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Genomics In The Journals: Feb 16, 2012

NEW YORK (GenomeWeb News) – In Nature Biotechnology, researchers from China, Taiwan, and Denmark describe the elaborate RNA editing patterns they uncovered through deep transcriptome sequencing of a lymphoblastoid cell line generated for a Han Chinese man whose genome was sequenced in 2008. Using a computational pipeline that weeds out false-positive RNA editing events based on genome and transcriptome sequence data, the team found almost 22,700 examples of RNA editing in protein-coding and non-coding sequences — most involving a switch from adenine to another base that's read as guanine during translation. Investigators also identified a few dozen editing sites in microRNAs, which they suspect have RNA editing-related regulatory roles.

"The evidence of extensive RNA editing identified in a human transcriptome underscores the necessity of an effective method to fully detect these events in order to further advance our understanding of human development and normal pathophysiological condition," BGI Executive Director Jun Wang, the study's corresponding author, said in a statement.


Researchers from the University of Toronto Hospital for Sick Children used a transposon mutagenesis system in mice to help characterize the genetic patterns associated with metastases for a pediatric brain cancer called medulloblastoma — work they describe in Nature. From their analyses of the mouse models, as well as follow-up experiments using human tumor samples, researchers found evidence that the medulloblastoma tumors traveling from the cerebellum to other parts of the brain and spinal cord harbor genetic patterns that resemble distinct sub-populations within the primary tumor, pointing to clonal selection of these populations.

"Clonal genetic events in the metastases can be demonstrated in a restricted sub-clone of the primary tumor," senior author Michael Taylor, from the hospital's neurosurgery division, and colleagues explain, "suggesting that only rare cells within the primary tumor have the ability to metastasize."


In a commentary in Nature, Utah Foundation for Biomedical Research investigator Gholson Lyon argues in favor of clinical standards for human genome studies. Drawing from his own experiences as a physician and researcher, Lyon called for standardized protocols for human genome sequencing and related studies on par with those used for clinical validation of laboratory tests, as well as training and funding to support such standards.

"Participants want to be involved in the research process and be told about any medically important findings," he wrote. "Therefore, I am suggesting that the entire process of DNA collection and genome sequencing for humans could and should be performed in a proper clinical environment so that physicians can immediately return all relevant genomic information much more easily and perhaps even link such information to medical records so that it is available for reanalysis as our knowledge expands."


A New England Journal of Medicine study explains how gene sequencing helped track down truncating mutations that can cause a heart condition called idiopathic dilated cardiomyopathy. A team from the US, UK, and Italy used Illumina and Sanger sequencing to sequence TTN — an extremely large gene coding for the muscle protein titin — in 312 individuals with dilated cardiomyopathy, 231 individuals with another form of cardiomyopathy, and 249 unaffected controls. In the process, the researchers found that TTN mutations were much more common in those with dilated cardiomyopathy than they were in healthy individuals or individuals with hypertrophic cardiomyopathy. TTN mutations also tracked with dilated cardiomyopathy in familial forms of the disease, and accounted for roughly one-quarter of familial and 18 percent of sporadic dilated cardiomyopathy cases that the group tested.

Based on their findings, study authors argue that "[i]ncorporation of sequencing approaches that detect TTN truncations into genetic testing for dilated cardiomyopathy should substantially increase test sensitivity, thereby allowing earlier diagnosis and therapeutic intervention for many patients with dilated cardiomyopathy."


By sequencing the 70 million base nuclear draft genome for a basal algal species called Cyanophora paradoxa — and examining the algae's predicted protein phylogeny, mitochondrial and plastid genome patterns, and transcriptional profiles — an international research team has learned more about the roots of photosynthesis in algae and plants. For example, results of the Science study suggest that the primary plant plastid was acquired in plant ancestors from cyanobacteria in a single event.

"Analysis of the gene-rich C. paradoxa genome unambiguously supports Plantae monophyly," study authors wrote, "laying to rest a long-standing issue in eukaryote evolution."


In Cell, a Wellcome Trust Sanger Institute-led team describes findings from a Tasmanian devil genome sequencing effort that it announced in 2010. The researchers sequenced a Tasmanian devil reference genome as well as a normal devil genome, and two cancer genomes from Tasmanian devil facial tumor disease (DFTD) samples collected in different parts of the Australian state. By analyzing patterns in the genomes, investigators found clues about the mutational processes behind the transmissible cancer, its evolution, and the genetic patterns that accompanied its march across Tasmania. For instance, results from the study suggest that DFTD has experienced genetic divergence as it moved from Tasmania's northeast to other parts of the state — findings that researchers verified through genotyping more than 100 DFTD samples collected across Tasmanian over seven years.

"This research is important because it allows us to understand the pattern of disease spread and this may help contain the epidemic," Sanger Director Mike Stratton, the study's senior author, said in a statement. "However, we also now need to use the genome sequence to understand more about how this cancer became transmissible."


Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.