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In Print: Aug 4, 2009

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Microarray Papers of Note Published in July 2009

Journal: Analytical Chemistry. 2009 Jul 15;81(14):5777-82.

Title: Microsphere-based rolling circle amplification microarray for the detection of DNA and proteins in a single assay.

Authors: T Konry; R Hayman; D Walt

The authors describe a high-density microarray for simultaneous detection of proteins and DNA in a single test. The authors used rolling circle amplification in the system as a signal amplification method for both protein and nucleic acid detection. The microsphere sensors were tested with synthetic DNA and purified recombinant protein analytes. The target DNA sequence was designed from a highly conserved gene that encodes the outer membrane protein P6 (OMP-P6) of both typeable and nontypeable strains of Haemophilus influenzae. The proinflammatory mediators IL-6 and IL-8 were selected as target proteins. Capture antibodies were first immobilized on fluorescently encoded microspheres. The microspheres were then loaded into the etched microwells of an imaging optical fiber bundle. A sandwich assay was performed for target proteins IL-6 and IL-8 using biotin-labeled secondary antibodies. Biotinylated capture DNA probes were then attached to the detection antibodies via an avidin bridge. A padlock probe, complementary to the target sequence, was subsequently hybridized to the capture probe. In the presence of the target sequence, the padlock probe was ligated, and this circular sequence was used for RCA. Following RCA, multiple fluorescently labeled signal probes were hybridized to each amplified sequence, and the microarray was imaged using an epi-fluorescence microscope, according to the authors. Using the assay, detection limits down to 10 femtometers and 1 picometer were achieved for proteins and target DNA, respectively.


Journal: Annals of Human Genetics. 2009 Jul 1. [Epub ahead of print]

Title: Combining microarray-based genomic selection with the Illumina Genome Analyzer platform to sequence diploid target regions.

Authors: D Okou; A Locke; K Steinberg; K Hagen; P Athri; A Shetty; V Patel; M Zwick

The authors of this paper optimized microarray-based genomic selection for use with the Illumina Genome Analyzer. A set of 202 fragments (304 kb in total) contained within a 1.7 Mb genomic region on human chromosome X was selected and sequenced in 10 female HapMap samples generating a total of 2.4 GB of DNA sequence. The authors maintain that data generated using array-based genomic selection and sequencing demonstrates that the approach can generate the "very high-quality sequence data necessary for human genetics research."


Journal: BMC Genomics. 2009 Jul 14;10 Suppl 2:S3.

Title: Application of chicken microarrays for gene expression analysis in other avian species.

Authors: T Crowley; V Haring; S Burggraaf; R Moore

In this study, the authors used a whole-genome long oligonucleotide chicken microarray to assess cross-species hybridization. They hybridized a number of different avian species to the array, and were able to distinguish ducks that were infected with avian influenza from uninfected ducks using the platform. The authors were also able to detect known chicken immunological genes in all of the hybridized avian species.


Journal: BMC Research Notes. 2009 Jul 24;2(1):150.

Title: An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping.

Authors: R Sasidharan; A Agarwal; J Rozowsky; M Gerstein

The authors developed an approach to compare transcripts identified from tiling microarray and MPSS sequencing data. They used the published rice and Arabidopsis datasets because they provide the "best matched sets of arrays and sequencing experiments." After scoring the arrays consistently in both the organisms, a first pass comparison revealed a small overlap in transcripts of 22 percent and 66 percent, respectively, in rice and Arabidopsis. However, by restricting their comparison to only protein-coding gene loci, the authors found a "very good overlap" between the two technologies.

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Journal: Cancer Research. 2009 Jul 15;69(14):5970-7.

Title: microRNA miR-196a-2 and breast cancer: a genetic and epigenetic association study and functional analysis.

Authors: A Hoffman; T Zheng; C Yi; D Leaderer; J Weidhaas; F Slack; Y Zhang; T Paranjape; Y Zhu

The authors performed a genetic association analysis by screening genetic variants in 15 microRNA genes and detected that a common sequence variant in hsa-miR-196a-2 was significantly associated with decreased breast cancer risk. They discovered that hypermethylation of a CpG island upstream of the miR-196a-2 precursor was also associated with reduced breast cancer risk. By delivering expression vectors containing either wild-type or mutant precursors of miR-196a-2 into breast cancer cells, the authors demonstrated that this variant led to less efficient processing of the miRNA precursor to its mature form as well as diminished capacity to regulate target genes. Subsequently, the authors used a whole-genome expression microarray to identify a cancer-relevant network formed by genes significantly altered following enforced expression of miR-196a-2. Mutagenesis analysis further showed that cell cycle response to mutagen challenge was significantly enhanced in cells treated with variant miR-196a-2 compared with cells treated with the wild-type. The authors suggest that miR-196a-2 might have a potentially oncogenic role in breast tumorigenesis, and the functional genetic variant in its mature region could serve as a biomarker for breast cancer susceptibility.


