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In Print: May 3, 2011

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Microarray Papers of Note Published April 2011

Journal: American Journal of Human Genetics. 2011 Apr 8;88(4):458-68.

Title: A genome-wide comparison of the functional properties of rare and common genetic variants in humans.

Authors: Zhu Q, et al.

The authors of this paper sequenced the complete genomes of 29 people of European origin to assess the relationship between the functional properties of variants and their population allele frequencies.They determined that the most common genetic variants in the human genome aren't the ones most likely to cause disease and posited that rare genetic variants are more likely linked to disease. The findings prompted the authors to argue that sequencing-based approaches, rather than array-based genome-wide association studies, are more likely to identify the rare variants behind common diseases.

BioArray News spoke with lead author Qianqian Zhu about this work last month (BAN 4/5/2011).


Journal: Analytical Chemistry. 2011 Apr 27. [Epub ahead of print]

Title: Ultrasensitive microarray detection of short RNA sequences with enzymatically modified nanoparticles and surface plasmon resonance imaging measurements.

Authors: Zhou W, et al.

The authors describe a method for short RNA detection that employs an enzymatic capture reaction onto DNA-modified silica nanoparticles, or SiNPs, followed by nanoparticle-enhanced surface plasmon resonance imaging. In the paper, SiNPs functionalized with 5'-phosphorylated single-stranded DNA were used with T4 RNA from a target solution. The authors claim that the detection method can be used to detect multiple ssRNA sequences at concentrations as low as 100 femtomolar in 500 microliters.


Journal: Analytical Chemistry. 2011 Apr 8. [Epub ahead of print]

Title: Drug-eluting microarrays for cell-based screening of chemical-induced apoptosis.

Authors: Kwon C, et al.

The authors designed a microarray platform for cell-based screening that can be carried out at the bench top. The device includes an array of 2,100 individual cell-based assays in a standard microscope slide format. A microarray of chemical-laden hydrogels addresses a matching array of cell-laden microwells, creating a microarray of sealed microscale cell cultures, each with unique conditions. They demonstrated the utility of the device by screening the extent of apoptosis and necrosis in MCF-7 breast cancer cells in response to exposure to a small library of chemical compounds.


Journal: Applied and Environmental Microbiology. 2011 Apr;77(8):2625-33.

Title: Development of a DNA microarray for enterococcal species, virulence, and antibiotic resistance gene determinations among isolates from poultry.

Authors: Champagne J, et al.

A DNA microarray called the Enteroarray was designed with probes targeting four species-specific taxonomic identifiers to discriminate among 18 different enterococcal species, while other probes were designed to identify 18 virulence factors and 174 antibiotic resistance genes. In total, 262 genes were used for species identification of enterococcal isolates, while characterizing their virulence potential through the simultaneous identification of endogenous antibiotic resistance and virulence genes. The new Enteroarray should prove to be a useful tool to genotype strains of enterococci and assess their virulence potential, according to the authors.


Journal: Applied Microbiology and Biotechnology. 2011 Apr 19. [Epub ahead of print]

Title: Profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems using 60-mer oligonucleotide microarray.

Authors: Pathak A, et al.

The authors developed an oligonucleotide microarray for the detection of biodegradative genes and bacterial diversity and tested it in five contaminated ecosystems. The array, called the BiodegPhyloChip, has 60-mer oligonucleotide probes comprising 14,327 unique probes derived from 1,057 biodegradative genes and 880 probes representing 110 phylogenetic genes from diverse bacterial communities. The biodegradative genes are involved in the transformation of 133 chemical pollutants. Application of the developed array using DNA extracted from five different contaminated sites led to the detection of 186 genes, including 26 genes unique to the individual sites.

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Journal: Autism Research. 2011 Apr;4(2):89-97.

Title: A genotype resource for postmortem brain samples from the Autism Tissue Program.

Authors: Wintle R, et al.

The Autism Tissue Program provides researchers with access to well-characterized postmortem brain tissues. In this paper, the authors describe an initiative to extract DNA from Brodmann area 19 in the brain, and genotype the samples using both the Affymetrix Genome-Wide Human SNP Array 6.0 and the Illumina Human1M-Duo DNA Analysis BeadChip. In total, 52 experimental samples, consisting of 27 subjects with confirmed or suspected autism and related disorders, five subjects with cytogenetically visible duplications of 15q, two with epilepsy, and 18 age-matched normal controls were processed, yielding genotype data in all cases.


