersed, and relatively few regions of copy number gain or loss. The good prognosis of this group was not attributable to the presence of tumors showing microsatellite instability. Supervised methods were employed to determine those genomic regions where copy number alterations correlate significantly with multiple indices of aggressive growth. Multivariate analysis identified DNA copy number loss at 18q12.2, harboring a single gene, BRUNOL4, which encodes the Bruno-like 4 splicing factor, as an independent prognostic indicator. The data show that the different patterns of DNA copy number alterations in primary tumors reveal prognostic information and can aid identification of novel prognosis-associated genes, according to the authors.

Journal: Journal of Pediatrics. 2010 Feb 5. [Epub ahead of print]

Title: Array comparative genomic hybridization as a diagnostic tool for syndromic heart defects.

Authors: Breckpot J, et al.

The authors of this paper used array CGH to analyze 150 patients with a syndromic congenital heart defect of unknown cause at 1 megabase resolution. Twenty nine of the patients, with normal results on 1 Mb aCGH, underwent re-analysis with a 244,000-oligonucleotide microarray. Using a logistic regression model, the authors assessed the predictive value of patient characteristics for causal imbalance detection. They also constructed an algorithm to evaluate the causality of copy number variants. With 1 Mb aCGH, they detected 43 structural variants not listed as clinically neutral polymorphisms, 26 of which were considered to be causal. A systematic comparison of the clinical features of these 26 patients to the remaining 124 patients revealed dysmorphism as the only feature with a significant predictive value for reaching a diagnosis with 1 Mb aCGH. With higher-resolution analysis in 29 patients, 75 variants not listed as clinically neutral polymorphisms were detected, two of which were considered to be causal. The authors concluded that molecular karyotyping yields an etiological diagnosis in at least 18 percent of patients with a syndromic CHD. They stated that higher-resolution evaluation results in an increasing number of variants of unknown significance.

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Journal: Journal of Virological Methods. 2010 Feb;163(2):445-51.

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 simultaneously a broad spectrum of 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 were 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.

Journal: Journal of Virological Methods. 2010 Feb;163(2):269-75.

Title: Development and clinical evaluation of a microarray for hepatitis C virus genotyping.

Authors: Park J, et al.

To identify hepatitis C virus genotypes, the authors of this paper designed an oligonucleotide array using 15 probes from the 5'-untranslated region. Reverse transcription was combined with asymmetric PCR to obtain an amplified product for hybridization without the need for a denaturation step. In addition, a biotin-labeled PCR product and streptavidin-Cy3 conjugate were cohybridized simultaneously. Clinical sera from Korean and French patients were then used to compare the chip results with those obtained by direct sequencing. The chip showed 100 percent accuracy for the commercial panels. Agreement levels between the chip and sequencing results at the genotype and subgenotype levels were 100 percent and 94.6 percent, respectively.

Journal: Lab on Chip. 2010 Feb 7;10(3):379-83.

Title: Simple benchtop patterning of hydrogel grids for living cell microarrays.

Authors: Zawko S, et al.

The authors describe a method for manufacturing substrates using woven nylon mesh to micropattern three-dimensional alginate hydrogel grids on glass slides. By using nylon mesh, the authors claim to have eliminated requirements for lithography, clean room equipment, and microarray printers to generate microarray patterns. In the paper, they demonstrated that glass slides micropatterned with hydrogel grids guide the attachment of single fibroblast cells and Schwann cell clusters in microarrays. The fibroblast arrays consisted of 70 micrometer square compartments at a density of 21,000 compartments per cm2. The Schwann cell arrays consisted of 100 micrometer square compartments at a density of 6,000 per cm2.

Journal: Lab on Chip. 2010 Feb 7;10(3):372-8.

Title: Multilayers of hydrogels loaded with microparticles: a fast and simple approach for microarray manufacturing.

Authors: Bally M, et al.

This paper describes a method of microarray creation by cutting stacked layers of biofunctionalized polystyrene particle layers embedded in a permeable agarose matrix. The three-dimensional constructs were obtained by consecutive dipping steps in a pre-gel solution. Model binding assays for the detection of rabbit and mouse IgG were performed as a proof of concept using a fluorescence microscope for readout. The limits of detection were in the low picomolar range for the sandwich assay while 1 IgG out of 50,000 background proteins could be detected in a reverse phase assay, according to the authors.

