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This Week in Genome Research: Nov 11, 2009

In Genome Research this week, a study out of Michael Wigler's lab at Cold Spring Harbor has looked at how tumor progression relates to genomic heterogeneity. To examine heterogeneous breast tumors, they developed a method called Sector-Ploidy-Profiling (SPP). SPP involves "macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization." Using the method, they found that breast tumors show two classes of genomic structural variation, monogenomic, which contain only one major clonal subpopulation of cells, and polygenomic, which contain multiple subpopulations.

Stanford University's Gavin Sherlock is lead author on research that used array CGH to find CNVs in five industrial fuel ethanol yeast strains, which produce billions of gallons of fuel ethanol a year from sugarcane. In the Saccharomyces cerevisiae strains, they saw amplifications of the telomeric SNO and SNZ genes, which are involved in synthesizing vitamins B6 and B1, suggesting that these duplications help the yeast grow better in medium lacking pyridoxine and with high sugar concentrations. A story at GenomeWeb Daily News adds perspective.

Researchers led in part by those at the Weizmann Institute of Science have looked globally at DNA methylation patterns in primate embryonic stem cells. Studying the DNA methylation patterns in monkey embryonic stem cells, fibroblasts, and ESCs created through somatic cell nuclear transfer, they found hundreds of regions that are hyper- or hypomethylated in fibroblasts compared to native ESCs and that these are conserved in human cells and tissues, they say. "Remarkably, the vast majority of these regions are reprogrammed in SCNT ESCs, leading to almost perfect correlation between the epigenomic profiles of the native and reprogrammed lines," they write in the abstract.

In a collaboration between scientists at the Weizmann Institute of Science, Lawrence Berkeley National Laboratory, the Joint BioEnergy Institute, and the Joint Genome Institute, they have constructed a single-base resolution transcriptome map of Sulfolobus solfataricus P2, a well-studied model archaeal organism. Looking at a mass of cDNA sequencing data, they were able to identify transcription start sites and operon structures for more than 1,000 transcriptional units. Unlike bacterial transcripts, they found that most Sulfolobus transcripts lack 5' UTR sequences, "suggesting that mRNA/ncRNA interactions differ between bacteria and archaea," they write.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.