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In Print: Jun 14, 2011

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Microarray Papers of Note Published May 2011

Journal: American Journal of Medical Genetics. 2011 May 27 [Epub ahead of print]

Title: Submicroscopic deletion in 7q31 encompassing CADPS2 and TSPAN12 in a child with autism spectrum disorder and PHPV.

Authors: Okamoto N, et al.

The authors performed array comparative genomic hybridization using a whole-genome oligonucleotide microarray in a patient with autism spectrum disorder and persistent hyperplastic primary vitreous. Submicroscopic deletions in 7q31 encompassing Ca2+ -dependent activator protein for secretion 2 and TSPAN12 were confirmed. They hypothesized that haploinsufficiency of CADPS2 and TSPAN12 contributes to ASDs and PHPV, respectively.


Journal: American Journal of Medical Genetics. 2011 May;155A(5):1152-6.

Title: Somatic/gonadal mosaicism in a syndromic form of ectrodactyly, including eye abnormalities, documented through array-based comparative genomic hybridization.

Authors: Filho A, et al.

The authors used array-based comparative genomic hybridization to study a family with two brothers who have a split hand/foot malformation and ocular abnormalities. Their sister and both parents are healthy. DNA of all five family members was analyzed using oligonucleotide-based DNA microarray and quantitative PCR. The two affected brothers were found to have a small duplication of approximately 539 kilobases at 10q24.32. The patients' sister and father do not have the microduplication, but qPCR showed that the mother's DNA carries the duplication in 20 percent of blood lymphocytes. The authors demonstrated that somatic/gonadal mosaicism is a mechanism that gives rise to SHFM. They also suggest that ocular abnormalities may be part of the clinical description of SHFM.


Journal: American Journal of Surgical Pathology. 2011 May 19. [Epub ahead of print]

Title: Evaluation of a gene expression microarray-based assay to determine tissue type of origin on a diverse set of 49 malignancies.

Authors: Beck A, et al.

The authors of this study evaluated the performance of Pathwork Diagnostics' Tissue of Origin Frozen Assay on 49 malignancies. They classified each case into one of four groups: common morphology from a tissue type included in the assay, uncommon morphology from a tissue type included in the assay, tumor from a tissue type not included in the assay, and malignancies of unknown primary. They reported a strong diagnostic performance for common morphologies from tissue types on the assay. At the same time, they noted a significant decline in performance for uncommon morphologies from tissue types included in the assay and for tumors from tissue types not included in the assay.


Journal: Analytical Chemistry. 2011 May 1;83(9):3610-3615.

Title: Enhanced colorimetric detection on porous microarrays using in situ substrate production.

Authors: Le Goff G, et al.

The authors report a technique for the enhanced colorimetric detection of multiplexed hybridization onto porous membrane-based microarrays. The approach combines the use of horseradish peroxidase as a label together with a chromogen substrate and a local production of the hydrogen peroxide required for substrate oxidation. The method was applied to the multiplex detection of SNPs in complex PCR samples. The background lowering was impacted here positively on the SNPs' detection by increasing the complementary/noncomplementary signal ratio.


Journal: Analytical Chemistry. 2011 May 31. [Epub ahead of print]

Title: Increased cross-platform microarray dataset correlation via substrate-independent nanofilms.

Authors: Spillman S, et al.

Recently developed substrate-independent nanofilms were used to generate concordant cross-platform microarray datasets on a diverse set of materials such as glass, mica, silicon, and polymer. Using model DNA and protein dose-response assays, the number of cross-platform datasets exhibiting high correlation increased from 33 percent to 86 percent when relying on platforms coated with the substrate-independent nanofilms as opposed to traditional surface coatings such as aminosilane and poly-L-lysine. The authors believe the substrate-independent nanofilms can be tailored through secondary modifications to improve assay performance.

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Journal: Applied Environmental Microbiology. 2011 May 13. [Epub ahead of print]

Title: Application of broad-range resequencing array RPM-TEI for detection of pathogens in desert dust samples from Kuwait and Iraq.

Authors: Leski T, et al.

The authors used multiplexed PCR and TessArae's RPM-TEI 1.0 resequencing microarray to screen samples of fine topsoil particles and airborne dust collected in 19 locations in Iraq and Kuwait for the presence of a broad range of human pathogens. The results indicated the presence of potential human pathogens, including Mycobacterium, Brucella, Coxiella burnetii, Clostridium perfringens, and Bacillus. The presence of C. burnetii, a "highly infectious potential biowarfare agent," was confirmed and detected in additional samples using real-time PCR, indicating a high prevalence of this organism in the analyzed samples.


Journal: Atherosclerosis. 2011 May;216(1):139-45.

Title: An APEX-based genotyping microarray for the screening of 168 mutations associated with familial hypercholesterolemia.

Authors: Dušková L, et al.

