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In Print: Oct 5, 2010

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Microarray Papers of Note Published September 2010

Journal: Analytical Biochemistry. 2010 Sep 15;404(2):244-6. Epub 2010 May 10.

Title: A visual chip-based coimmunoprecipitation technique for analysis of protein-protein interactions.

Authors: Chen Q, et al.

The authors of this study developed a chip-based coimmunoprecipitation platform for analysis of protein-protein interactions. The system combines the advantages of an antibody microarray, traditional coimmunoprecipitation, and a silver enhancement detection method, according to the paper's abstract. The chip was fabricated by spotting anti-Flag antibody on aldehyde-modified slides, and the resulting platform could assay immunoprecipitate from a small amount of crude cell lysates containing Flag-bait and Myc-prey, according to the authors. The interaction signals are visible using biotinylated anti-Myc antibody and colloidal gold-labeled streptavidin followed by a silver enhancement detection method.


Journal: Cancer Prevention Research. 2010 Sep 28. [Epub ahead of print]

Title: Loss of inositol polyphosphate 5-phosphatase is an early event in development of cutaneous squamous cell carcinoma.

Authors: Sekulic A, et al.

To identify genetic changes associated with early stages of cutaneous squamous cell carcinoma development, the authors of this study analyzed a series of 40 archived skin tissues ranging from normal skin to invasive SCC. Using high-resolution array-based comparative genomic hybridization, they identified deletions of a region on chromosome 10q harboring the INPP5A gene in 24 percent of examined SCC tumors. Subsequent validation by immunohistochemistry on an independent sample set of 71 SCC tissues showed reduced INPP5A protein levels in 72 percent of primary SCC tumors. Decrease in INPP5A protein levels seems to be an early event in SCC development, as it also is observed in nine of 26 examined actinic keratoses, the earliest stage in SCC development. The authors claim that the observed frequency and pattern of loss indicate that INPP5A, a negative regulator of inositol signaling, may play a role in development and progression of cutaneous SCC tumors.


Journal: Clinica Chimica Acta. 2010 Sep 6;411(17-18):1187-94. Epub 2010 Mar 27.

Title: Multiplex detection of CpG methylation using microarray combining with target-selection-padlock probe.

Authors: Shi X, et al.

Microarray technology combed with bisulfite-PCR offers a high-throughput approach for detection of DNA methylation, according to the authors of this study. However, the use of microarray-based DNA methylation analysis has been limited by the low throughput of sample preparation due to the difficulty in simultaneous amplification of multiple targets. To overcome this, a set of target-selection-padlock probes was designed to capture the target sequences containing the queried CpG sites from bisulfite-treated genomic DNA. All targets were then amplified by a pair of common primers. The methylation status of multiple targets was detected by single-base extension on an oligonucleotide microarray based on a polyacrylic acid-covered surface. The assay analyzed promoter methylation of eight tumor suppressor genes in 12 colorectal cancer samples and two normal control samples. The authors believe their method may be useful for a large-scale screen of DNA methylation in cancer cell lines and clinical samples.


Journal: Cytometry. 2010 Sep;77(9):881-9.

Title: Cell microarrays for the screening of factors that allow the enrichment of bovine testicular cells.

Authors: Anglin E, et al.

The authors of this paper sought to demonstrate that surface-engineered microarrays can be used for the screening and identification of factors that allow the enrichment and isolation of rare cells from tissue-derived heterogeneous cell populations. In particular, they focused on the enrichment of bovine testicular cells including type A spermatogonia and Sertoli cells. Microarray slides were coated with a copolymer synthesized from poly(ethylene glycol) methacrylate and glycidyl methacrylate to enable both the prevention of cell attachment between printed spots and the covalent anchoring of various factors such as antibodies, lectins, growth factors, extracellular matrix proteins, and synthetic macromolecules on printed spots, according to the authors. Microarrays were then incubated with mixed cell populations from freshly isolated bovine testicular tissue. Overall, cell attachment was evaluated using CellTracker staining, whereas differential attachment of testicular cells was determined by immunohistochemistry staining with Plzf and vimentin antibodies as markers for type A spermatogonia and Sertoli cells, respectively. Based on the results, the authors claim that surface engineered cell-based microarrays can be used to identify factors that allow the selective capture of rare cells from tissue isolated heterogeneous mixtures.

