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In Print: Last Week's Microarray Papers of Note: Feb 26, 2013


No association between general cognitive ability and rare copy number variation.
Behav Genet. 2013 Feb 17. [Epub ahead of print]
McRae A, Wright M, Hansell N, et al.

The authors investigated the role of rare CNVs on general cognitive ability in a sample of 800 individuals using variants called from the Illumina 610K SNP genotyping array with the software QuantiSNP. They assessed three measures of CNV burden: total CNV length, number of CNVs, and average CNV length, for both deletions and duplications in combination and separately. No correlation was found between any of the measures of CNV burden and individuals' intelligence quotients.

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform.
Epigenetics. 2013 Feb 19;8(3).
Marabita F, Almgren M, Lindholm M, et al.

While the Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation, the authors claim that the design of an appropriate analysis pipeline faces challenges due to the convolution of biological and technical variability, as well as the presence of a signal bias between Infinium I and II probe design types. For this study, they performed a comparative analysis of different pipelines, targeting the problems of reducing the technical variability, eliminating the probe design bias, and reducing the batch effect by exploiting two data sets that included technical replicates and that were profiled for DNA methylation.

Differences in microRNA detection levels are technology and sequence dependent.
RNA. 2013 Feb 19. [Epub ahead of print]
Leshkowitz D, Horn-Saban S, Parmet Y, et al.

In this study, the authors compared the detection performance of three high-throughput commercial platforms for microRNA expression profiling: Agilent and Affymetrix microarrays and Illumina next-generation sequencing. The ability to detect miRNAs was shown to depend strongly on the platform and on miRNA modifications and sequence, and detected miRNA expression levels were not consistent between platforms. A detailed exploration of a large number of attributes, including base composition, sequence structure, and isoform miRNA attributes, suggested their impact on miRNA expression detection level.

Development of a solid-phase receptor-based assay for the detection of cyclic imines using a microsphere-flow cytometry system.
Anal Chem. 2013 Feb 19;85(4):2340-7.
Rodríguez L, Vilariño N, Molgó J, et al.

The authors developed a receptor-based detection method for marine toxins. The assay relies on the immobilization of specific receptors on the surface of carboxylated microspheres and the competition of cyclic imines with biotin-α-bungarotoxin for binding to these proteins. The amount of biotin-α-BTX bound to the surface of the microspheres is quantified using phycoerythrin-labeled streptavidin, and the fluorescence is analyzed using a Luminex 200 system.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.