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This Week in Genome Biology: Mar 10, 2010

In Genome Biology this week, researchers in Australia present a scaling normalization method for the differential expression analysis of RNA-seq data. The authors write that, because RNA-seq is likely to become the choice platform for interrogating RNA, and because normalization is an essential step in the analysis, their method proves to be simple. It shows "dramatically improved results ... in simulated and publicly available data sets," they add.

Researchers in Singapore present their tool for comprehensive chromatin interaction analysis with paired-end tag sequencing, or ChIA-PET, in Genome Biology this week. The authors write that the ChIA-PET software can be used to study genome-wide long-range chromatin interactions bound by protein factors. The researchers report that their technology is "fast, accurate, comprehensive, user-friendly, and open source."

Yale University and Wellcome Trust Sanger Institute scientists report their identification and analysis of unitary pseudogenes in humans and other primates. The team writes that although unitary pseudogenes represent only a small portion of all annotated pseudogenes in the genome, they constitute distinct functional losses over time, shedding light on human and primate evolution. They found 11 unitary pseudogenes to be polymorphic, containing both fuctional and nonfunctional alleles in the human population.

European researchers this week present XGAP, a "software model for the genotype and phenotype community." The team writes that users can either download standard XGAP or generate a custom version using a tool with programming interfaces to R-software and web services. "Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans," the team writes.

The Scan

Study Find Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

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.