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In Print: Last Week's Microarray Papers of Note: Oct 15, 2013

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Multiplex detection of antibiotic resistance genes using padlock probes.
Diagn Microbiol Infect Dis. 2013 Oct;77(2):118-25.
Barišić I, et al.

The authors present on a 100-plex assay based on padlock probes in combination with a microarray that allows the simultaneous large-scale identification of highly diverse β-lactamases. The specificity of the assay was performed using 70 clinical bacterial isolates, recovering 98 percent of the β-lactamase nucleotide sequences present.


A high density SNP genotyping array for rice biology and molecular breeding.
Mol Plant. 2013 Oct 11. [Epub ahead of print]
Chen H, et al.

The authors describe the development of a high density rice SNP array. SNP probes were designed by screening more than 10,000,000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives.


Allele-specific qRT-PCR demonstrates superior detection of single nucleotide polymorphisms as genetic markers for West Nile virus compared to Luminex and quantitative sequencing.
J Virol Methods. 2013 Oct 9. [Epub ahead of print]
Worwa G, et al.

The authors compared in vivo and in vitro competitive fitness among West Nile viruses by marking three reference viruses with five synonymous nucleotide substitutions in the envelope gene region of the genome. Phenotypic neutrality of the mutants was assessed by competitive replication in cell culture and genetic stability of the substituted nucleotides was confirmed by direct sequencing, Luminex technology, quantitative sequencing, and quantitative RT-PCR. The authors found that while Luminex technology and quantitative sequencing provided semi-quantitative or qualitative measurements, qRT-PCR demonstrated the best quantitation and specificity in the detection of RNA from wildtype and mutants viruses.

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