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This Week in Nature : Jun 21, 2012

An international team led by investigators at the Broad Institute this week reports whole-exome sequences for 103 human breast cancers of diverse subtypes and matched-normal DNA as well as whole-genome sequences for 22 breast cancer/normal pairs. In its analysis of these sequences, the team confirmed recurrent somatic mutations in PIK3CA11, TP536, AKT112, GATA313, and MAP3K110 in the cancer samples and identified recurrent mutations in the CBFB transcription factor gene and deletions of its partner, RUNX1. The team also discovered a recurrent MAGI3-AKT3 fusion that was enriched in triple-negative breast cancers lacking estrogen and progesterone receptors and ERBB2 expression, it reports. "The MAGI3-AKT3 fusion leads to constitutive activation of AKT kinase, which is abolished by treatment with an ATP-competitive AKT small-molecule inhibitor," the researchers add in their Nature report.

Elsewhere in Nature, members of the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project report whole-genome sequences for 37 medulloblastoma tumors and matched normal blood samples. After discovering 136 genes harboring somatic mutations in this discovery set, the team sequenced those genes in an additional 56 medulloblastomas. Overall, the team found recurrent mutations in 41 genes not previously implicated in medulloblastoma, several of which "target distinct components of the epigenetic machinery in different disease subgroups, such as regulators of H3K27 and H3K4 trimethylation in subgroups 3 and 4, and CTNNB1-associated chromatin re-modelers in WNT-subgroup tumors," the authors write.

A trio of investigators at the US National Institute of Allergy and Infectious Diseases discusses the H5N1 avian influenza virus publication issue, saying that even though the National Science Advisory Board for Biosecurity eventually recommended that more-complete manuscripts be published in full, "controversy about this and similar research remains." (This controversy, and the issues surrounding it, was also discussed and debated at the American Society for Micrbiology annual meeting in San Francisco.) Of the H5N1 transmissibility studies, the NIAID team says "some would argue that even this background research should not have been done, or should henceforth be classified and made available only to 'approved' scientists who would be vetted by yet-to-be-determined mechanisms," though had the work not been done and made available, "the field of influenza research would have been considerably impeded and our current state of knowledge and readiness for responding to future outbreaks and/or pandemics would be lessened," it adds.

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.