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In Print: Apr 13, 2010

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Microarray Papers of Note Published March 2010

Journal: American Journal of Human Genetics. 2010 Mar 12;86(3):454-61.

Title: Identification of a recurrent microdeletion at 17q23.1q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities.

Authors: Ballif B, et al.

Segmental duplications are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination and have been suggested to be important in chromosome evolution and human genomic instability, according to the authors of this paper. In this study, they report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization. The individuals discussed have common features, including mild to moderate developmental delay, microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome, according to the authors.


Journal: Analytical Biochemistry. 2010 Mar 10. [Epub ahead of print]

Title: Sensitive detection of multiplex toxins using antibody microarray.

Authors: Lian W, et al.

This paper presents a protein antibody microarray assay system for the specific detection of bioterrorism agents, including ricin, cholera toxin, and staphylococcal enterotoxin B. The Ab microarray uses a sandwich format that consists of capture Abs, analytes, biotinylated detection Abs, and avidin-conjugated nanoparticle. The system was used to detect toxins spiked in milk, apple cider, and blood samples. The authors believe their study highlights the role of pAb and NP in increasing selectivity and sensitivity of toxin detection in a microarray format.


Journal: Applied Microbiology and Biotechnology. 2010 Mar;86(2):681-91.

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

Authors: Borneman A, et al.

Oenococcus oeni is a bacterium used during winemaking. Large numbers of O. oeni strains show differences in commercially important industrial phenotypes. To ascertain the basis of these phenotypic differences, the authors of this study mapped the genomic content of ten wine strains of O. oeni using array-based comparative genome hybridization. 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 determined that the genome of O. oeni is likely to be much larger than that 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 Mar 15;25(7):1789-95.

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

Authors: Ozkumur E, et al.

This paper proposes a method for 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. The authors argue that the capabilities of the method are demonstrated by high-throughput sensing of solid-phase hybridization of oligonucleotides. For example, 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. 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 high confidence interval, according to the authors. They believe their approach eliminates the need for using labels or secondary reagents to monitor oligonucleotide hybridization.


Journal: Diagnostic Molecular Pathology. 2010 Mar;19(1):9-14.

Title: Comparison of microarray analysis of fine needle aspirates and tissue specimen in thyroid nodule diagnosis.

Authors: Kundel A, et al.

The authors of this study evaluated whether ex vivo fine needle aspirates and tissue samples could be used interchangeably with microarrays and whether the method of acquisition affects the precision of the gene list that is generated. To assess whether FNA samples provide adequate material for reliable gene expression analysis, paired tissue and FNA samples were collected from 13 thyroid nodules: 7 malignant, 6 benign. RNA was extracted from each specimen, converted to complementary DNA, and hybridized to Affymetrix U-133 GeneChips. Cluster analysis was then performed using 61 genes predetermined to differentiate benign from malignant nodules. The authors concluded that FNA is a reliable alternative to tissue samples in predicting malignancy with microarrays.

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Journal: Expert Reviews in Molecular Medicine. 2010 Mar 9;12:e8.

Title: The clinical context of copy number variation in the human genome.

Authors: Lee C, et al.

In this review, the authors place copy number variants into their historical and medical contexts, focusing on how CNVs can be recognized, documented, characterized, and interpreted in clinical diagnostics. They also discuss how CNVs can cause disease or influence adaptation to an environment. According to the authors, the potential is immense for CNVs to explain and predict disorders and traits that have long resisted understanding. However, they warn that creative solutions are needed to manage the sudden and overwhelming burden of expectation for laboratories and clinicians to assay and interpret these complex genomic variations as awareness permeates medical practice.


Journal: Journal of Clinical Virology. 2010 Mar;47(3):282-5.

Title: Resequencing microarray for detection of human adenoviruses in patients with conjunctivitis.

Authors: Woo P, et al.

The authors of this paper tested to see if their high-density resequencing microarray platform could be applied to detection of viruses in conjunctival swabs for patients with conjunctivitis. To do this, every four or five bacterial culture-negative conjunctival swab samples were pooled and subject to viral detection using the TessArray Resequencing Pathogen Microarray-Flu 3.1. Assay results were then compared with human adenovirus hexon gene PCR sequencing and viral culture. The authors determined that their resequencing microarray is as sensitive as PCR for detection of HAdV in conjunctival swabs but, unlike viral culture and hexon gene PCR sequencing, the resequencing microarray platform was not able to differentiate the type and species of HAdV.


Journal: Journal of Medical Genetics. 2010 Mar;47(3):195-203.

Title: Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder.

Authors: Fernandez B, et al.

Recurrent microdeletions and microduplications of approximately 555 kilobases at 16p11.2 confer susceptibility to autism spectrum disorder in up to 1 percent of ASD patients, the authors of this study note. In this paper, they report five autistic probands identified by microarray analysis with copy number variation of 16p11.2, specifically three deletions and two duplications. Each patient was assessed for ASD and dysmorphic features. The authors also describe a deletion-positive 26-month-old female who has developmental delay and autistic features.


