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In Print: Last Week's Microarray Papers of Note: Oct 9, 2012


Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways.
Oncogene. 2012 Oct 4;31(40):4409-19.
Dallosso A, Oster B, Greenhough A, et al.

The authors used Illumina Beadchip methylation arrays to identify long-range epigenetic silencing across 800 kilobases of chromosome 5q31 in colorectal adenomas and carcinomas relative to normal colonic epithelial DNA. The gene PCDHGC3 was hypermethylated in 60.7 percent of cases, and subsequent analyses led the authors to conclude that PCDH LRES is an important tumour suppressor locus in colorectal cancer, and that PCDHGC3 may be a strong marker and driver for adenoma-carcinoma transition.

DMET-Analyzer: automatic analysis of Affymetrix DMET Data.
BMC Bioinformatics. 2012 Oct 5;13(1):258.
Guzzi P, Agapito G, Di Martino M, et al.

The authors developed the described software tool for automatic association analysis of patient genomes using data generated on Affymetrix's DMET panel. The proposed system allows users to automate the analysis of DMET SNP data, automatically annotate DMET SNP data and search existing databases of SNPs, and associate SNPs with pathways through PharmaGKB, a knowledge base for pharmacogenomic studies. The system is freely available for academic purposes here.

Hydrodynamic resettability for a microfluidic particulate-based arraying system.
Lab Chip. 2012 Oct 8. [Epub ahead of print]
Sochol R, Dueck M, Li S, et al.

The authors present a single-layer hydrodynamic methodology for releasing high numbers of microparticles after a microfluidic arraying process. Experiments with suspended streptavidin-coated polystyrene microbeads revealed resetting efficiencies of 100 percent. They claim the resettable microarray could be readily integrated into bead-based or cell-based microfluidic platforms to enable the retrieval of high numbers of microparticles and microarray reusability.

Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico.
BMC Genomics. 2012 Oct 5;13(1):530.
Gardner L, Jayasundara N, Castilho P, et al.

The authors constructed a 4x44K array from T. Thynnus ESTs sourced from reproductive tissues to study the reproductive physiology of bluefin tunas. The aim of this particular study was to compare transcription profiles from the ovaries and testes of mature T. Thynnus to establish sex-specific variations underlying their reproductive physiology.

Comparative transcriptome profiling in winter wheat grown under different agricultural practices.
J Agric Food Chem. 2012 Oct 5. [Epub ahead of print]
Tenea G, Cordeiro Raposa F, Maquet A.

Comparative transcriptome profiling was conducted on winter wheat flag leaves of several cultivars growing in open fields under different agricultural production systems. Ten transcripts differentially expressed in organic and conventional growing conditions were identified in Tommi and Centenaire cultivars and transcript abundance profiles of selected probe sets were independently confirmed by quantitative reverse-transcription PCR analysis, tested on Tommi, Centenaire, and Cubus cultivars from different growing year and geographical sites.

Microarray evaluation of specific IgE to allergen components in elite athletes.
Allergy. 2012 Oct 4. [Epub ahead of print]
Bonini M, Marcomini L, Gramiccioni C, et al.

The authors of this study evaluated Phadia's ImmunoCAP ISAC microarray to detect IgE antibodies to specific or cross-reacting allergen components in 72 athletes with different allergic phenotypes. ImmunoCAP ISAC detected the presence of sIgE in 90 percent of poly-sensitized athletes and in 100 percent of allergic controls.

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.