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Journal: Genome Research. 2010 Sep 1. [Epub ahead of print]

Title: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.

Authors: Teer J, et al.

The authors of this paper compared three methods of enrichment for genomic regions of interest for targeted sequencing: molecular inversion probes, solution hybrid selection, and microarray-based genomic selection. Using HapMap DNA samples, they compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes. For sequence analysis, the authors developed a Bayesian genotype-assigning algorithm called Most Probable Genotype. They found that all three capture methods were effective, but sensitivities varied. The authors also observed a low false-positive rate with all three methods. They concluded that the three genomic enrichment methods are "highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data."


Journal: Haematologica. 2010 Sep;95(9):1481-8.

Title: Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia.

Authors: Okamoto R, et al.

The authors of this study compared two different sets of high-density SNP array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples. The patients' samples were randomly acquired from among Caucasian and Asian populations and hybridized to either Affymetrix 50K or 250K SNP arrays. The array data were investigated with the Copy Number Analysis for GeneChips software for allele-specific copy number analysis. The authors' analysis of adult ALL cases led to the identification of new potential target lesions relevant for the pathogenesis of ALL. However, no unequivocal pattern of submicroscopic genomic alterations was found to separate adult ALL from pediatric ALL. Apart from different therapy regimen, differences of prognosis between adult and pediatric ALL are probably based on genetic subgroups according to cytogenetically detectable lesions but not focal genomic copy number microlesions, the authors concluded.


Journal: Human Mutation. 2010 Sep 16. [Epub ahead of print]

Title: Detection of clinically relevant exonic copy-number changes by array CGH.

Authors: Boone P, et al.

The authors of this study designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy number change occurred within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of the array to detect clinically relevant copy number variants with sub-kilobase resolution, according to the authors. They claim that their custom-designed, exon-targeted oligonucleotide array can detect intragenic copy-number changes in patients with various clinical phenotypes.


Journal: Journal of Clinical Microbiology. 2010 Sep 15. [Epub ahead of print]

Title: Hepatitis C virus genotyping using an oligonucleotide microarray based on the NS5B sequence.

Authors: Gryadunov D, et al.

The authors of this paper describe a microarray-based molecular technique for identifying the hepatitis C virus genotype and subtype. It uses low-density, hydrogel-based biochips containing genotype and subtype-specific oligonucleotides based on the sequences of the NS5B region of the HCV genome. Altogether, the biochip contains 120 oligonucleotides that identify specific genotypes and subtypes. The procedure included amplification of a 380-nucleotide fragment of NS5B and its hybridization on the biochip. Tests on 345 HCV-positive samples showed that the assay agreed with NS5B sequencing 100 percent for the genotype and 99.7 percent for the subtype. The hybridization on the microarray and the NS5B sequence were in 100 percent agreement for identifying the most common subtypes. Based on their results, the authors believe their tool is "promising" for HCV genotyping, "especially for implementing the new anti-HCV drugs that require accurate identification of clinically relevant subtypes."


Journal: Journal of Medical Genetics. 2010 Sep 12. [Epub ahead of print]

Title: Submicroscopic genomic alterations in Silver-Russell syndrome and Silver-Russell-like patients.

Authors: Bruce S, et al.

Silver-Russell syndrome features fetal and postnatal growth restriction and variable dysmorphisms. While genetic and epigenetic aberrations on chromosomes 7 and 11 are commonly found in SRS, a large fraction of SRS cases remain with unknown genetic etiology, according to the authors of this study. They screened 22 patients with a diagnosis of SRS and their parents using Affymetrix 250K Sty microarrays. Several analytical approaches were used to identify genomic aberrations such as copy number changes, loss of heterozygosity, and uniparental disomy. Unexpected submicroscopic genomic events with pathogenic potential were found in three patients with molecularly unexplained SRS that was mild, the authors wrote. They believe the findings emphasize that SRS is heterogeneous in genetic etiology and that unbiased genome-scale screens may reveal new genotype-phenotype correlations.

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Journal: Journal of Medical Genetics. 2010 Sep;47(9):586-94.

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.

They authors of this study explored the possibilities for implementing prenatal analysis by using the Affymetrix 250K SNP array platform to screen 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. Aberrations were detected in 17 of 38 fetuses, six of whom with a previously identified chromosomal abnormality and 11 with previously normal or balanced karyotypes. Of the latter, the detected aberration was de novo 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 clinically relevant abnormalities either were novel copy number variants or concerned a uniparental disomy. The authors concluded that microarray use is "important" in prenatal analysis, based on the fact that "identified, clinically relevant, aberrations would have gone undetected with most targeted approaches."


