June 2010

Mark your calendars for a special seminar on "A draft sequence of the Neandertal genome and comparison to modern human genomes" by David Reich from Harvard Medical School. The talk will be held this Thursday, June 3rd, at 2 PM in Schiciano Auditorium A.

Reich was part of the team led by Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology that just reported the first draft sequence of the Neandertal genome in Science. It is Reich's comparison of the Neandertal genome to the human genome that suggests interbreeding occurred in the Middle East, where both modern humans and Neandertals lived tends of thousands of years ago. There are no Neandertal sequences that are consistently found in all carriers; instead, each carrier lineage has “a different bit of Neanderthal in them,” Reich told NPR.

We would also like to draw your attention to two other special events. There will be a communications workshop for scientists held on Monday, June 7th, at 4 PM. The workshop co-sponsored by the IGSP and given by communications expert Tim Miller will be videotaped for use by the National Science Foundation. On Thursday, June 17th, the IGSP and Office of Postdoctoral Services will present part 5 in their Summer 2010 Grant Series "NSF Funding from the Inside." For more details, please see our events calendar.

The IGSP would also like to give a special welcome to the 14 undergraduate research fellows who have just arrived to spend 10 weeks of their summers with us. The students include five from North Carolina Central University, six from Duke, one from William Jewell College in Missouri, one from The University of Wisconsin-Madison and one from Fayetteville State University. Welcome summer fellows!

Genetic Ancestry Tests Imperfect Say Researchers
A report produced by Charmaine Royal and colleagues for the American Society of Human Genetics says that genetic tests sold directly to consumers to help people trace their ancestry are imperfect and may lead some to draw unfounded conclusions about their heritage, according to Reuters. The news was also covered by GenomeWeb and Bloomberg. Read the original commentary in The American Journal of Human Genetics.

Science and the Stimulus Effect
In a Genome Technology feature, Hunt Willard discusses the impact of stimulus funds on scientific research at the IGSP and beyond. The article highlights funds won by Willard and Mark Delong to build a high-performance computing system.

Swathi Padmanabhan: Student Studies Commercial Barriers to HPV Vaccine
Duke News profiles IGSP undergraduate Swathi Padmanabhan and her research efforts to assess the patents associated with the very popular and expensive HPV vaccine and their implications for access in India. Padmanabhan's mentors include Bob Cook-Deegan and Shubha Chandrasekharan.

Genomes to Health: The Path to Better and More Personal Cancer Care
In an Age of Personalized Medicine blog post, Geoff Ginsburg says "At Duke, we have been wrestling with how to translate genomic science and information into something that can be made practical and accessible to patients and their physicians." The post features the relaunched GenomesToHealth clinical trials website and the emerging trials network.

Pentagon Virus Detector Knows You're Sick Before You Do
A DARPA-funded research project spearheaded by Geoff Ginsburg and colleagues including Chris Woods and Aimee Zaas aims to create a gadget that can detect viral infection hours before the first sniffles, Wired.com reports.

Gene Makes Kids More Vulnerable to Bullying's Effects
A twin study exploring the connection between the stress-related gene 5-HTT and bullying can’t directly pin the kids’ emotional problems on the gene-bullying combo, “but it is about as close as it is possible to get," Terrie Moffitt told Science News.

Using Fish to Illuminate the Architecture of Inherited Disease
A research team led by Nico Katsanis has developed a way to simultaneously look at the effects of 125 mutations occurring in 14 different genes, physorg.com reports. Read the original report in Proceedings of the National Academy of Sciences.

Game Systems Crunching on Scientific Problems
With scientific programming tools developed by Mike West and colleagues, the same technology that enables realistic combat scenes and fluid-looking touchdown passes in computer gaming systems is being put to use on solving complex problems in biomedical research. Read the original paper that describes these new tools in the Journal of Computational and Graphical Statistics.

Striking Down of Myriad Patents Opens Up Talk About Their Effect
"If [the Myriad decision] were partially reversed, there will be some lingering uncertainty about what kinds of claims are allowable and which ones aren't," Bob Cook-Deegan told Genome Technology. But, he adds, if the case moves on, perhaps even all the way to the Supreme Court, it would change practices at the patent office and the interpretation of many claims granted in the past.

