Chromosome instability leaves its mark

Jonathan R Pollack

SUMMARY: Genomic instability is a common feature of human cancer. A new study identifies a putative gene expression signature of chromosome instability in solid tumors, with

CONTEXT: …has been known, available methods to measure aneuploidy, such as flow cytometry–based ploidy analysis, FISH, CGH and LOH analysis, have yet to be widely adopted in the clinical management of patients with solid tumors. Whether gene…

Nature Genetics 38, 973 – 974 (01 Sep 2006) News and Views

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

Andrew J Sharp, Sierra Hansen, …, Evan E Eichler

SUMMARY: Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of

CONTEXT: …abnormalities had also been excluded. None had been previously analyzed by array comparative genomic hybridization (CGH). Parents or guardians of all subjects provided informed consent, and the protocol was reviewed and approved by…

Nature Genetics 38, 1038 – 1042 (01 Sep 2006) Letters

Using array-comparative genomic hybridization to define molecular portraits ofprimary breast cancers

S-F Chin, Y Wang, N P Thorne, A E Teschendorff, S E Pinder, M Vias, A Naderi, I Roberts, N L Barbosa-Morais, M J Garcia, N G Iyer, T Kranjac, J F R Robertson, S Aparicio, S Tavaré, I Ellis, J D Brenton, C Caldas

SUMMARY: We analysed 148 primary breast cancers using BAC-arrays containing 287 clones representing cancer-related gene/loci to obtain genomic molecular portraits. Gains were detected in 136

CONTEXT: …analysis to subtype breast cancers. Cytogenetic methods, including conventional comparative genomic hybridization (CGH), have revealed chromosomal regions that are frequently altered in breast tumors (Kallioniemi et al., 1994;…

Oncogene (25 Sep 2006) Oncogenomics

Small dsRNAs induce transcriptional activation in human cells

Long-Cheng Li^*,, Steven T. Okino, Hong Zhao, Deepa Pookot, Robert F. Place, Shinji Urakami, Hideki Enokida, and Rajvir Dahiya^*,

Department of Urology, Veterans Affairs Medical Center and University of California, San Francisco, CA 94121

…… In conclusion, we have identified several dsRNAs that activate gene expression by targeting noncoding regulatory regions in gene promoters. These findings reveal a more diverse role for small RNA molecules in the regulation of gene expression than previously recognized and identify a potential therapeutic use for dsRNA in targeted gene activation.

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

Timothy R. Lezon^*, Jayanth R. Banavar^*, Marek Cieplak, Amos Maritan, and Nina V. Fedoroff^,¶,||

Pennsylvania State University.

We describe a method based on the principle of entropy maximization to identify the gene interaction network with the highest probability of giving rise to experimentally observed transcript profiles. In its simplest form, the method yields the pairwise gene interaction network, but it can also be extended to deduce higher-order interactions. Analysis of microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies a gene interaction network that reflects the intracellular communication pathways that adjust cellular metabolic activity and cell division to the limiting nutrient conditions that trigger metabolic oscillations. The success of the present approach in extracting meaningful genetic connections suggests that the maximum entropy principle is a useful concept for understanding living systems, as it is for other complex, nonequilibrium systems.