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This Week in Science: Aug 31, 2012

Researchers led by the Max Planck Institute for Evolutionary Anthropology's Svante Pääbo present a 30x coverage genome sequence of a Denisovan individual in Science this week. To analyze the DNA from the ancient hominin, the researchers turned to a single-stranded DNA library preparation "as it will double its representation in the library." They add that they generated uniform overage of the genome and found that genetic diversity among Denisovans was low. They further estimate the divergence between Denisovans and present-day humans to have occurred 800,000 years ago. As our sister publication GenomeWeb Daily News reports, Pääbo and his colleagues also compared the Denisovan genome to ones from modern populations and found Denisovan sequences in Papua New Guineans as well as in aboriginal populations from Australia and the Philippines.

Also in Science, Reza Vafabakhsh and Taekjip Ha from the University of Illinois at Urbana-Champaign report the DNA that is short than 100 base pairs in length is quite bendable. They developed a single-molecule fluorescence resonance energy transfer-based assay to monitor DNA cyclization. From applying this approach, they found that "the looping rate has a weak length dependence between 67 and 106 bp." Vafabakhsh and Ha note that many DNA-protein interactions likely take advantage of such looping.

Finally, researchers at New York's Memorial Sloan-Kettering Cancer Center write that mutations in TSC1, which regulates activation of the mTOR pathway, are linked to everolimus sensitivity in bladder cancer patients. Using whole-genome sequencing, the researchers studied the tumor genome of a patient who showed a durable response to everolimus and found a number of missense mutations and indels, including a deletion in TSC1 and a nonsense mutation in NF2. In a follow-up cohort, the Sloan-Kettering researchers found additional TSC1 mutations, and further found that "patients with TSC1-mutant tumors remained on everolimus longer than those with wild-type tumors (7.7 versus 2.0 months, P = 0.004) with a significant improvement in time to recurrence (4.1 versus 1.8 months; hazard ratio=18.5, 95% CI: 2.1-162, P = 0.001)."

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.