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In Print: Jul 20, 2010

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Microarray Papers of Note Published June 2010

Journal: American Journal of Medical Genetics. 2010 Jun;152A(6):1398-410.

Title: Array CGH in molecular diagnosis of mental retardation — a study of 150 Finnish patients.

Authors: Siggberg L, et al.

The authors report the results of an array comparative genomic hybridization study of 150 karyotypically normal Finnish patients with idiopathic mental retardation and/or dysmorphic features and malformations. Using high-resolution microarray analysis, they sought to identify clinically relevant microdeletions and microduplications in these patients. The results were confirmed using other methods and compared with findings reported in recent publications and internet databases. Small aberrations of potential clinical significance were found in 28 percent of the 150 patients. Eight of the identified aberrations are known to cause syndromes, four affected the X chromosome in males, four were familial, and 13 have yet to be associated with a phenotype, according to the authors.


Journal: Analytica Chimica Acta. 2010 Jun 25;671(1-2):92-8.

Title: Printed protein microarrays on unmodified plastic substrates.

Authors: Moschallski M, et al.

The authors describe the single-step production of protein microarrays on unmodified plastic substrates, based on the printing of polymer-protein mixtures and the photochemical attachment of the obtained microstructures to the plastic chip surfaces. According to the paper, in the photochemical process, three reactions occur simultaneously: transformation of the polymer into hydrogel dots, covalent binding of the forming gel to the substrate, and covalent immobilization of the proteins to the three-dimensional hydrogel scaffold. In one experiment, the authors used anti-bovine serum albumin as a protein and a water swell-able polymer network based on polydimethylacrylamide as a scaffold, which is photochemically crosslinked using benzophenone as a crosslinking agent, resulting in a "large amount of probes per spot."


Journal: Applied Biochemistry and Biotechnology. 2010 Jun 3. [Epub ahead of print]

Title: Implementation of random bacterial genomic DNA microarray chip (RBGDMC) for screening of dominant bacteria in complex cultures.

Authors: Kim B, et al.

The random bacterial genomic DNA microarray chip, or RBGDMC, was fabricated using random genomic DNA fragments obtained from the fragmentation of bacterial genome by using four different pairs of restriction enzymes. The authors of this study found the chip could discriminate bacterial species in the same genus and resulted in the determination of dominant bacteria in enriched cultures. The identification of a dominant bacterial species was successfully conducted in the co-culture of three different bacteria using the RBGDMC. In addition, the analysis of the chip data could confirm if any of the selected bacteria was the most abundant or if some bacteria were enriched and became the dominant species within the consortium after the samples were prepared from the repeated cultures of real sludge in a complex medium, according to the authors.


Journal: Astrobiology. 2010 Jun;10(5):499-508.

Title: High-density 16S microarray and clone library-based microbial community composition of the phoenix spacecraft assembly clean room.

Authors: Vaishampayan P, et al.

The bacterial diversity and comparative community structure of a clean room used for assembling the Phoenix spacecraft was characterized throughout the spacecraft assembly process using 16S rRNA gene cloning and sequencing and DNA microarray technologies. Samples were collected from several locations of the clean room at three time points: before Phoenix's arrival, during hardware assembly, and after the spacecraft was removed for launch. Bacterial diversity comprised of all major bacterial phyla during assembly was found to be statistically different from samples collected before the arrival and after the departure of the Phoenix. Due to cleaning and decontamination protocols during assembly, bacterial diversity was reduced following departure. Comparative community analysis based on array results revealed similar overall trends as were seen in clone libraries, but the high-density phylogenetic microarray detected larger diversity in all sampling events, according to the authors.


Journal: Biochemistry. 2010 Jun 24. [Epub ahead of print]

Title: Identification and characterization of the carbohydrate ligands recognized by pertussis toxin via a glycan microarray and surface plasmon resonance.

Authors: Millen S, et al.