Journal: Experimental and Molecular Medicine. 2009 Jul 31;41(7):462-70.

Title: Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

Authors: S Jung; S Shin; S Yim; H Choi; S Lee; Y Chung

To achieve high-resolution copy number analysis integrated with expression profiles, the authors developed a human 30,000-probe oligonucleotide-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using an MDA-MB-231 cell line. They compared the alterations detected by the oligo array with those detected by the 3,000 bacterial artificial chromosome array for validation. The oligoarray identified the single copy difference "more accurately and sensitively" than the BAC array, the authors found. Overall, they argue that their 30K oligoarray-CGH system can be a "reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost."


Journal: Genes, Chromosomes, and Cancer. 2009 Jul;48(7):603-14.

Title: A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect.

Authors: L Agnelli; L Mosca; S Fabris; M Lionetti; A Andronache; I Kwee; K Todoerti; D Verdelli; C Battaglia; F Bertoni; G Deliliers; A Neri

Multiple myeloma is characterized by marked genomic heterogeneity, according to the authors. To better understand the genomic complexity of MM, they analyzed a panel of 45 patients using combined fluorescence in situ hybridization and microarray approaches. First, they generated genome-wide profiles of 41 MMs and four plasma cell leukemias, using a self-developed procedure to infer exact local copy numbers for each sample. Subsequent analysis identified a "significant fraction" of patients showing near-tetraploidy. A conventional hierarchical clustering analysis showed that near-tetraploidy, 1q gain, hyperdiploidy, and recursive deletions at 1p and chromosomes 13, 14, and 22 were the main aberrations driving samples grouping. Mapping information was integrated with gene-expression profiles of the tumor samples, and a multiclass analysis of transcriptional profiles characterizing the different clusters showed marked gene-dosage effects, the authors wrote. Additionally, they identified several loci in which gene expression correlated with the occurrence of loss of heterozygosity.

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Journal: Genome Research. 2009 Jul 10. [Epub ahead of print]

Title: High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications.

Authors: T Shaikh; X Gai; J Perin; J Glessner; H Xie; K Murphy; R O'Hara; T Casalunovo; L Conlin; M D'arcy; E Franckelton; E Geiger; C Haldeman-Englert; M Imielinski; C Kim; L Medne; K Annaiah; J Bradfield; E Dabaghyan; A Eckert; C Onyiah; S Ostapenko; F Otieno; E Santa; J Shaner; R Skraban; R Smith; J Elia; E Goldmuntz; N Spinner; E Zackai; R Chiavacci; R Grundmeier; E Rappaport; S Grant; P White; H Hakonarson

The authors presented a database of copy number variations detected in 2,026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. The large cohort included Caucasians (65.2 percent) and African-Americans (34.2 percent), and was analyzed for CNVs in a single study using a uniform array platform and computational process, the authors reported. As a result of that effort, they catalogued and characterized 54,462 individual CNVs, 77.8 percent of which were identified in multiple unrelated individuals. These non-unique CNVs mapped to 3,272 distinct regions of genomic variation spanning 5.9 percent of the genome. 51.5 percent of these variants were previously unreported, and more than 85 percent are rare. Also, the authors used the data set to distinguish CNVs with pathologic significance from normal variants. BioArray News spoke with co-authors Tamim Shaikh and Hakon Hakonarson about the project last month (see BAN 7/21/2009).


Journal: Journal of Translational Medicine. 2009 Jul 28;7(1):65. [Epub ahead of print]

Title: Development of a microarray platform for FFPET profiling: application to the classification of human tumors.

Authors: S Duenwald; M Zhou; Y Wang; S Lejnine; A Kulkarni; J Graves; R Smith; J Castle; G Tokiwa; B Fine; H Dai; T Fare; M Marton

The authors developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of formalin-fixed, paraffin-embedded samples. They profiled a set of 50 fresh-frozen breast cancer samples and assigned class labels according to an existing signature, and then profiled 50 matched FFPE samples to test how well the FFPE data predicted the same class labels. According to their results, the authors' platform can accurately sort FFPE samples into class labels derived from FF classifiers. Additionally, a classifier derived from FFPE samples can reliably provide the same sorting power as a classifier derived from matched FF samples, the authors report. According to the authors, their approach may be useful in generating hypotheses from the archives of FFPE samples, and could lead to prognostic and predictive classifiers that could be used to segregate patients for clinical trial enrollment or to guide patient treatment.


Journal: Journal of Virological Methods. 2009 Jul 25. [Epub ahead of print]

Title: A low-density oligonucleotide microarray for the detection of viral and atypical bacterial respiratory pathogens.

Authors: G Cannon; M Carr; Z Yandle; K Schaffer; R Kidney; G Hosny; A Doyle; J Ryan; R Gunson; T Collins; W Carman; J Connell; W Hall

The authors describe a PCR-based, low-density oligonucleotide microarray for the detection of 16 viral and two atypical bacterial pathogens. The array exhibited "comparable sensitivities and specificities" to RT-PCR, the authors state. Additionally, the authors argue that arrays incorporate "an intrinsic redundancy as multiple and non-identical probes per target on the array allow direct intra-assay confirmation of positives."

