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This Week in Genome Research: Aug 21, 2014

Canadian researchers introduce a computational method for discerning copy number and loss of heterozygosity patterns from tumor genome sequence data. The probabilistic model, known as TITAN, is designed to provide clues about copy number architecture in mixed cell populations, the team says, including the clonal populations that make up a tumor sample. For their proof-of-principle study, the investigators used this approach to assess copy number alterations and loss of heterozygosity in both simulated cell mixtures — meant to represent ovarian tumors — and actual genome sequence data for almost two-dozen breast tumor genomes.

Infection by the malaria parasite Plasmodium falciparum prompts expression shifts involving genes in the innate immune system, according to a transcriptomic study of more than 100 Indonesians infected by the parasite. Researchers from Japan, Egypt, Indonesia, and Germany used RNA sequencing on patient blood samples to simultaneously see human and P. falciparum transcripts during infection, including those associated with specific clinical features. The analysis highlighted changes in the expression of TLR2, TICAM2, and other genes in the same innate immune pathway that appeared to coincide with malaria severity, for example. It also pointed to genetic variants in humans and parasites that seem to contribute to infection features.

A team based in China and the US describes a new, recurrent fusion transcript in a form of brain cancer called glioma. The researchers detected dozens of in-frame fusion transcripts when they did RNA sequencing on 272 grade II, III, or IV gliomas, including recurrent fusions that involved transcripts from FGFR3 and TACC3, RNF213 and SLC26A11, and PTPRZ1 and MET. The latter, PTPRZ1-MET, fusion was specific to two forms of glioma, they note, appearing only in grade III astrocytoma or secondary glioblastoma samples. Moreover, the newly detected fusion tended to correspond with especially aggressive tumors and poor outcomes in the glioblastoma patients, study authors note, suggesting it may be prognostically important.