The authors of this paper examined the binding of pertussis toxin using a glycan microarray. Of the 53 positive hits, all fell into four general groups. One group represents sialylated biantennary compounds with an N-glycan core terminating in alpha2-6-linked sialic acid. The second group consists of multiantennary compounds with a canonical N-glycan core, but lacking terminal sialic acids, which represents a departure from the previous understanding of PTx binding to N-glycans. The third group consists of Neu5Acalpha2-3(lactose or N-acetyllactosamine) forms that lack the branched mannose core found in N-glycans. The fourth group of compounds consists of Neu5Acalpha2-8Neu5Acalpha2-8Neu5Ac. Quantitative analysis by surface plasmon resonance of the relative affinities of PTx for terminal Neu5Acalpha2-3 versus Neu5Acalpha2-6, as well as the affinities for the trisaccharide Neu5Acalpha2-8Neu5Acalpha2-8Neu5Ac versus disaccharide, revealed identical global affinities, even though the amount of bound glycan varied by between four and five fold. The authors suggest that the conformational space occupied by a glycan can play an important role in binding, independent of affinity.


Journal: Clinical & Experimental Allergy. 2010 Jun;40(6):911-21.

Title: Cross-sectional survey on immunoglobulin E reactivity in 23,077 subjects using an allergenic molecule-based microarray detection system.

Authors: Scala E, et al.

The aim of this study was to make a cross-sectional evaluation of the raw prevalence of IgE reactivity to allergenic molecules in serum samples from a cohort of Italian patients. A microarray system was subsequently developed for specific IgE detection using 75 different allergenic molecules. Sera were collected from 23,077 unselected consecutive individuals complaining about any allergic disease. The authors found 16,408 of 23,077 patients had IgE to at least one of 75 allergenic molecules. Prevalence varied depending on the age range considered, and showed a different behavior in the lifetime sensitization process. Unsupervised two-way hierarchical clustering analysis generated distinctive patterns of reactivity as the result of IgE recognition of either homologous allergens belonging to different biological sources or non-homologous belonging to the same biological source, according to the authors. They concluded that allergen-based microarrays are a tool for the detection of IgE-related sensitization to panels of allergens and give a precise evaluation for an IgE-based epidemiology.


Journal: Fertility and Sterility. 2010 Jun;94(1):114-9.

Title: Genome-based expression profiling as a single standardized microarray platform for the diagnosis of endometrial disorder: an array of 126-gene model.

Authors: Tseng L, et al.

The authors of this study aimed to assess the molecular signatures underlying endometrial disorder using a cDNA microarray. Endometrial tissues were obtained from 28 normal cycling women undergoing endometrial biopsy. RNA was extracted from each tissue and all labeled samples were hybridized to Affymetrix Human U133 plus 2.0 array. Hierarchical cluster analysis with the Mahalanobis distance revealed a 126-gene model, where genes are up-regulated at mid-secretory phase, moderately expressed at late-secretary phase, and down-regulated at late-secretory phase. The authors believe that microarray-based genome expression profiling should be used as a single standardized platform for diagnosis of endometrial disorders.

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Journal: Journal of Clinical Pathology. 2010 Jun;63(6):513-7.

Title: Feasibility of using tissue microarray cores of paraffin-embedded breast cancer tissue for measurement of gene expression: a proof-of-concept study.

Authors: Drury S, et al.

The authors of this study set out to determine whether 0.6 mm cores of formalin-fixed paraffin-embedded tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer. Four matched 0.6 mm cores of invasive breast tumor and two 10 micrometer whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan assays were performed on the 21 genes of the Genomic Health Oncotype DX Breast Cancer assay. Expression of the 16 recurrence-related genes was normalized to the set of five reference genes, and the recurrence score was calculated. The authors found that RNA yield was lower from 0.6 mm cores than from 10 micrometer whole sections, but was still more than sufficient to perform the assay. They concluded that FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximize RNA yield and to allow for standard histopathological assessment. Still, the authors argued that 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.


Journal: Journal of Immunological Methods. 2010 Jun 30;358(1-2):23-34.

Title: An extended antibody microarray for surface profiling metastatic melanoma.

Authors: Kaufman K, et al.

The authors of this paper developed an antibody microarray for profiling the surface proteome of melanoma cells, which could be used to sub-classify melanoma and predict the clinical behavior of the melanoma, patient outcome, and treatment response. According to the paper, 48 antibodies were selected based on their correlation with melanoma development, progression, and prognosis, and were printed on nitrocellulose slides. The immobilized antibodies capture live cells expressing corresponding antigens to produce a cell-binding dot pattern representing the surface antigen profile of the melanoma. Surface antigen signatures were determined for a normal melanocyte and six melanoma cell lines and cell suspensions prepared from 10 surgically excised melanoma lymph node metastases. A procedure for obtaining separate surface antigen profiles for melanoma cells and leukocytes from clinical lymph node samples was also developed using anti-CD45 magnetic beads.


