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In Print: Last Week's Microarray Papers of Note: Aug 26, 2014


The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.
Nature. 2014 Aug 25. [Epub ahead of print]
Wang C, et al.

The authors generated Illumina RNA-seq and Affymetrix microarray data from the same liver samples of rats exposed in triplicate to varying degrees of perturbation by 27 chemicals representing multiple modes of action. RNA-seq outperformed microarray in digital gene expression verification as assessed by quantitative PCR, with the gain mainly due to its improved accuracy for low-abundance transcripts, according to the authors. Nonetheless, classifiers to predict MOAs perform similarly when developed using data from either platform. They concluded that the endpoint studied and its biological complexity, transcript abundance, and the genomic application are important factors in transcriptomic research and for clinical and regulatory decision making.

Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies.
BMC Biotechnol. 2014 Aug 21;14(1):78. [Epub ahead of print]
Sharma H, et al.

The authors have developed a microarray with manageable volumes using a soft gel. In this study, they introduced new applications based on the array, including C2D2P, in which the cells in each well are converted from DNA to protein in parallel; next-generation-sequencing-non-dependent microbiome analysis; and others.

Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome.
Eur J Hum Genet. 2014 Aug 20. [Epub ahead of print]
Kuechler A, et al.

Whole-exome sequencing analysis revealed de novo intragenic variants in SET domain-containing five in two patients with intellectual disability. One patient carried a nonsense variant, and the other an 81 basepair deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5.