Journal: Journal of Molecular Diagnostics. 2010 Sep;12(5):670-9.

Title: Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics.

Authors: Shao L, et al.

The authors of this study developed a custom genome-wide oligonucleotide microarray interrogating 493 genes involved in hematological disorders. They analyzed 55 patients with hematological neoplasms using the microarray. In 33 patients with apparent normal conventional cytogenetic analysis, aneuploidy or isochromosomes were detected in 12 percent of the patients by aCGH. In 17 patients with chronic lymphocytic leukemia who were initially investigated by using a panel of standard fluorescence in situ hybridization probes, additional copy number changes that were not interrogated by the FISH panel were detected in 47 percent of the patients by aCGH. In five patients with known abnormal karyotypes, aCGH identified the origin of two marker chromosomes and detected microdeletions at five breakpoints involved in three apparent balanced translocations. The authors suggest that a subset of potentially significant genomic alterations is missed by currently available cytogenetic techniques, and recommend the use of array-CGH in diagnosis and follow-up in patients with hematological neoplasms.


Journal: Journal of Proteome Research. 2010 Sep 29. [Epub ahead of print]

Title: Serum autoantibody profiling using a natural glycoprotein microarray for the prognosis of early melanoma.

Authors: Liu Y, et al.

The authors developed a natural glycoprotein microarray to discover serum autoantibodies to distinguish between patients with node-negative melanoma and node-positive melanoma. Dual-lectin affinity chromatography was used to extract glycoproteins from a melanoma cell line. Liquid-based reverse phase separation and microarray platforms were then applied to separate and spot these natural proteins on nitrocellulose slides. The serum autoantibodies were investigated by exposing these proteins to sera from 43 patients at different stages of early melanoma. Recombinant proteins were used to confirm results using a sample set with 79 patients with diagnosed melanoma. According to the authors, the glycoarray platform can be used to profile autoantibodies that could be used as serum biomarkers for prognosis of melanoma.


Journal: Lab on a Chip. 2010 Sep 13. [Epub ahead of print]

Title: Micromolded arrays for separation of adherent cells.

Authors: Wang Y, et al.

The authors of this paper describe a cell microarray-based approach for isolating viable single cells or colonies from a mixed population. Arrays of microwells with bases composed of detachable concave elements, termed microrafts, were fabricated by a dip-coating process using a polydimethylsiloxane mold as the template and the array substrate, according to the authors. Cells plated on the microarray settled and attached at the center of the wells due to the microrafts' concavity. Individual microrafts were dislodged by the action of a needle inserted through the compliant polymer substrate. For cell analysis and isolation, cells of interest were identified using a standard inverted microscope and microrafts carrying target cells were dislodged with the needle. The released cells could be collected, cultured and clonally expanded, according to the authors.


Journal: Molecular & Cellular Proteomics. 2010 Sep 10. [Epub ahead of print]

Title: Sequential multiplex analyte capturing for phospho-protein profiling.

Authors: Poetz O, et al.

While microarray-based sandwich immunoassays can simultaneously detect dozens of proteins, their use in quantifying large numbers of proteins is hampered by cross-reactivity and incompatibilities caused by the immunoassays themselves, according to the authors of this study. They claim that sequential multiplex analyte capturing addresses these problems by repeatedly probing the same sample with different sets of antibody-coated, magnetic suspension bead arrays. To demonstrate this, they used suspension bead array-based assays to probe tumor cell line lysates for the abundance of seven different receptor tyrosine kinases and their degree of phosphorylation. Using the arrays, the authors were able to measure the complex phosphorylation pattern of the epidermal growth factor receptor in the same sample from the same cavity.

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Journal: Nature Genetics. 2010 Sep 12. [Epub ahead of print]

Title: Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma.

Authors: Thorleifsson G, et al.

