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In Print: Last Week's Microarray Papers of Note: Sep 10, 2013


A predictive factor of the quality of microarray comparative genomic hybridization analysis for formalin-fixed paraffin-embedded archival tissue.
Diagn Mol Pathol. 2013 Sep;22(3):174-80.
Nakao K, et al.

The authors searched for a predictive factor of the performance of FFPE DNA in aCGH analysis. DNA was extracted from 63 FFPE archival tissue samples of various tissue types, followed by CGH analysis using high-density oligonucleotide microarrays. A derivative log ratio spread, or DLRSpread, was used to assess the overall quality of each aCGH result. According to the authors, the DLRSpread correlated significantly with the double-stranded DNA ratio of tumor DNA, storage time, and the degree of labeling with Cy5.

Simultaneous light-directed synthesis of mirror-image microarrays in a photochemical reaction cell with flare suppression.
Anal Chem. 2013 Sep 6. [Epub ahead of print]
Sack M, et al.

The authors describe a photochemical reaction cell that allows for the simultaneous synthesis of microarrays on two substrates. The reaction cell positions both substrates within the limited depth-of-focus of the optical system while maintaining the necessary reagent flow conditions. The resulting microarrays are mirror images of each other but otherwise identical, according to the authors

Signatures of selection identify loci associated with milk yield in sheep.
BMC Genet. 2013 Sep 3;14(1):76. [Epub ahead of print]
Moioli B, et al.

A genome-wide scan using the Illumina SNP50K Beadchip was performed in the attempt to identify genomic regions associated with milk productivity in sheep. The ovine genomic regions encoding putative candidate genes were compared with the corresponding areas in Bos taurus, the annotated bull genome, allowing the detection of two genes, the Palmdelphin and the Ring finger protein 145. According to the authors, these genes encoded non-synonymous mutations correlated with the marker alleles.

The Scan

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.

Study Examines Relationship Between Cellular Metabolism, DNA Damage Repair

A new study in Molecular Systems Biology finds that an antioxidant enzyme shifts from mitochondria to the nucleus as part of the DNA damage response.

Stem Cell Systems Target Metastatic Melanoma in Mouse Model

Researchers in Science Translational Medicine describe a pair of stem cell systems aimed at boosting immune responses against metastatic melanoma in the brain.

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.