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In Print: Last Week's Microarray Papers of Note: Sep 25, 2012

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Genomic variation in seven Khoe-San groups reveals adaptation and complex African history.
Science. 2012 Sep 20. [Epub ahead of print]
Schlebusch C, Skoglund P, Sjödin P, et al.

Using SNP chips, the authors of this study genotyped 220 southern Africans and found that the Khoe-San diverged from other populations more than 100,000 years ago, but that structure within the Khoe-San dated back to about 35,000 years ago. Additionally, genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. The authors also found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development.

BioArray News spoke recently with corresponding author Mattias Jakobsson about the study (see related story, this issue).


Evaluating coverage of exons by HapMap SNPs
Genomics. 2012 Sept 19. [Epub ahead of print]
Donga X, Zhonga T, Xuc T, et al.

In this study, the authors used the concept of haplotype blocks to evaluate the coverage of five SNP sets including the HapMap and four commercial arrays, for every exon in the human genome. They found that although some chips can reach similar coverage as the HapMap, only about 50 percent of exons are completely covered by haplotype blocks of HapMap SNPs. They suggest that further high-resolution genotyping methods are required to provide adequate genome-wide power for identifying variants.


Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication
New Phytol. 2012 Sep 20. [Epub ahead of print]
Wang Y, Bai X, Yan C, et al.

In this study, a genome, three small RNA populations, and a degradome of O. rufipogon were sequenced on the Illumina platform and the expression levels of microRNAs were profiled using microRNA chips. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could be a target of domestication.


Genomic arrays in chronic lymphocytic leukemia routine clinical practise: are we ready to substitute conventional cytogenetics and FISH techniques?
Leuk Lymphoma. 2012 Sep 20. [Epub ahead of print]
Puiggros A, Puigdecanet E, Salido M, et al.

The aim of this study was to compare genomic arrays with G-banding cytogenetics and fluorescence in situ hybridization in CLL testing to see if arrays could replace current techniques in routine procedures. The researchers analyzed 70 CLL patients using the Cytogenetics Whole-Genome 2.7M array and CytoScan HD array from Affymetrix, as well as CGC and FISH with the classic CLL panel. Although abnormality detection was higher when arrays are applied, one case with del(11q) and three with del(17p) were missed by genomic arrays due to their limited sensitivity. The authors concluded that the complete substitution of CGC and FISH by genomic arrays in laboratories could negatively affect the management of some patients harboring 11q or 17p deletions and that arrays should be maintained as a complementary tool to the current techniques.


Evolutionary insights into scleractinian corals using comparative genomic hybridizations.
BMC Genomics. 2012 Sep 21;13(1):501.
Aranda M, Desalvo M, Bayer T, et al.

The authors performed comparative genomic hybridizations with different coral species using an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies via heterologous hybridization.


Genome-wide activation of latent donor splice sites in stress and disease.
Nucleic Acids Res. 2012 Sep 23. [Epub ahead of print]
Nevo Y, Kamhi E, Jacob-Hirsch J, et al.

Using a splicing-sensitive microarray, the authors found that stress-induced activation of latent splicing is widespread across the human transcriptome, and suggest that latent splicing may underlie certain diseases. In addition, analyses of data from the Gene Expression Omnibus revealed widespread activation of latent splicing in cells grown under hypoxia and in certain cancers such as breast cancer and gliomas.

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Science Papers Present GWAS of Brain Structure, System for Controlled Gene Transfer

In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.