The authors of this study conducted a genome-wide association study for primary open-angle glaucoma in 1,263 cases and 34,877 controls from Iceland. Using Illumina HumanHap300 or HumanHapCNV370 bead chips, they identified a common sequence variant at 7q31. The authors then replicated the association in sample sets of 2,175 POAG cases and 2,064 controls from Sweden, the UK, and Australia and in 299 POAG cases and 580 unaffected controls from Hong Kong and Shantou, China. The risk variant identified is located close to CAV1 and CAV2, both of which are expressed in the trabecular meshwork and retinal ganglion cells that are involved in the pathogenesis of POAG, according to the authors.


Journal: New England Journal of Medicine. 2010 Sep 23;363(13):1211-21.

Title: A large-scale, consortium-based genome-wide association study of asthma.

Authors: Moffatt M, et al.

The authors carried out a genome-wide association study by genotyping 10,365 persons with physician-diagnosed asthma and 16,110 unaffected persons, all of whom were matched for ancestry. They used random-effects pooled analysis to test for association in the overall study population and in subgroups of subjects with childhood-onset asthma, later-onset asthma, severe asthma, and occupational asthma. Using Illumina's 650K array, the authors observed associations of genome-wide significance between asthma and five SNPs. They concluded that asthma is genetically heterogeneous and that a few common alleles are associated with disease risk at all ages.


Journal: PLoS One. 2010 Sep 20;5(9). pii: e12822.

Title: A novel hepatitis C virus genotyping method based on liquid microarray.

Authors: Duarte C, et al.

The authors of this paper describe the use of a liquid microarray for HCV genotyping. This array is based on the 5' UTR — the most highly conserved region of HCV — and the variable region NS5B sequence. Plasma samples from 78 patients infected with viruses with genotypes and subtypes as determined by Siemens' Versant HCV Genotype Assay LiPA were tested with the new liquid microarray method. Using liquid arrays, the authors were able to successfully determine the genotypes of 74 of the 78 samples previously genotyped using the Versant assay. No genotype discordance was found for any sample and HCV was successfully genotyped with both methods. According to the authors, liquid microarray assays may be added to the list of methods suitable for HCV genotyping.


Journal: PLoS One. 2010 Sep 1;5(9). pii: e12346.

Title: Fruit and soil quality of organic and conventional strawberry agroecosystems.

Authors: Reganold J, et al.

The authors used microarrays to test if there are significant differences in fruit and soil quality from 13 pairs of commercial organic and conventional strawberry agroecosystems in California. At multiple sampling times for two years, the team evaluated three varieties of strawberries for mineral elements, shelf life, phytochemical composition, and organoleptic properties, as well as traditional soil properties and soil DNA using arrays. They found that the organic farms had strawberries with longer shelf life, greater dry matter, and higher antioxidant activity and concentrations of ascorbic acid and phenolic compounds, but lower concentrations of phosphorus and potassium. They also found the organically farmed soils to have more total carbon and nitrogen, greater microbial biomass and activity, and higher concentrations of micronutrients. Organically farmed soils also exhibited greater numbers of endemic genes and greater functional gene abundance and diversity for several biogeochemical processes, such as nitrogen fixation and pesticide degradation.


Journal: Proceedings of the National Academy of Sciences. 2010 Sep 7. [Epub ahead of print]

Title: Microbes and Health Sackler Colloquium: Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways.

Authors: van Baarlen P, et al.

To explore in vivo mucosal responses of healthy adults to probiotics, the authors of this study used arrays to obtain transcriptomes in an intervention study after a double-blind placebo-controlled cross-over design. In the mucosa of the proximal small intestine of healthy volunteers, probiotic strains from the species Lactobacillus acidophilus, L. casei, and L. rhamnosus each induced differential gene-regulatory networks and pathways in the human mucosa. Further analyses revealed that these transcriptional networks regulate major basal mucosal processes and uncovered remarkable similarity to response profiles obtained for specific bioactive molecules and drugs.


Journal: Science Translational Medicine. 2010 Sep 15;2(49):49ra67.

Title: Personalized epigenomic signatures that are stable over time and covary with body mass index.

Authors: Feinberg A, et al.

The authors performed an unbiased genome-scale analysis of around 4 million CpG sites in 74 individuals with comprehensive array-based relative methylation analysis. They found 227 regions that showed "extreme" inter-individual variability across the genome, which are enriched for developmental genes based on Gene Ontology analysis. Half of these regions were stable within individuals over an average of 11 years and defined a personalized epigenomic signature. Four of the regions showed covariation with body mass index consistently at two study visits and were located in or near genes previously implicated in regulating body weight or diabetes.

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