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In Print: Last Week's Microarray Papers of Note: Apr 16, 2013


Array CGH as a first line diagnostic test in place of karyotyping for postnatal referrals — results from four years' clinical application for over 8,700 patients.
Mol Cytogenet. 2013 Apr 5;6(1):16.
Ahn J, Bint S, Bergbaum A, Mann K, et al.

The authors relate their experience with using array comparative genomic hybridization as a first line test in place of G-banded chromosome analysis. Of the 8,794 patients tested with array CGH, a quarter had CNVs either in known pathogenic regions or in other regions where imbalances have not been reported in the normal population. Of these CNVs, the authors report that 87 percent were less than five megabases in size and would likely not be detected by G-banded chromosome analysis.

Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array.
BMC Genomics. 2013 Apr 8;14(1):229.
Liu J, Zhang L, Xu L, et al.

The authors analyzed the genomes of three sheep breeds using Illumina's Ovine SNP50 BeadChip array. A total of 238 CNV regions were identified and analyzed using the algorithms PennCNV and CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response.

Aptamer microarray as a novel bioassay for protein-protein interaction discovery and analysis.
Biosens Bioelectron. 2013 Apr 15;42:248-55.
Chen L, Tzeng S, Peck K

The authors investigated the use of an aptamer microarray for protein-protein interaction discovery and analysis. To accomplish this, they assayed a mixture of fluorescence-labeled thrombin and Escherichia coli proteins with the chip. Ultimately, they were able to study a network of protein-protein, protein-DNA, and DNA-DNA interactions and their interaction orders using the array, in addition to PPI discovery.

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.