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Genomics In The Journals: Feb 9, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, an international group reports on a chromosome 11 locus linked to lower tuberculosis risk, found through an association study that relied on imputation from 1000 Genomes Project data. Researchers genotyped 1,329 individuals from Ghana with tuberculosis and 1,847 without the disease, using 1000 Genomes data on individuals of African descent to impute nearly 11 million more variants. From their discovery group data, combined with replication studies involving additional cases and controls from Ghana, The Gambia, Indonesia, and Russia, the team narrowed in on SNPs downstream of the chromosome 11 gene WT1 with significant ties to tuberculosis susceptibility.


In the Journal of Neurosurgery, Virginia Commonwealth University researchers describe gene expression changes that occur in glioma cells after levels of a transcription factor called Wilm's tumor protein are suppressed using small interfering RNA. In the absence of the transcription factor, previously linked to some malignant forms of glioma and other cancers, the team found decreased invasiveness in the cells tested. Their microarray and other experiments indicate that this change coincides with a shift in gene expression that includes muted expression of CD97. On the other hand, they found that an uptick in CD97 expression promoted enhanced glioma invasiveness.


Italian and American researchers used microRNA deep sequence data to look for miRNA profiles that correspond to progression, invasiveness, and outcomes in a form of breast cancer called ductal carcinoma in situ — work they describe in the early, online version of Proceedings of the National Academy of Sciences.

The team compared miRNA profiles in six normal breast tissue samples, eight ductal carcinoma in situ samples, and 80 biopsies from more advanced, invasive ductal carcinomas, identifying miRNA patterns characterizing transitions between these states. Along with nine signature miRNAs that distinguish in situ from invasive ductal carcinomas, the investigators uncovered miRNA signatures linked to survival time and time to metastasis. One miRNA, miR-210, turned up in all three signatures, spurring additional experiments focused on protein-coding genes that it regulates.

"These findings suggest that this 'micro-signature' might be used to identify [ductal carcinoma in situ] tumors that are at high-risk for becoming invasive cancer," senior author Carlo Croce, human cancer genetics director at Ohio State University, said in a statement.


A Stanford University team explores genetic variants suspected of making some people more sensitive to the anthrax toxins than others in another PNAS study. The researchers saw dramatic differences in sensitivity to the Bacillus anthracis-produced protective antigen protein, which mediates anthrax toxin entry into cells, when they looked at 234 lymphoblastoid cell lines generated for African, European, or Asian individuals sampled through the international HapMap project. Through RT-PCR and other experiments, they found ties between anthrax toxin sensitivity and expression levels of CMG2, a gene coding for a receptor utilized by the protective antigen.

"Our results reveal extensive human diversity in cell lethality dependent on [protective antigen]-mediated toxin binding and uptake," Stanford genetics and medicine researcher Stanley Cohen, the study's senior author, and colleagues wrote, "and identify individual differences in CMG2 expression level as a determinant of this diversity."


A gene-centric meta-analysis of individuals enrolled through dozens of studies has found that many of the same genetic loci seem to contribute to type 2 diabetes risk in different populations. As they explain online in the American Journal of Human Genetics, researchers genotyped tens of thousands of individuals from 39 previous studies using the ITMAT-Broad-CARe array, which looks at 50,000 SNPs across around 2,000 genes suspected of influencing metabolism-, cardiovascular-, and inflammation-related traits.

The international team's analyses of data from individuals within different ancestries not only verified known risk loci, but also uncovered type 2 diabetes-associated variants not found before. Together, the new and known diabetes-related sites in the genome corresponded to diabetes risk in individuals from European, African American, Hispanic, and Asian populations, they reported, suggesting overlap between risk variants in these populations.

"[O]ur results demonstrate that this type of large multiethnic genome-wide screening study should lead to identification of additional [type 2 diabetes] genetic variants relevant to multiple ethnic groups," co-corresponding author Richa Saxena, a researcher affiliated with Massachusetts General Hospital, said in a statement.


Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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