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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

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.