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This Week in Genome Research: Nov 27, 2013

Spanish researchers used transcriptome sequencing to uncover molecular subtypes of chronic lymphocytic leukemia with notable clinical characteristics — work they describe online in Genome Research. The team did deep RNA sequencing on normal B cell sub-populations and tumor samples from nearly 100 individuals with CLL. The sequences revealed CLL-associated shifts in splicing profiles for some 2,000 genes, along with a slew of transcripts showing differential expression between the tumor and normal B cell samples. Moreover, researchers identified two gene expression clusters that coincided with molecular CLL subgroups that had different time-to-treatment patterns, marking the disease activity and lag before therapeutics intervention is required.

A combination of transcriptome and somatic rearrangement profiling helped a team from the Netherlands characterize heterogeneity within advanced ovarian cancer tumors that had not yet been exposed to treatment. Using multiple samples from three women with ovarian cancer, the researchers identified a wide range of rearrangements and expression patterns, even within individual patients and tumors. The findings "highlight the plasticity of ovarian cancer genomes," study authors say, "which may contribute to their strong capacity to adapt to changing environmental conditions and give rise to the high rate of recurrent disease following standard treatment regimes."

Ohio State University Comprehensive Cancer Center's Maura Gillison and colleagues describe the genomic instability they detected around human papillomavirus insertion sites in HPV-positive cancer cell lines and tumor samples. The team performed genome sequencing on 10 HPV-positive or -negative cell lines derived from head and neck or cervical cancers — along with two more HPV-positive tumors originating in the tonsil area or other parts of the oral cavity. Together with viral transcript information, the genome sequences made it possible to pick up instability and rearrangements in the cancer samples, particularly near apparent HPV insertion sites. Our sister publication GenomeWeb Daily News has more on the study, here.