Journal: Journal of Medical Genetics. 2010 Jun 24. [Epub ahead of print]

Title: Identification of clinically significant, submicroscopic chromosome alterations and UPD in fetuses with ultrasound anomalies using genome-wide 250K SNP array analysis.

Authors: Faas B, et al.

The authors of this study sought to explore prenatal application of genome-wide SNP arrays. Using the Affymetrix 250K NspI SNP array, they analyzed DNA from 38 prenatally karyotyped fetuses with ultrasound anomalies. Analyses were performed after termination of pregnancy, intrauterine fetal death, or birth on DNA isolated from fetal or neonatal material. The authors detected aberrations in 17 of 38 fetuses, six of whom had a previously identified chromosomal abnormality and 11 with previously normal or balanced karyotypes. Of the latter, the detected aberration occurred in a de novo manner and was considered of clinical relevance in five cases, inherited from a healthy parent in four cases, and de novo yet with unclear clinical relevance in two cases. The authors concluded that in at least 16 percent of fetuses with ultrasound anomalies and a normal or balanced karyotype, causal aberrations were detected.


Journal: Molecular Cytogenetics. 2010 Jun 29;3(1):11. [Epub ahead of print]

Title: Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH.

Authors: Neill N, et al.

To determine the difference in detection rate between similarly designed bacterial artificial chromosome and oligo arrays, the authors of this study developed whole-genome BAC and oligonucleotide microarrays and validated them in a side-by-side comparison of 466 consecutive clinical specimens. Of the 466 cases studied, 67 had a copy-number imbalance of potential clinical significance detectable by the whole-genome BAC array, and 73 had a copy-number imbalance of potential clinical significance detectable by the whole-genome oligo array. However, because both platforms identified copy number variants of unclear clinical significance, the authors designed a systematic method for the interpretation of copy number alterations and tested an additional 3,443 cases by BAC array and 3,096 cases by oligo array. Of those cases tested on the BAC array, 17.6 percent were found to have a copy-number abnormality of potential clinical significance, while the detection rate increased to 22.5 percent for the cases tested by oligo array. In addition, the authors validated the oligo array for detection of mosaicism and found that it could routinely detect mosaicism at levels of 30 percent and greater. The authors concluded that, while BAC arrays have faster turnaround times, the increased detection rate of oligo arrays makes them attractive for clinical cytogenetic testing.


Journal: Nature. 2010 Jun 9. [Epub ahead of print]

Title: Functional impact of global rare copy number variation in autism spectrum disorders.

Authors: Pinto D, et al.

The authors of this study analyzed the genome-wide characteristics of rare copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants, especially so for loci previously implicated in either ASD and/or intellectual disability. Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2, and the X-linked DDX53–PTCHD1 locus. The authors also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. The authors believe their results reveal genetic and functional targets in ASD that may lead to final connected pathways.


Journal: Nature. 2010 Jun 9. [Epub ahead of print]

Title: The genome-wide structure of the Jewish people.

Authors: Behar D, et al.

Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers, genome-wide patterns of variation across the geographic span of Jewish diaspora communities and their respective neighbors have yet to be addressed. The authors of this study used high-density bead arrays to genotype individuals from 14 Jewish diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. The authors found that principal component and structure-like analyses identified previously unrecognized genetic substructure within the Middle East. While most Jewish samples form a tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired diaspora host populations, Ethiopian Jews and Indian Jews cluster with neighboring autochthonous populations in Ethiopia and western India, respectively, despite clear paternal links.


Journal: Nucleic Acids Research. 2010 Jun;38(10):e116.

Title: Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.

Authors: Mokry M, et al.

