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In Print: Jun 9, 2009

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Microarray-Related Papers of Note Published in May 2009

Journal: American Journal of Medical Genetics. 2009 May;149A(5):914-8.
Title: aCGH detects partial tetrasomy of 12p in blood from Pallister-Killian syndrome cases without invasive skin biopsy.
Authors: A Theisen; J Rosenfeld; S Farrell; C Harris; H Wetzel; B Torchia; B Bejjani; B Ballif; L Shaffer

Abstract: Pallister-Killian syndrome is a genetic disorder characterized by mental retardation, seizures, streaks of hypo- or hyperpigmentation, and dysmorphic features. PKS is associated with tissue-limited mosaic partial tetrasomy of 12p, usually caused by an isochromosome 12p. The mosaicism is usually detected in cultured skin fibroblasts or amniotic cells and rarely in phytohemagluttinin-stimulated lymphocytes, which suggests stimulation of T-lymphocytes may distort the percentage of abnormal cells. In this study, the authors report on seven individuals with partial tetrasomy of 12p characterized by Signature Genomic Laboratories. In each case, array comparative genomic hybridization using genomic DNA extracted from whole peripheral blood detected copy-number gain for all clones for the short arm of chromosome 12. In comparison, in all but one case, fluorescence in situ hybridization on metaphases from cultured lymphocytes did not detect the copy-number gain. The authors argue that their findings demonstrate the usefulness of aCGH with genomic DNA from whole peripheral blood to detect chromosome abnormalities that are not present in stimulated blood cultures and would otherwise require invasive skin biopsies for identification.


Journal: American Journal of Medical Genetics. 2009 May;149A(5):887-93.
Title: High resolution SNP based microarray mapping of mosaic supernumerary marker chromosomes 13 and 17: delineating novel loci for apraxia.
Authors: J Kogan; E Miller; S Ware

Abstract: In this study, the authors present the clinical and molecular analysis of a patient with de novo mosaic supernumerary marker chromosomes (17) and SMC (13). High-resolution SNP-based microarray mapping identified the parent of origin for the SMCs and allowed delineation of the breakpoints, which include a 5.1 megabase duplication from 17p11.2 to 17q11.2 as well as duplication of chromosome 13 that includes 2.2 Mb from 13q11 to 13q12.11. The results demonstrate the utility of SNP microarray-based methodology for mapping disease-causing genes, including those within SMCs, and provide the opportunity to identify novel candidate genes for verbal apraxia, the authors state.


Journal: American Journal of Dermatopathology. 2009 May;31(3):218-22.
Title: The utility of the DNA microarray scanner to simplify the immunofluorescence evaluation of autoimmune bullous diseases.
Authors: S Iwamoto; A Iwamoto; J Cha; T Clark; M Lu; C Breen; J Bhawan; V Falanga

Abstract: The authors used a DNA microarray scanner as a digital fluorescence microscope to simplify the diagnosis of autoimmune bullous diseases. Frozen sections of skin biopsies were taken from three patients with bullous pemphigoid and one patient each with lichen planus pemphigoides, linear immunoglobulin A disease, and dermatitis herpetiformis. After incubation with cyanine-labeled antibodies, the tissues were scanned at 5-µm resolution using an instrument originally designed to study gene expression. The microarray scanner's large field of view, unlike that of fluorescence microscopy, allowed a view of the entire specimen, considerably easing the orientation of tissue. In conclusion, the authors argue that the advantages of the microarray scanner over standard fluorescence microscopy include speed, technical ease, large field of view, potential for visualizing multiple antibodies simultaneously in a tissue, and convenience of digital image archiving.


Journal: American Journal of Psychiatry. 2009 May;166(5):540-56.
Title: Genomewide association studies: history, rationale, and prospects for psychiatric disorders.
Authors: Psychiatric GWAS Consortium Coordinating Committee; S Cichon; N Craddock; M Daly; S Faraone; P Gejman; J Kelsoe; T Lehner; D Levinson; A Moran; P Sklar; P Sullivan

Abstract: The authors conducted a literature review of the history and empirical basis of genome-wide association studies, the rationale for GWAS of psychiatric disorders, results to date, limitations, and plans for GWAS meta-analyses. They found that GWAS of large samples have detected associations of common SNPs and of rare copy number variants with psychiatric disorders. Also, they predict that more findings are likely, since larger GWAS samples detect larger numbers of common susceptibility variants, with smaller effects. The authors noted that the Psychiatric GWAS Consortium is conducting GWAS meta-analyses for schizophrenia, bipolar disorder, major depressive disorder, autism, and attention deficit hyperactivity disorder. Based on results for other diseases, larger samples will be required, they state. The contribution of GWAS will depend on the true genetic architecture of each disorder, the authors argue.