The authors performed molecular genetic analysis of 1,945 Czech familial hypercholesterolemia probands to design an arrayed primer extension-based genotyping DNA microarray, which they call the FH chip. The FH chip contains the APOB mutation p.Arg3527Gln, all 89 LDLR point mutations and small DNA rearrangements detected in Czech FH patients, and 78 mutations frequent in other European and Asian FH populations. The validation phase revealed the sensitivity and specificity of the FH chip platform to be 100 percent and 99.1 percent, respectively.


Journal: Cellular Oncology. 2011 May 6. [Epub ahead of print]

Title: Gene copy number variation in male breast cancer by aCGH.

Authors: Tommasi S, et al.

The aim of this study was to investigate DNA imbalances of male breast cancer patients by array comparative genomic hybridization and compare them with a female breast cancer dataset. The authors used Agilent Technologies' Human Genome CGH Microarray Kit 44B and 44 K to compare genomic alterations in 25 male breast cancer tissues studied at the National Cancer Center of Bari, Italy, and 16 female breast cancer deposited with the Gene Expression Omnibus. Data analysis was performed with BioDiscovery's Nexus Copy Number 5.0 software. All the 25 male and 16 female breast cancer samples displayed some chromosomal instability, the authors discovered, but male samples presented a lower frequency of genetic alterations both in terms of loss and gains.


Journal: Cellular Oncology. 2011 May 11. [Epub ahead of print]

Title: Ultra-fast processing of gigapixel tissue microarray images using high performance computing.

Authors: Wang Y, et al.

According to the authors of this study, the processing of tissue microarray slides is "time-consuming, bottlenecking a potentially high-throughput platform." They developed an analysis approach based on a high-performance cluster and centralized dynamic load balancing and evaluated it on non-small cell lung cancer tissue microarrays for complex analysis of tissue pattern and immunohistochemical positivity. According to the paper, the automated processing of a slide containing 230 patient samples could be sped up by a factor of 22 using the approach, bringing the analysis time to one minute, and more than 90 arrays could be analyzed simultaneously.


Journal: Clinical Cancer Research. 2011 May 24. [Epub ahead of print]

Title: Genome-wide analysis of promoter methylation associated with gene expression profiles of pancreatic adenocarcinomas.

Authors: Vincent A, et al.

The goal of this study was to comprehensively identify CpG island methylation alterations between pancreatic cancers and normal pancreata and their associated gene expression alterations. The authors used a microarray to analyze the methylation profile of 27,800 CpG islands covering 21 megabases of the human genome in nine pairs of pancreatic cancer versus normal pancreatic epithelial tissues as well as in three matched pairs of pancreatic cancer versus lymphoid tissues from the same individual. They identified dozens of aberrantly methylated and differentially expressed genes in pancreatic cancers including a more comprehensive list of hypermethylated and silenced genes that have not been previously described as targets for aberrant methylation in cancer.

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Journal: European Journal of Human Genetics. 2011 May;19(5):547-54.

Title: Deletions flanked by breakpoints 3 and 4 on 15q13 may contribute to abnormal phenotypes.

Authors: Rosenfeld J, et al.

Non-allelic homologous recombination between segmental duplications in proximal chromosome 15q breakpoint regions can lead to microdeletions and microduplications, but the significance of these alterations is unclear. The authors of this paper identified six individuals with deletions limited to the BP3-BP4 interval and an additional four individuals with deletions of the BP3-BP5 interval from 34,046 samples submitted for clinical testing by microarray-based comparative genomic hybridization. Of four individuals with BP3-BP4 deletions for whom parental testing was conducted, two were apparently de novo and two were maternally inherited. A comparison of clinical features, available for five individuals in the study, with those in the literature showed common features of short stature, microcephaly, hypotonia, and premature breast development in some individuals. The authors suggest that this deletion may have a role in abnormal phenotypes in some individuals.


Journal: Fertility & Sterility. 2011 May 14. [Epub ahead of print]

Title: Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.

Authors: Treff N, et al.

The authors conducted pre-implantation genetic diagnosis for a woman with a balanced translocation causing Alagille syndrome. PGD was applied to 48 embryos. Real-time polymerase chain reaction, SNP microarray, and fluorescence in situ hybridization all demonstrated 100 percent consistency, although FISH failed to detect aneuploidies observed by comprehensive SNP microarray-based analyses. Two blastocysts were identified to be normal for all three factors using SNP microarray technology alone. The two normal embryos were transferred back to the patient, resulting in the delivery of a healthy boy with a normal karyotype.


Journal: Journal of Human Genetics. 2011 May 26. [Epub ahead of print]

Title: 16p13.11 duplication is a risk factor for a wide spectrum of neuropsychiatric disorders.

Authors: Ramalingam A, et al.

The chromosome 16p13.11 heterozygous deletion is associated with neuropsychiatric disorders including intellectual disabilities, autism, schizophrenia, epilepsy and attention-deficit hyperactivity disorder, but the clinical significance of its reciprocal duplication is not clearly defined yet. The authors of this study evaluated 1,645 consecutive pediatric patients with various developmental disorders by high-resolution microarray-based comparative genomic hybridization and identified four deletions and eight duplications within the 16p13.11 region. The authors believe the data lends support for the pathogenic involvement of this duplication in patients who carry it.