The authors of this study explored the use of short fragment libraries to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. According to the authors, high enrichment specificity was obtained with a relative even base coverage. Up to 98 percent of the target-sequence was covered more than 20 times at an average coverage depth of about 200 times. To verify the accuracy of SNP-mutation detection, the authors evaluated 384 known non-reference SNPs in the targeted regions. At approximately 200 times average sequence coverage, they were able to survey 96.4 percent of 1.69 megabases of genomic sequence with 4.2 percent false negative calls. Using the same settings, a total of 1,197 candidate variants were detected. Verification experiments revealed eight false positive calls, indicating an overall false positive rate of less than 1 per approximately 200,000 base pairs.


Journal: Nucleic Acids Research. 2010 Jun 1;38(11):e121.

Title: Evaluating oligonucleotide properties for DNA microarray probe design.

Authors: Xia X, et al.

According to the authors, most current microarray oligonucleotide probe design strategies are based on probe design factors, which include probe hybridization free energy, probe minimum folding energy, dimer score, hairpin score, homology score, and complexity score. In this study, they evaluated the impact of these PDFs on probe performance using four sets of microarray comparative genome hybridization data, which included two array manufacturing methods and the genomes of two species. In all data sets, the authors determined PDFs related to probe secondary structure to be the most significant factors linearly correlated with probe hybridization intensities. They also developed a new PDF, pseudo probe binding energy, by iteratively fitting dinucleotide positional weights and dinucleotide stacking energies until the average residue sum of squares for the model was minimized. The authors determined that PPBE showed a better correlation with probe sensitivity and a better specificity than all other PDFs, though they noted that training data are required to construct a PPBE model prior to designing new oligonucleotide probes.


Journal: Plant Methods. 2010 Jun 30;6:16.

Title: A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus.

Authors: Sansaloni C, et al.

The authors of this study developed a high-density DArT genome-profiling resource that they believe has potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Specifically, they developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree, whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. The authors believe their DArT array will deliver between 1,000 and 2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees and provide high-genome coverage for researchers studying Eucalyptus.


Journal: PLoS One. 2010 Jun 28;5(6):e11355.

Title: Peptide-MHC cellular microarray with innovative data analysis system for simultaneously detecting multiple CD4 T-cell responses.

Authors: Ge X, et al.

Aiming to characterize multiple Ag-specific populations of T cells, the authors of this study co-immobilized peptide:DR0401 complexes, anti-CD28, anti-CD11a, and cytokine-capture antibodies on the surface of chamber slides to generate a functional array that was able to detect rare Ag-specific T cell populations from previously primed in vitro T cell cultures. A statistical methodology was also developed to facilitate batch processing of raw array-like data into standardized endpoint scores, which linearly correlated with total Ag-specific T cell inputs. In applying these methods to analyze influenza A viral antigen-specific T cell responses, the authors both determined prominent viral epitopes and demonstrated the heterogeneity of antiviral cellular responses in healthy individuals. Additionally, by applying the methods to examine the insulin producing beta-cell autoantigen specific T cell responses, the authors observed little difference between autoimmune diabetic patients and healthy individuals, suggesting an association between diabetes status and peripheral autoreactive T cells.


Journal: PLoS One. 2010 Jun 23;5(6):e11285.

Title: Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.

Authors: Wu C, et al.

Using a high-density PhyloChip microarray, the authors of this study examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence, according to the authors. The first approach relied on 503 operational taxonomic units common to all fecal samples analyzed, with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of four bacterial classes (Bacilli, Bacteroidetes, Clostridia and alpha-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these four classes from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip-analyzed studies.


Journal: Proceedings of the National Academy of Sciences. 2010 Jun 1;107(22):9923-8.

Title: Analysis of factorial time-course microarrays with application to a clinical study of burn injury.

Authors: Zhou B, et al.

Time-course microarray experiments are capable of capturing dynamic gene expression profiles. The authors of this paper developed a method to evaluate factor effects by pooling information across the time course while accounting for multiple testing and non-normality of the microarray data. The method extracts gene-specific response features and models their dependency on the experimental factors. Both longitudinal and cross-sectional time-course data can be handled by this approach, according to the authors. In this study, the authors applied their method to analyze the impact of age on the temporal gene response to burn injury in a large-scale clinical study. Their analysis revealed that 21 percent of the genes responsive to burn are age-specific, among which expressions of mitochondria and immunoglobulin genes are differentially perturbed in pediatric and adult patients by burn injury.

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.