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Journal: Biomacromolecules. 2009 May 11;10(5):1163-72.
Title: Multifunctional polymer coatings for cell microarray applications.
Authors: M Kurkuri; C Driever; G Johnson; G McFarland; H Thissen; N Voelcker

Abstract: In this study, multifunctional polymer surface chemistries were developed for a cell microarray application with the aim of screening cellular interactions with surface immobilized factors. The coatings were prepared by the deposition of an allylamine plasma polymer pinning layer followed by the deposition of random copolymers of glycidyl methacrylate and polyethylene glycol methacrylate. The coatings were then characterized by X-ray photoelectron spectroscopy, infrared spectroscopy, ellipsometry, and contact angle measurements. A variety of proteins as well as synthetic polymers were printed onto copolymer-coated slides using a high-precision contact microarrayer. Printing conditions were optimized for a fluorescently labeled model protein in regard to the temperature, humidity, pin geometry, concentration, and pH of the printing solution. In conclusion, the suitability of the surface chemistry for the evaluation of cellular responses to surface immobilized factors in a microarray format was demonstrated using HeLa cells, according to the authors.


Journal: BMC Biotechnology. 2009 May 27;9(1):51. [Epub ahead of print]
Title: A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis.
Authors: E Barros; C van Staden; S Lezar

Abstract: Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa, but the most serious problem affecting the quality and yield of solid wood products is the occurrence of end splitting in logs, according to the authors. The selection of E. grandis planting stock that exhibit preferred wood qualities is a priority of the South African forestry industry. In this study, the authors used microarray-based DNA-amplified fragment length polymorphism analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven different E. grandis trees. Specifically, a 1,578-probe cDNA microarray was designed by arraying 768 cDNA-AFLP clones and 810 cDNA library clones from seven individual E. grandis trees onto silanized slides. The authors claim the chip could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programs.


Journal: BMC Genomics. 2009 May 12;10:221.
Title: Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.
Authors: J Bloom; Z Khan; L Kruglyak; M Singh; A Caudy

Abstract: The authors compared full-length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of a comparable cost to a gene expression microarray, the authors focused on data obtainable from a single lane of an Illumina 1G sequencer. They compared the sequencing data to a microarray experiment profiling two divergent strains of S. cerevisiae. According to the authors, neither technology is decisively better at measuring differential gene expression. Additionally, they report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full-length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.


Journal: BMC Genomics. 2009 May 29;10(1):253. [Epub ahead of print]
Title: Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array.
Authors: T Coram; M Settles; X Chen

Abstract: In this study, the authors developed a protocol to assay sense- and antisense-strand transcription on the 55K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription expression array. They claim their study is the first to use a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof of concept. According to the authors, the study identified 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Ultimately, they argue that the study demonstrates the use of an adapted labeling protocol and a 3'IVT GeneChip array for large-scale identification of antisense transcription in wheat.

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Journal: Clinica Chimica Acta. 2009 May 13. [Epub ahead of print]
Title: A fast modified protocol for random-access ultra-high density whole-genome scan: A tool for personalized genomic medicine, positional mapping, and cytogenetic analysis.
Authors: K Lau; C Mak; K Leung; T Tsoi; H Tang; C Lam

Abstract: The authors describe a modified PCR purification protocol without batch-size limitation for whole-genome scan using ultra-high density SNP microarrays. In the protocol, enzyme-digested PCR products are purified with the use of magnetic beads. Separation of the magnetic particles applies magnetic stand devices instead of vacuum pumps. To test the protocol, the authors genotyped 17 genomic samples and three whole genome amplified samples. They argue that, using the protocol, they were able to identify the breakpoint localization of a ring chromosome in a female and locate the disease gene in a consanguineous family affected by limb-girdle muscular dystrophy.