Journal: Journal of Microbiology Methods. 2010 Mar;80(3):223-30.

Title: Diagnostic microarray for human and animal bacterial diseases and their virulence and antimicrobial resistance genes.

Authors: Peterson G, et al.

The objective of this study was to develop a spotted microarray for rapid identification and characterization of bacterial pathogens and their antimicrobial resistance genes. The authors designed an array consisting of 489 70-mer probes that detect 40 bacterial pathogens of medical, veterinary and zoonotic importance; associated genes that encode resistance for antimicrobial and metal resistance; and DNA elements that are important for horizontal gene transfer among bacteria.


Journal: Journal of Molecular Diagnostics. 2010 Mar 19. [Epub ahead of print]

Title: Development of a diagnostic microarray assay to assess the risk of recurrence of prostate cancer based on PITX2 DNA methylation.

Authors: Schatz P, et al.

DNA methylation of PITX2 has been established in several studies as a prognostic biomarker for breast and prostate cancer. To facilitate its use in a diagnostic setting, the authors of this study transferred the PITX2 biomarker to the Affymetrix GeneChip System. A customized microarray called the Epichip PITX2 was designed to determine the methylation state of the PITX2 promoter. Specifically, determination of PITX2 methylation in formalin-fixed, paraffin-embedded tissue samples from a cohort of 157 prostatectomy patients resulted in an excellent level of concordance of the clinical classification, as well as the measured output between the research assay and the Epichip PITX2, the authors wrote. They believe the Epichip PITX2 is a reliable diagnostic tool for assessing the methylation status of PITX2, which could lead to an improved outcome prediction in cancer patients following radical prostatectomy. BioArray News spoke with the authors last month (BAN 3/30/2010).


Journal: Journal of Plant Physiology. 2010 Mar 1;167(4):301-10.

Title: Use of a custom array to study differentially expressed genes during blood orange (Citrus sinensis L. Osbeck) ripening.

Authors: Bernardi J, et al.

The authors designed a flesh-specific oligonucleotide array to study gene expression during blood orange ripening. The custom array was hybridized using samples of Moro, a pigmented cultivar, and Cadenera, a common cultivar, at three different ripening stages: the immature phase, the halfway point of maturation, and the full ripening. Of the 301 probes on the array, 27 in total, corresponding to 20 different transcripts, indicated differential expression in stage-to-stage and cultivar-to-cultivar comparisons. Transcripts encoding for anthocyanin biosynthesis represented most of the total over-expressed probes. The remaining differentially expressed transcripts were functionally associated with primary metabolism as flavor biosynthesis, defense, and signal transduction.


Journal: Journal of Virological Methods. 2010 Mar 18. [Epub ahead of print]

Title: Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses.

Authors: Zhang Y, et al.

The authors present an array that can detect a wide spectrum of 169 plant virus species from 13 different genera. The array was constructed using an automated probe design protocol that generated a minimal number of probes to detect viruses at the genus level. The designed arrays showed a high specificity and sensitivity when tested with a set of standard virus samples, according to the authors. Field samples collected from a severe disease outbreak of Panaxnotoginseng farms in Yunnan, China, in 2001 were screened using the array. A potyvirus infection was identified as being associated with the disease.

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Journal: Langmuir. 2010 Mar 16;26(6):4130-5.

Title: Tandem surface microfluidic lithography and activation to generate patch pattern biospecific ligand and cell arrays.

Authors: Pulsipher A, et al.

The authors describe a method that combines microfluidic lithography and oxidative activation to pattern and chemically alter selective regions of self-assembled monolayers on gold for subsequent chemoselective ligand immobilization. They demonstrated that PCC, a mild oxidant, can be used to convert hydroxyl-terminated SAMs to aldehydes and decorated with a variety of oxyamine-containing molecules. The authors used this method to create a biospecific ligand platform for peptide-mediated, cell adhesion arrays.


Journal: Leukemia Research. 2010 Mar 18. [Epub ahead of print]

Title: Prognostic classification of patients with acute lymphoblastic leukemia by using gene copy number profiles identified from array-based comparative genomic hybridization data.

Authors: Usvasalo A, et al.

In this study, the authors aimed to define a prognostic classifier for acute lymphoblastic leukemia based on DNA copy number alterations of adolescent and young adult patients using microarray CGH and the relapse status of the patients. As a result of prognostic model identification procedure, they discovered a model of four genes: BAK1, CDKN2C, GSTM1, and MT1F, the copy number profile combinations of which differentiated young ALL patients at diagnosis depending on their risk of relapse. The performance of the model was poorer on other age groups. Still, the authors suggested that the approach produces models simple and accurate enough for potential use in ALL routine classification.