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Journal: Molecular and Cellular Proteomics. 2010 Feb 16. [Epub ahead of print]

Title: Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies.

Authors: Schröder C, et al.

The authors present protocols for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In an initial study, they demonstrated the applicability of the protocols to proteins derived from urine samples. They identified differences between urine samples from pancreatic cancer patients and healthy individuals and between genders.

Journal: Nature. 2010 Feb 18;463(7283):893-8.

Title: Signatures of mutation and selection in the cancer genome.

Authors: Bignell G, et al.

The authors of this study used microarray-based experiments and targeted sequencing to identify signatures of selection and mutation in nearly 750 cancer cell lines. They found 2,428 somatic homozygous deletions, including deletions affecting tumor suppressor genes as well as deletions occurring at fragile sites in the genome. By exploiting structural signatures in the genome, the team was able to tease apart deletions involving cancer genes from those at fragile sites. To do this, the researchers used Affymetrix SNP 6.0 arrays to genotype and find copy number changes in 746 publicly available cancer cell lines, mapping breakpoints coinciding with the edges of amplifications and deletions and losses of heterozygosity. They then surveyed the locations of homozygous deletions, integrated this data with sequence and expression information on dozens of known cancer genes, and came up with structural signatures for differentiating between cancer gene deletions and deletions at fragile sites.

Journal: Nature. 2010 Feb 18;463(7283):899-905.

Title: The landscape of somatic copy-number alteration across human cancers.

Authors: Beroukhim R, et al.

The authors of this study looked at more than two dozen cancers, mapping the copy number changes within the cancer genomes. In the process, they found an unexpectedly high amount of overlap between copy number changes in various kinds of cancer. Specifically, the authors used the Affymetrix 250 K Sty array to assess 2,509 cancer samples. They then combined this with publicly available data on another 622 samples. Together, these 3,131 samples represented 26 cancer types. When the team compared copy number profiles in the cancer samples with those in nearly 1,500 normal tissue samples, they turned up 75,500 gains and 55,101 losses in the cancer genomes. Many of these somatic copy number changes affected known tumor suppressor genes or genes involved in cell cycle related pathways, though genes involved in apoptosis were also well represented. Numerous copy number alterations overlapped between different cancer types. The authors suggested that it may eventually be possible to glean insights from the pattern of genomic alterations in a tumor rather than just where it originates in the body.

Journal: Nature Genetics. 2010 Mar;42(3):234-9.

Title: Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions.

Authors: Van Deerlin V, et al.

By performing a genome-wide association study involving post-mortem tissue samples from more than 500 individuals with so-called frontotemporal lobar degeneration, these researchers pinpointed several SNPs in a linkage disequilibrium block in a chromosome 7 region called 7p21. Through a series of validation and follow-up experiments, they found these risk SNPs fall in and around a gene called TMEM106B, affecting its expression in brain and other tissues.

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Journal: Nucleic Acids Research. 2010 Feb 21. [Epub ahead of print]

Title: Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments.

Authors: Jourdren L, et al.

The authors describe Teolenn, a universal probe design workflow developed with a customizable module framework that allows fixed or variable length oligonucleotide generation. The software also provides quality scores for each of the designed probes. In order to assess the relevance of these scores, the authors performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. The authors show that their scoring pipeline correlates with signal quality for 97.2 percent of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities.

Journal: Nucleic Acids Research. 2010 Feb 25. [Epub ahead of print]

Title: Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays.

Authors: Lee C, et al.

The authors of this paper have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software EvolSTAR is also described. EvolSTAR uses neighborhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries, according to the authors. They believe their kit is an efficient large-scale evolutionary biosurveillance tool.

Journal: PLoS One. 2010 Feb 23;5(2):e9366.

Title: Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset.

Authors: Gamazon E, et al.

The authors mapped the 1000 Genomes Project genotypic data to the Affymetrix GeneChip Human Exon 1.0ST array, which had been used in their previous studies and for which gene expression data had been made publicly available. They also evaluated the potential impact of these SNPs on the differentially spliced probesets they had identified previously. Though the 1000 Genomes Project data allowed a comprehensive survey of the SNPs in this particular array, they argued that the same approach can be applied to other microarray platforms. They also presented a detailed catalog of SNP-containing probesets and transcript clusters that can be considered in evaluating findings using the exon array as well as benefit the design of follow-up experiments and data re-analysis.

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