Journal: Colloids and Surfaces. 2009 May 1;70(2):259-65.
Title: Enhancement of sensitivity of SPR protein microarray using a novel 3D protein immobilization.
Authors: H Tanaka; M Hanasaki; T Isojima; H Takeuchi; T Shiroya; H Kawaguchi

Abstract: The authors developed a method to prepare a three-dimensional protein-based hydrogel that is composed of protein-polymer hybrid nanoparticles. In this study, they designed a protein microarray whose 3D nanoparticle hydrogel spots were prepared by dispensing a small volume of the solution of protein-polymer mixture on a substrate. As the dispensed solution had a short time for cross-linking before it dried, the resulting hydrogel was of a loosely cross-linked, thin spongy structure. Because of this, the authors argue, the reaction ratio between ligands and analytes was improved in this system compared with the large volume system for a surface plasmon resonance protein microarray.


Journal: Heart Rhythm. 2009 May;6(5):634-41.
Title: Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae.
Authors: J Smith; J Lowe; S Kovvali; J Maller; J Salit; M Daly; M Stoffel; D Altshuler; J Friedman; J Breslow; C Newton-Cheh

Abstract: The authors examined 1,604 individuals from the island of Kosrae, Federated States of Micronesia, an isolated founder population, to identify common genetic determinants of arrhythmia. A genome-wide association study was performed on a subset of 1,262 individuals genotyped using the Affymetrix GeneChip Human Mapping 500K microarray. The authors found that the PR interval and its subcomponents showed substantial heritability in a South Pacific islander population and were associated with common genetic variation in SCN5A.


Journal: Journal of Investigative Dermatology. 2009 May;129(5):1219-24.
Title: MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling.
Authors: M Glud; M Klausen; R Gniadecki; M Rossing; N Hastrup; F Nielsen; K Drzewiecki

Abstract: To explore whether formalin-fixed, paraffin-embedded material would be suitable for microRNA profiling in melanocytic lesions, the authors compared miRNA expression patterns in FFPE versus fresh frozen samples, obtained from 15 human melanocytic nevi. Out of resulting microarray data, they identified 84 miRNAs that were expressed in both types of samples and represented an miRNA profile of melanocytic nevi. The study's results showed a high correlation in miRNA expression between paired FFPE and fresh frozen material. The data were further validated by quantitative RT-PCR. In conclusion, the authors argue that FFPE specimens of melanocytic lesions are suitable as a source for miRNA microarray profiling.


Journal: Journal of Molecular Diagnostics. 2009 May;11(3):226-37.
Title: Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA.
Authors: S Yatsenko; C Shaw; Z Ou; A Pursley; A Patel; W Bi; S Cheung; J Lupski; A Chinault; A Beaudet

Abstract: The authors evaluated the ability of bacterial artificial chromosome and oligonucleotide-based array comparative genomic hybridization analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. The authors determined that using sex-mismatched reference DNAs in array CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, masking potential pathogenic genomic imbalances. To optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, they suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs.


Journal: Journal of Virological Methods. 2009 May 3. [Epub ahead of print]
Title: Microarray immunoassay for the detection of grapevine and tree fruit viruses.
Authors: I Abdullahi; M Rott

Abstract: In this work, an antibody microarray procedure was developed and its usefulness for the detection of plant viruses demonstrated. Using the conventional monoplex enzyme-linked immunosorbent assay technique as a benchmark, the procedure was used to detect several grapevine and tree fruit viruses. Using a direct labeling approach, Arabis mosaic virus and Grapevine fanleaf virus were detected after incubating the antibody array with alkaline phosphatase-conjugated viral extract. Indirect detection using a double or triple antibody sandwich format also resulted in good reaction signals, using either a chromogenic or fluorescence dye. In a multiplex system, four grapevine viruses were detected without compromising sensitivity and specificity. In conclusion, the authors found that, compared to ELISA, the antibody microarray system is similar with respect to sensitivity and specificity, and a high correlation.

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Journal: Nature. 2009 May 28;459(7246):569-73.
Title: Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.
Authors: J Glessner; K Wang; C Cai; O Korvatska; C Kim; S Wood; H Zhang; A Estes; C Brune; J Bradfield; M Imielinski; E Frackelton; J Reichert; E Crawford; J Munson; P Sleiman; R Chiavacci; K Annaiah; K Thomas; C Hou; W Glaberson; J Flory; F Otieno; M Garris; L Soorya; L Klei; J Piven; K Meyer; E Anagnostou; T Sakurai; R Game; D Rudd; D Zurawiecki; C McDougle; L Davis; J Miller; D Posey; S Michaels; A Kolevzon; J Silverman; R Bernier; S Levy; R Schultz; G Dawson; T Owley; W McMahon; T Wassink; J Sweeney; J Nurnberger; H Coon; J Sutcliffe; N Minshew; S Grant; M Bucan; E Cook; J Buxbaum; B Devlin; G Schellenberg; H Hakonarson

Abstract: The authors present the results from a whole-genome copy number variation study on a cohort of 859 autism spectrum disorder cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to identify CNVs conferring susceptibility to ASDs. In addition to previously reported ASD candidate genes, the authors reported new susceptibility genes encoding neuronal cell-adhesion molecules. Also, CNVs within or surrounding genes involved in the ubiquitin pathways were affected by CNVs not observed in controls. Although the identified variants may be individually rare, according to the authors, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, and indicate that these two gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.


