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)."