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In Print: Last Week's Microarray Papers of Note: May 28, 2013


Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history.
Investig Genet. 2013 May 20;4(1):9. [Epub ahead of print]
Lao O, Altena E, Becker C, et al.

The authors collected data on a total of 999 Dutch individuals sampled at 54 sites across the country at 443,816 autosomal SNPs using Affymetrix's Genome-Wide Human SNP Array 5.0. They detected a genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern, and a southern group. They also observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands.

Genetic analysis of candidate SNPs for metabolic syndrome in obstructive sleep apnea (OSA).
Gene. 2013 May 25;521(1):150-4.
Grilo A, Ruiz-Granados ES, Moreno-Rey C, et al.

To better understand the relationship between obstructive sleep apnea and metabolic syndrome, the authors genotyped 384 SNPs in 387 subjects using the Illumina BeadXpress platform. They determined that obstructive sleep apnea and metabolic syndrome do not share major genetic determinants, although both syndromes share common epidemiological and clinical features.

Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing.
Eur J Hum Genet. 2013 May 22. [Epub ahead of print]
Wiszniewska J, Bi W, Shaw C, et al.

To provide comprehensive clinical testing for both copy number variants and copy-neutral absence of heterozygosity, the authors enhanced their custom-designed high-resolution oligonucleotide array to provide exon-targeted coverage of 1,860 genes with 60,000 SNP probes. Of the 3,240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases showed at least one AOH region greater than 10 megabases in size. Though their array array has a lower density of SNP probes than other commercially available SNP arrays, they authors report that their chip reliably detected AOH events as well as exonic CNVs beyond the detection limitations of SNP genotyping.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.