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Journal: Molecular & Cellular Proteomics. 2009 Jul 28. [Epub ahead of print]

Title: Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high-density protein microarrays.

Authors: I Babel; R Barderas; R Díaz-Uriarte; J Martínez-Torrecuadrada; M Sánchez-Carbayo; J Casal

The authors used commercial protein microarrays containing 8,000 human proteins to examine 20 sera samples from colorectal cancer patients and healthy subjects to identify autoantibody patterns and associated antigens. They found that 43 proteins were differentially recognized by tumoral and reference sera in the protein microarray. Five immunoreactive antigens, Pim-1, MAPKAPK3, STK4, SRC and FGFR4, showed the highest prevalence in cancer samples. A diagnostic enzyme-linked immunsorbent assay based on the combination of MAPKAPK3 and ACVR2B proteins yielded specificity and sensitivity values of 73.9 percent and 83.3 percent, respectively, for CRC discrimination after using an independent set sample containing 94 sera representative of different stages of progression and control subjects, the authors found.


Journal: Nature. 2009 Jul 8. [Epub ahead of print]

Title: A highly annotated whole-genome sequence of a Korean individual.

Authors: J Kim; Y Ju; H Park; S Kim; S Lee; J Yi; J Mudge; N Miller; D Hong; C Bell; H Kim; I Chung; W Lee; J Lee; S Seo; J Yun; H Woo; H Lee; D Suh; S Lee; H Kim; M Yavartanoo; M Kwak; Y Zheng; M Lee; H Park; J Kim; O Gokcumen; R Mills; A Zaranek; J Thakuria; X Wu; R Kim; J Huntley; S Luo; G Schroth; T Wu; H Kim; K Yang; W Park; H Kim; G Church; C Lee; S Kingsmore; J Seo

The authors provide a highly annotated, whole-genome sequence for a Korean individual, known as AK1. They determined the genome of AK1 using a combined approach that included whole-genome shotgun sequencing, targeted bacterial artificial chromosome sequencing, and high-resolution comparative genomic hybridization using custom microarrays featuring more than 24 million probes. Alignment to a reference composite of several ethnic clades disclosed nearly 3.45 million SNPs, including 10,162 non-synonymous SNPs, and 170,202 deletion or insertion polymorphisms.


Journal: Nucleic Acids Research. 2009 Jul;37(12):e89.

Title: Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.

Authors: S Kamalakaran; J Kendall; X Zhao; C Tang; S Khan; K Ravi; T Auletta; M Riggs; Y Wang; A Helland; B
Naume; N Dimitrova; A Børresen-Dale; J Hicks; R Lucito

The authors developed a high-resolution microarray that detects the methylation status of more than 25,000 CpG islands in the human genome. They performed experiments to demonstrate low system noise in the methodology and that the array probes have a high signal-to-noise ratio. The authors validated methylation measurements between different cell lines to demonstrate the accuracy of measurement. They also identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. According to the authors, the methodology can identify methylation profiles in cancer and can differentiate any CpG methylation alterations.


Journal: Nucleic Acids Research. 2009 Jul 17. [Epub ahead of print]

Title: Importance of randomization in microarray experimental designs with Illumina platforms.

Authors: R Verdugo; C Deschepper; G Muñoz; D Pomp; G Churchill

The authors assayed multiple samples on Illumina BeadChips in an ordered series of arrays. They performed two experiments using the same samples but different hybridization designs. The authors compared a confounded BeadChip design with a randomized BeadChip. An ordinal effect of array position on intensity values was observed in both experiments. The authors demonstrate that there is an increased rate of false-positive results in the confounded design and that attempts to correct for confounded effects by statistical modeling reduce power of detection for true differential expression. They argue that simple analysis models without post hoc corrections provide the best results possible for a given experimental design. Normalization also improved differential expression testing in both experiments but randomization was the most important factor for establishing accurate results. They conclude that lack of randomization cannot be corrected by normalization or by analytical methods. Proper randomization is essential for successful microarray experiments, they state.


Journal: Proceedings of the National Academy of Sciences. 2009 Jul 21;106(29):12019-24.

Title: Global discovery of primate-specific genes in the human genome.

Authors: S Tay; J Blythe; L Lipovich

The genomic basis of primate phenotypic uniqueness remains obscure, despite increasing genome and transcriptome sequence data availability, according to the authors. To discover primate-specific genes, the authors screened a catalog of 38,037 human transcriptional units compiled from EST and cDNA sequences in conjunction with the FANTOM3 transcriptome project. Of the 33 primate-specific TUs found with human Affymetrix microarray probe support, 21 were differentially expressed in human teratozoospermia, the authors report. These primate-specific genes can be used for future functional studies, they state.

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.