Journal: Journal of Medical Microbiology. 2011 May 26. [Epub ahead of print]

Title: Microarray-based detection of extended virulence and antimicrobial resistance gene profiles in phylogroup B2 Escherichia coli of human, meat and animal origin.

Authors: Jakobsen L, et al.

To study connections between Escherichia coli-causing urinary tract infections in human intestines and meat and food-production animals, the authors of this study screened an E. coli phylogroup B2 strain collection of geographical and temporally matched isolates from UTI patients, community-dwelling humans, imported and Danish broiler chicken meat, Danish broiler chickens, imported and Danish pork, and healthy Danish pigs. The isolates were subjected to microarray analysis for 315 virulence genes and variants and 82 antimicrobial resistance genes and variants. In total, 133 different virulence and antimicrobial resistance genes were detected in at least one UTI isolate. The group's findings suggest that B2 E. coli from meat and animal origin can be the source of most of the virulence and antimicrobial resistance genes detected in uropathogenic E. coli isolates and there is a general resemblance of animal, meat, and UTI E. coli based on extended gene profiling.

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Journal: Journal of Proteome Research. 2011 May 31. [Epub ahead of print]

Title: Proteomic analyses of lung lysates from short-term exposure of Fischer 344 rats to cigarette smoke.

Authors: Pelech S, et al.

A cigarette smoke exposure study was conducted in rats to identify changes in lung proteins. Lung lysates from control verses treated animals were screened with 650 antibodies for changes in signaling protein levels and phosphorylation using antibody microarray technology. Over 100 of the top protein hits were assessed by immunoblotting. The top smoke-altered proteins were further evaluated using reverse lysate microarrays. The authors believe that changes in identified proteins may serve as early indicators of lung damage.


Journal: Microbial Ecology. 2011 May 17. [Epub ahead of print]

Title: Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland.

Authors: Kelly L, et al.

Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterized using the PhyloChip microarray platform and clone library analysis of 16S rRNA genes, revealing the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site, host to a rhyolitic/andesitic lava flow, than that present at the Hnausahraun site, which hosts a basaltic lava flow. Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, the authors argue that rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks.


Journal: Molecular Cytogenetics. 2011 May 9;4:13.

Title: Comparative genomic hybridization on microarray (a-CGH) in constitutional and acquired mosaicism may detect as low as 8 percent abnormal cells.

Authors: Valli R, et al.

The authors constructed a case of synthetic mosaicism by mixing the DNA of three patients carrying altogether seven chromosome imbalances with normal sex-matched DNA. Dilutions were prepared mimicking between 5 percent and 15 percent levels of mosaicism. Oligomer-based array comparative genomic hybridization was applied on the patients' DNA. The use of array-CGH on the synthetic mosaics proved to be able to detect as low as 8 percent abnormal cells in the tissue examined.


Journal: Nature. 2011 May 25. [Epub ahead of print]

Title: Transcriptomic analysis of autistic brain reveals convergent molecular pathology.

Authors: Voineagu I, et al.
The researchers used Illumina Ref8v3 arrays to profile gene expression patterns in post-mortem brain tissue from 19 individuals with autism spectrum disorders and 17 unaffected individuals. The team focused on three brain regions: the superior temporal gyrus and prefrontal cortex, both in the cortex, as well as the cerebellar vermis in the cerebellum. Some 444 genes showed significant expression differences in cortex samples of those with ASD versus controls, compared to just two in the cerebellum.

BioArray News sister publication GenomeWeb Daily News reported on the findings last month.


Journal: Proceedings of the National Academy of Sciences. 2011 May 17. [Epub ahead of print]

Title: Expression of trypanotolerance in N'Dama x Boran crosses under field challenge in relation to N'Dama genome content.

Authors: Orenge C, et al.

Investigators used a combination of gene expression profiling and transcriptome and targeted gene sequencing to characterize African cattle breeds that are sensitive or relatively resistant to Trypanosoma congolense infection. Specifically, they used Affymetrix Bovine Genome arrays to assess gene expression patterns in liver, spleen, and lymph node samples cattle from N'Dama and Boran cattle before T. congolense infection, 21 days after infection, and 35 days after infection, assessing 25 animals from each breed overall. The search yielded two genes that appear to have undergone trypanosomiasis-related selective sweeps: TICAM1 and ARHGAP15.


Journal: Proceedings of the National Academy of Sciences. 2011 May 31;108(22):9026-31.

Title: Counting individual DNA molecules by the stochastic attachment of diverse labels.

Authors: Fu G, et al.

The authors developed a strategy for single-molecule counting termed stochastic labeling, where random attachment of a diverse set of labels converts a population of identical DNA molecules into a population of distinct DNA molecules suitable for threshold detection. The conceptual framework for stochastic labeling is demonstrated by determining the absolute and relative number of selected genes after stochastically labeling approximately 360,000 different fragments of the human genome. The approach takes advantage of microarray and sequencing technologies to count absolute numbers of multiple targets. Stochastic labeling should be useful for determining the absolute numbers of RNA or DNA molecules in single cells, the authors state.

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