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In Print: Last Week's Microarray Papers of Note: Oct 23, 2012


North African populations carry the signature of admixture with Neandertals.
PLoS One. 2012;7(10):e47765.
Sánchez-Quinto F, Botigué L, Civit S, et al.

Using arrays, the authors analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. They found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans.

High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.
Genes Chromosomes Cancer. 2012 Oct 17. [Epub ahead of print]
Hasselblatt M, Isken S, Linge A, et al.

Atypical teratoid/rhabdoid tumor is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 locus in chromosome band 22q11.2. To identify potential additional genetic alterations, the authors performed a high-resolution genome-wide analysis using Affymetrix's OncoScan FFPE Express on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. The analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral loss of heterozygosity, suggesting the absence of recurrent genomic alterations other than SMARCB1 in AT/RT.

Comparative transcriptome analysis of tobacco (Nicotiana tabacum) leaves to identify aroma compound-related genes expressed in different cultivated regions.
Mol Biol Rep. 2012 Oct 19. [Epub ahead of print]
Lei B, Zhao X, Zhang K, et al.

To identify genes that are differentially expressed in tobacco in response to environmental changes and to decipher the mechanisms by which aromatic carotenoids are formed in tobacco, an Agilent tobacco gene expression microarray was adapted for transcriptome comparison of tobacco leaves derived from three cultivated regions of China: Kaiyang, Weining, and Tianzhu. Further analysis indicated that the genes that were differentially expressed among the three cultivated regions were associated with the light reaction of photosystem II, response to stimuli, and secondary metabolism.

Matched molecular pair analysis of small molecule microarray data identifies promiscuity cliffs and reveals molecular origins of extreme compound promiscuity.
J Med Chem. 2012 Oct 22. [Epub ahead of print]
Dimova D, Hu Y, Bajorath J.

The authors analyzed patterns of compound promiscuity in a publicly available small-molecule microarray data set using matched molecular pair formalism. On the basis of their analysis, they introduced "promiscuity cliffs" as pairs of structural analogs with single-site substitutions that lead to large magnitude differences in apparent compound promiscuity involving between 50 and 97 unrelated targets. On the basis of their analysis, the authors determined that promiscuity is not an inherent feature of molecular scaffolds but can be induced by small chemical substitutions.

Replication of bipolar disorder susceptibility alleles and identification of two novel genome-wide significant associations in a new bipolar disorder case-control sample.
Mol Psychiatry. 2012 Oct 16. [Epub ahead of print]
Green E, Hamshere M, Forty L, et al.

The authors conducted a genotyping study using a custom Illumina Infinium HD genotyping array, the ImmunoChip, in a sample of 1,218 bipolar disorder cases and 2,913 controls that have not been used in any studies previously reported independently or in meta-analyses. They report on two new associations: rs7296288, an intergenic polymorphism on chromosome 12 located between RHEBL1; and rs3818253, an intronic SNP on chromosome 20q11.2 in the gene TRPC4AP, which lies in a high linkage disequilibrium region along with the genes GSS and MYH7B.

The genetic prehistory of southern Africa.
Nat Commun. 2012 Oct 16;3:1143.
Pickrell J, Patterson N, Barbieri C, et al.

The authors report data from 23 populations analyzed at over half a million SNPs, using a genome-wide array designed for studying human history. Based on the array data, they claim the southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which they show separated within the last 30,000 years. They also found that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began about 1,200 years ago.

The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.