Journal: Nature Genetics. 2009 May 31. [Epub ahead of print]
Title: HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.
Authors: A Daly; P Donaldson; P Bhatnagar; Y Shen; I Pe'er; A Floratos; M Daly; D Goldstein; S John; M Nelson; J Graham; B Park; J Dillon; W Bernal; H Cordell; M Pirmohamed; G Aithal; C Day

Abstract: Drug-induced liver injury is an important cause of serious liver disease. The antimicrobial agent flucloxacillin is a common cause of DILI, but the genetic basis for susceptibility remains unclear. The authors conducted a genome-wide association study using 866,399 markers in 51 cases of flucloxacillin DILI and 282 controls matched for sex and ancestry. The study showed an association peak in the major histocompatibility complex region with the strongest association seen for rs2395029[G], a marker in complete linkage disequilibrium with HLA-B*5701. More MHC genotyping, which included 64 flucloxacillin-tolerant controls, confirmed the association with HLA-B*5701, the authors state. The authors claim the findings have the potential to improve diagnosis of this serious disease.


Journal: Nucleic Acids Research. 2009 May;37(8):e61.
Title: Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips.
Authors: Y Lee; H Chen; C Tsai; C Tsai; A Chao; T Wang

Abstract: The authors report that labeling extension values, or LEVs, which are correlation coefficients between probe intensities and probe positions, are highly correlated with the gene expression levels on eukaryotic Affymetrix microarray data. By analyzing LEVs and GEVs in the publicly available cel files of 20 Affymetrix microarray types covering 13 species, the authors found that correlations between LEVs and GEVs only exist in eukaryotic RNAs, but not in prokaryotic ones. In conclusion, the authors argue that LEVs provide a new filtering parameter for microarray analysis of gene expression and it may improve the inter- and intralaboratory comparability of Affymetrix GeneChip data.


Journal: Nucleic Acids Research. 2009 May 31. [Epub ahead of print]
Title: Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays.
Authors: A Bonham; T Neumann; M Tirrell; N Reich

Abstract: The authors developed a high-throughput total internal reflectance fluorescence protein binding microarray (TIRF-PBM) assay to systematically investigate transcription regulatory protein complexes binding to DNA with varied specificity and affinity. The approach is based on the coupling of total internal reflectance fluorescence spectroscopy, swellable hydrogel double-stranded DNA microarrays, and dye-labeled regulatory proteins. This coupling makes it possible to determine both the equilibrium binding specificities and kinetic rates for multiple protein-DNA interactions in a single experiment, the authors stated. According to the authors, TIRF-PBM provides an extendible platform for multi-protein transcription factor investigation.


Journal: Veterinary Parasitology. 2009 May 26;162(1-2):106-15.
Title: Use of a candidate gene array to delineate gene expression patterns in cattle selected for resistance or susceptibility to intestinal nematodes.
Authors: R Araujo; T Padilha; D Zarlenga; T Sonstegard; E Connor; C Van Tassel; W Lima; E Nascimento; L Gasbarre

Abstract: Using arrays, the authors investigated the expression patterns of 381 genes with known association to host immune responses. Hybridization targets were derived from previously characterized bovine cDNAs. A total of 576 reporters were spotted onto glass slides in two sets of four replicates. Two color, comparative hybridizations across both mesenteric lymph node and small intestine mucosa RNA samples were done between animals with previously demonstrated phenotypic differences based on natural exposure to gastrointestinal nematodes over a six-month exposure period. A total of 138 significant hybridization differences were detected by mixed model analysis of variance. According to the authors, the results indicated that immune responses against GI nematode infections involve multiple response pathways. Higher levels of expression for IgE receptor, integrins, complement, monocyte/macrophage and tissue factors are related to resistance. In contrast, higher levels of expression for immunoglobulin chains and TCRs are related to susceptibility. Identification of these genes provides a framework to better understand the genetic variation underlying parasite resistance.

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Right Whales' Decline

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In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.