Journal: Biosensors and Bioelectronics. 2011 Apr 8. [Epub ahead of print]

Title: Silicon biochips for dual label-free and fluorescence detection: Application to protein microarray development.

Authors: Cretich M, et al.

A silicon chip for protein microarray development, fabrication, and validation is described in the paper. According to the authors, the chip allows, within a single experiment performed on the same surface, label-free imaging of arrayed protein probes coupled with high-sensitivity fluorescence detection of the molecular interaction counterparts. The authors claim the array can be used in the assay development process to image arrays, check consistency and quality of the protein array, quantify the amount of immobilized probes, and detect fluorescence of bioassays.


Journal: Biosensors and Biolelectronics. 2011 Apr 15;26(8):3688-91.

Title: Single-molecule-counting protein microarray assay with nanoliter samples and its application in the dynamic protein expression of living cells.

Authors: Li L, et al.

The authors describe a single-molecule-counting microarray assay for quantification of proteins. The target proteins spotted on the substrate were modified with primary antibodies of the proteins and blocked with ethanolamine and BSA using a pin-tool type microarraying robot. Then, biotinylated secondary antibodies of the proteins were bound to the proteins to form sandwich immunocomplexes. After labeling, the image of the microarray was acquired using a homemade single-molecule microarray reader.


Journal: Bioinformatics. 2011 Apr 15;27(8):1052-1060.

Title: Performance assessment of copy number microarray platforms using a spike-in experiment.

Authors: Halper-Stromberg E, et al.

The authors evaluated the sensitivity and specificity of six platforms provided by four leading vendors using a spike-in experiment. They determined that the Roche NimbleGen and Agilent Technologies array platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, they said that Illumina and Affymetrix algorithms that leverage SNP information made up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer, they concluded.


Journal: BMC Molecular Biology. 2011 Apr 12;12(1):15. [Epub ahead of print]

Title: A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon).

Authors: Leelatanawit R, et al.

Poor reproductive maturation in captive male broodstock of the black tiger shrimp Penaeus monodon is a serious problem in the farming industry, according to the authors of this paper. A cDNA microarray, the UniShrimpChip, was constructed from P. Monodon EST libraries of 12 tissues, containing 5,568 non-redundant cDNA clones from 10,536 unique cDNA in the database. The UniShrimpChip was used to study testicular development by comparing gene expression levels of wild brooders from the west and east coasts of Thailand and domesticated brooders with different ages.

BioArray News met with the Thai researchers during a site visit to their lab in Bangkok last year (BAN 3/9/2010).

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Journal: Clinical Pediatrics. 2011 Apr 27. [Epub ahead of print]

Title: Diagnostic yield of genetic testing in children diagnosed with autism spectrum disorders at a regional referral center.

Authors: Roesser J, et al.

The medical records of 507 children were abstracted for genetic testing and factors associated with chromosomal microarray testing. Abnormalities were found on karyotype in 2.3 percent and in DNA for fragile X in 0.04 percent. The authors conclude that the diagnostic yield of the genetic testing was low in this population. Additionally, they state that CMA can be considered as part of the initial genetic screening in children with ASD in most situations.


Journal: Epigenetics. 2011 Apr 1;6(4):410-5.

Title: Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms.

Authors: Rajendram R, et al.

In this study, the authors verified the accuracy of two array methods — methylated DNA immunoprecipitation coupled with CpG island microarrays and sodium bisulfite conversion-based microarrays — in predicting regional methylation levels as measured by pyrosequencing of bisulfite converted DNA. To test the accuracy of these methods they used the Agilent Human CpG island and the Illumina HumanMethylation27 microarrays and compared microarray outputs to the data from targeted BC-pyrosequencing assays from several genomic regions of corresponding samples. They observed relatively high correlation with BC pyrosequencing data for both array platforms. However, the Agilent array was less reliable in predicting intermediate levels of DNA methylation.


Journal: Genome Research. 2011 Apr 25. [Epub ahead of print]

Title: Natural genetic variation caused by small insertions and deletions in the human genome.

Authors: Mills R, et al.

The authors report on almost 2 million small insertions and deletions, or indels, that range from 1 basepair to 10,000 basepairs in length in the genomes of 79 diverse humans. The variants include 819,363 small indels that map to human genes. Small indels frequently were found in the coding exons of these genes, and several lines of evidence indicate that such variation is a major determinant of human biological diversity. Microarray-based genotyping experiments revealed that many of of the reported indels had high levels of linkage disequilibrium with both HapMap SNPs and with high-scoring SNPs from genome-wide association studies.