Journal: Nature. 2010 Apr 8;464(7290):898-902.

Title: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.

Authors: Vonholdt B, et al.

The authors conducted a genome-wide survey of more than 48,000 SNPs in dogs and their wild progenitor, the grey wolf. They show in the paper that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from East Asia, as suggested by mitochondrial DNA sequence data. These results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages, the authors write. Additionally, they believe the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create phenotypic diversity.


Journal: Nature Biotechnology. 2010 Mar 28. [Epub ahead of print]

Title: High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity.

Authors: Närvä E, et al.

The authors present a high-resolution study of human embryonic stem cells using an Affymetrix SNP 6.0 array. Analysis of 17 different hESC lines maintained in different laboratories identified 843 CNVs between 50 kilobases and 3 megabases in size. The authors identified, on average, 24 percent of the loss of heterozygosity sites and 66 percent of the CNVs changed in culture between early and late passages of the same lines. Thirty percent of the genes detected within CNV sites had altered expression compared to samples with normal copy number states, of which more than 44 percent were functionally linked to cancer, the authors found.


Journal: Nucleic Acids Research. 2010 Mar 1;38(5):e28.

Title: Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.

Authors: Pozhitkov A, et al.

The authors of this paper examined hybridization isotherms generated on different microarray platforms using a ribosomal RNA target and then investigated hybridization signals at equilibrium and after stringent wash. Hybridization signal at equilibrium was achieved by treating the microarray with isopropanol, which prevents nucleic acids from dissolving into solution. Their results suggest that: a) the shape of hybridization isotherms varied by microarray platform with some being hyperbolic or linear, and others following a power-law; b) at equilibrium, fluorescent signal of different probes hybridized to the same target were not similar even with excess of target; and c) the amount of target removed by stringent washing depended upon the hybridization time, the probe sequence, and the presence or absence of nonspecific targets.


Journal: Nucleic Acids Research. 2010 Mar 17. [Epub ahead of print]

Title: Evaluating oligonucleotide properties for DNA microarray probe design.

Authors: Xia X, et al.

Most current microarray oligonucleotide probe design strategies are based on probe design factors, or PDFs, such as probe hybridization free energy, probe minimum folding energy, dimer score, hairpin score, homology score and complexity score. The authors of this paper assessed the impact of these PDFs on probe performance using four sets of microarray comparative genome hybridization data, including two array manufacturing methods and the genomes of two species. They found that PDFs related to probe secondary structure are the most significant factors linearly correlated with probe hybridization intensities. PHFE, homology and complexity score correlated significantly with probe specificities, but in a non-linear fashion. The authors developed a new PDF called 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. According to the authors, PPBE showed a better correlation with probe sensitivity and a better specificity than all other PDFs, although training data are required to construct a PPBE model prior to designing new oligonucleotide probes.


Journal: Nucleic Acids Research. 2010 Mar 22. [Epub ahead of print]

Title: Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells.

Authors: Dougherty JD, et al.

A method is described for the affinity purification of the process of translating mRNA from genetically labeled cell populations. The method allows quantitative comparisons of the genes employed by each specific cell type. This paper also presents a statistic called the specificity index that can be used for comparative quantitative analysis to identify genes enriched in specific cell populations across a large number of profiles. This measure correctly predicts in situ hybridization patterns for many cell types, according to the authors. In this paper, they apply the measure to a large survey of CNS cell-specific microarray data to identify those genes that are significantly enriched in each population.


Journal: Pediatrics. 2010 Mar 15. [Epub ahead of print]

Title: Clinical genetic testing for patients with autism spectrum disorders.

Authors: Shen Y, et al.

The authors of this study performed various tests on a cohort of 933 patients for a diagnosis. Clinical genetic testing included G-banded karyotype, fragile X testing, and chromosomal microarray to test for submicroscopic genomic deletions and duplications. The authors compared the diagnostic yield of clinically significant genetic changes and determined that CMA had the highest detection rate among clinically available genetic tests for patients with ASD. Though they noted that the interpretation of microarray data is complicated by the presence of both novel and recurrent copy-number variants of unknown significance, the authors argued that CMA should be considered as part of the initial diagnostic evaluation of patients with ASD.


Journal: Science. 2010 Mar 18. [Epub ahead of print]

Title: Variation in transcription factor binding among humans.

Authors: Kasowski M, et al.

The authors of this study examined genome-wide differences in transcription factor binding in several humans and a single chimpanzee using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase and a key regulator of immune responses, NFkappaB (p65), were mapped in ten lymphoblastoid cell lines and 25 percent and 7.5 percent of the respective binding regions were found to differ between individuals. Binding differences were frequently associated with SNPs and genomic structural variants and were often correlated with differences in gene expression, suggesting functional consequences of binding variation, according to the authors. The authors said their results indicate that many differences in individuals and species occur at the level of TF binding and provide insight into the genetic events responsible for these differences.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.