Orchid Agonistes
"Celeste was the product of emogenics, the breeding programme to optimize genes and environments for those with heightened sensitivities to external stimuli," writes Misha Angrist in a fictional account of the future published in the journal Nature.

A Paired End Sequencing Strategy to Map the Complex Landscape of Transcription Initiation
In an advanced online publication of Nature Methods, Jun Zhu and Uwe Ohler show that a paired-end transcription start site analysis is a powerful method to uncover the transcriptional complexity of eukaryotic genomes.

Intratumor Heterogeneity and Precision of Microarray-Based Predictors of Breast Cancer Biology and Clinical Outcome
Mike Datto and colleagues conclude in the Journal of Clinical Oncology that intratumor heterogeneity, although present at the level of individual gene expression, does not preclude precise microarray-based predictions of tumor behavior or clinical outcome in breast cancer patients.

Informed Consent in Genomics and Genetic Research
In the Annual Review of Genomics and Human Genetics, Amy McGuire of Baylor College of Medicine and the IGSP's Laura Beskow discuss the features of genetic and genomic research that challenge established norms of informed consent and consider alternatives that have been proposed.

The Prospect of Genome-Guided Preventive Medicine: A Need and Opportunity for Genetic Counselors
Given their expertise in genetic science, risk assessment and communication, and a patient-centered approach to practice, genetic counselors are poised to play a critical role in facilitating the incorporation of genomic health risks into the burgeoning field of genome-guided preventive medicine, writes Julianne O'Daniel in the Journal of Genetic Counseling.

Genetic Sensitivity to the Environment: The Case of the Serotonin Transporter Gene and Its Implications for Studying Complex Diseases and Traits
In the American Journal of Psychiatry, Avshalom Caspi, Terrie Moffitt and Ahmad Hariri review the ways in which genotype by environment (G X E) interactions can be tested with large and small samples, how G X E research can be carried out before and after replicated gene discovery, the use of G X E research as a tool for gene discovery, and the importance of validation.

Genome-Wide Association Study of Lp-PLA(2) Activity and Mass in the Framingham Heart Study
In PLoS Genetics, Jeanette McCarthy, Geoff Ginsburg and colleagues report that genetic polymorphisms may contribute to inter-individual variation in the activity and mass of Lp-PLA(2), an enzyme that is an emerging risk factor and therapeutic target for cardiovascular disease.

A Transcription Factor Affinity-Based Code for Mammalian Transcription Initiation
Uwe Ohler and Molly Megraw are authors on a Genome Research report that predicts transcription start sites for ~70% of mammalian microRNAs based on currently available data.

Uwe Ohler has been awarded a grant from the National Science Foundation's Faculty Early Career Development program (CAREER) for a project entitled "Computational modelling and analysis of gene expression patterns from microscopy image data." The effort will involve close collaborations between biologists working on animal and plant model systems to ensure that methods developed are widely applicable.

Recent IGSP Graduate Xander Nuttle was selected by the Biology faculty at Duke to receive this year's Biology Faculty Award, which is given to the biology major deemed to have achieved the highest level of excellence in their academic and research interests and who has great promise for a career in biological research. Xander will attend the University of Washington in Seattle, where he plans to pursue a Ph.D. in the Genome Sciences. Learn more about Xander and his research in Greg Wray's lab here.

The National Institutes of Health has announced The Centers of Excellence in Genomic Sciences (CEGS) program to establish academic Centers for advanced genome research. CEGS projects will address critical issues in genomic science, proposing a solution that would be a very substantial advance.

The National Science Foundation plans to award a total of $22 million annually under its Advances in Biological Informatics program, which aims to support the development of informatics tools and resources "that have the potential to advance, or transform, research in biology."

The National Institutes of Health plans to spend $6 million to fund 30 grants for investigators seeking to discover new molecular probes for use in automated, high-throughput screening research.

The National Eye Institute has announced funding for clinical vision research studies, including efforts to improve the early diagnosis of ocular diseases and to develop and test new treatments and interventions or predictors of response to treatment.