Journal: Human Molecular Genetics. 2011 Apr 19. [Epub ahead of print]

Title: Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis.

Authors: Kim M, et al.

The authors profiled gene expression and DNA methylation of three cell states of in vitro hepatogenesis — human embryonic stem cell, definitive endoderm, and hepatocyte — using microarray analysis. Among 525 state-specific expressed genes, 67 showed significant negative correlation between gene expression and DNA methylation. State-specific expression and methylation of target genes were validated by quantitative reverse transcription-PCR and pyrosequencing, respectively.


Journal: Human Reproduction.011 Apr;26(4):941-9.

Title: PGD for a complex chromosomal rearrangement by array comparative genomic hybridization.

Authors: Vanneste E, et al.

The authors performed preimplantation genetic diagnosis using array comparative genomic hybridization. Selection of embryos for transfer was only based on copy number status of the chromosomes involved in both rearrangements. In two PGD cycles, nine and seven embryos were analyzed by the array, leaving three and one embryos suitable for transfer, respectively. In both cycles a single embryo was transferred, resulting in pregnancy following the second cycle.


Journal: Human Reproduction. 2011 Apr 18. [Epub ahead of print]

Title: PGD for reciprocal and Robertsonian translocations using array comparative genomic hybridization.

Authors: Fiorentino F, et al.

The authors describe the clinical application of array comparative genomic hybridization to screen for unbalanced translocation derivatives and aneuploidy of all 24 chromosomes. Cell biopsy was carried out on cleavage-stage embryos. Single cells were first lysed and DNA amplified by whole-genome amplification. WGA products were then processed by array CGH using BluGnome 24sure+ arrays. Balanced euploid embryos were then selected for transfer on day 5 of the same cycle.

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Journal: Journal of Virology. 2011 Apr;85(8):3780-91.

Title: Exploring the fitness landscape of an RNA virus by using a universal barcode microarray.

Authors: Lauring A, et al.

The authors developed a molecular barcoding strategy in which viral subpopulations are tagged with unique 20-nucleotide sequences. According to the authors, the behavior of these subpopulations can be monitored using a universal barcode microarray. In this paper, they demonstrated the performance of the barcode microarray platform using poliovirus, a model RNA virus. Using this platform, they explored the fitness landscape occupied by an artificial quasispecies consisting of 48 randomly mutagenized clones. The authors were able to rapidly derive precise fitness measurements for a majority of these clones and identified a neutral space surrounding the wild type.


Journal: Langmuir. 2011 Apr 13. [Epub ahead of print]

Title: Plasmon resonance imaging measurements.

Authors: Seefeld T, et al.

A four-chamber microfluidic biochip was fabricated for the detection of multiple proteins and nucleic acids from microliter volume samples via surface plasmon resonance imaging. The 18 mm × 18 mm biochip consisted of four 3 μL microfluidic chambers attached to an SF10 glass substrate, each of which contained three individually addressable SPRI gold thin film microarray elements. Microarrays of single-stranded DNA and RNA were fabricated by either chemical or enzymatic attachment reactions in these microchannels. The SPRI microarrays were then used to detect femtomole amounts of DNA and proteins.


Journal: Molecular Biosystems. 2011 Apr 5. [Epub ahead of print]

Title: A PNA microarray for tomato genotyping.

Authors: Tedeschi T, et al.

A peptide nucleic acid microarray was designed for the simultaneous identification of several SNPs characteristic of seven different tomato varieties. Highly selective arginine-based monomer containing PNAs were used in order to obtain very selective probes. PNA-microarrays based on these probes were prepared and applied to SNP discrimination in model experiments using oligonucleotide mixtures simulating the different sequences of the seven tomato varieties. The strength and the limitations of such a system for SNP recognition are discussed in the paper.


Journal: Nature Biotechnology. 2011 Apr 30;28(3):282-90.

Title: Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA).

Authors: Stoevesandt O, et al.

The authors describe a so-called "DNA-array-to-protein-array" method for microarraying proteins expressed by cell-free systems in situ on the surface of an array. An array on one slide acts as the template for generating a protein array on a second slide, mediated by a cell free lysate between the two juxtaposed slides. In this paper, they reused the same array several times, and then used the method to generate a microarray of 116 diverse proteins.

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