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In Print: Last Week's Microarray Papers of Note: Dec 3, 2013


SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato.

BMC Genomics. 2013 Nov 27;14(1):835. [Epub ahead of print]

Corrado G, et al.

The authors genotyped 214 tomato accessions, including cultivated landraces, commercial varieties, and wild relatives, using a custom-made Illumina SNP-panel. They reported that that adaptation and selection have led to a genomic signature in cultivated landraces, and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. They believe their work is a step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study.

Clin Microbiol Infect. 2013 Nov 26. [Epub ahead of print]

Halligan E, et al.

The authors compared Luminex's Gastrointestinal Pathogen Panel with conventional testing over eight-months to determine diagnostic accuracy, turnaround times, laboratory costs, use of isolation facilities and user acceptability. They reported higher detection rates and turnaround times in some instances, and argue that the GPP is likely to be of greater benefit to cases that present within the first four days of hospital admission.

KRAS gene codon 12 mutation detection enabled by gold nanoparticles conducted in a nanobioarray chip.

Anal Biochem. 2013 Nov 26. [Epub ahead of print]

Sedighi A, et al.

The authors aimed to distinguish between mutant and wild-type KRAS gene codon 12 targets by relying on single temperature hybridization, enabled by the use of gold nanoparticles, on a bioarray created within nanofluidic channels.

Clinical utility of chromosomal microarray analysis in prenatal diagnosis: report of first 6 months in clinical practice.

J Matern Fetal Neonatal Med. 2013 Nov 26. [Epub ahead of print]

Klugman S, et al.

The authors studied the clinical utility of chromosomal microarray analysis in prenatal diagnosis in a clinical setting in New York City. Benign familial variants were the most common finding. Variants of uncertain significance were frequent, especially when fathers were not available for testing. And most patients undertook CMA as part of evaluation of an ultrasound anomaly.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.