August 2009

The Next Generation of Genome Structure and Function

The IGSP is fortunate to have two facilities that can address the research needs of investigators interested in large-scale DNA sequencing projects to explore genome structure, variation and function.

The Genomic Analysis Facility, directed by Kevin Shianna within the IGSP Center for Human Genome Variation, has developed a very high-throughput pipeline for sequencing whole human genomes, in addition to a variety of other collaborative projects, using 11 recently acquired Illumina Genome Analyzer IIx machines. (See the April/May GenomeLIFE for more.) For information and consultation, contact Kevin Shianna at k.shianna@duke.edu or 684-0598.

The DNA Sequencing Facility, directed by Greg Wray within the IGSP Center for Evolutionary Genomics, offers a range of fee-for-service technologies based on both the Illumina Genome Analyzer and Roche/454 Genome Sequencer FLX. Duke researchers working within the core are sequencing the complete genomes of everything from lichen - with its two symbiotic genomes - to a small parrot called a budgerigar. Meanwhile, others are analyzing the microbial ecology of premature baby poop, looking for rare RNA splicing events between the malaria parasite and its human host, and conducting fine-scale mapping of open chromatin throughout the genome.

"The range of projects has expanded vastly in the last year," said Greg Wray, the facility's faculty director. "They showcase what the facility can do." In addition to DNA sequence, the new instruments can measure DNA replication, gene activity, chromatin composition and the chemical structure of DNA.

In some cases, Facility Manager Lisa Bukovnik and her staff of five can run the genome analysis from start to finish. In others, particularly if someone wants to do something totally new, researchers should expect to have greater involvement. Once the sequencing machines have done their thing, the facility now offers additional support in analyzing all the data. Bioinformatician Ty Wang can help researchers as little or as much as they like for an hourly fee.

For a consultation about your next-gen project, contact Lisa Bukovnik at lisa.bukovnik@duke.edu or 660-7436.

Vital Signs with Dr. Sanjay Gupta: Military Medical Technology
CNN's Vital Signs featured Geoff Ginsburg and his team's DARPA-funded efforts to develop a device that harnesses the power of the genome to predict the onset of infectious disease before symptoms appear. "You can imagine in the field a device that could be used everyday and...you'd know you were going to be fine for the next three days."

What Can Baboons Teach Us About Fighting Malaria?
A BBC Science in Action report features research by Greg Wray, Susan Alberts and Jenny Tung that reveals surprising commonalities in how baboons and humans resist malaria and related parasites.

Family History Predicts Frequency, Severity of Mental Illness
Quizzing young people for less than 30 minutes about their family history of depression, anxiety or substance abuse can result in predictions of whether and how severely they will develop the disorders, according to a new report by Avshalom Caspi and Terrie Moffitt in the Archives of General Psychiatry.

Five Questions on Race, Identity and Health with Charmaine Royal
A Duke Research five-question interview features Charmaine Royal on race, identity and health. "I believe that the value and usefulness of ancestry testing rest largely with the test-taker or seeker," she says.

Collins Seen as Boon to NIH
In a blog post from The Scientist magazine, Bob Cook-Deegan suggests that, if confirmed as the new NIH director, Francis Collins may be able to help "heal some of the ideological rifts that have opened up in biomedical research policy."

New Alzheimer's Gene Pinpointed
A gene identified by IGSP member Allen Roses appears to be highly predictive of not only the risk of developing Alzheimer's disease, but also the approximate age at which the disease will begin to manifest itself, The Wall Street Journal reports.

Finding the Constant in Bacterial Communication
New insights into how bacteria communicate with one another are essential to the advancement of the new field of synthetic biology, where populations of genetically altered bacteria may be "programmed" to do useful things. The original findings by Lingchong You and his group appeared in Molecular Systems Biology.

Disclosure of APOE Genotype for Risk of Alzheimer's Disease
Bob Cook-Deegan is a collaborator on a New England Journal of Medicine study that found no significant short-term psychological risks of disclosing APOE status to adult children of patients with Alzheimer's disease.

Common Variants Conferring Risk of Schizophrenia
Anna Need, Dongliang Ge, Kevin Shianna and David Goldstein are coauthors on a deCODE genetics-led study published in Nature implicating the MHC region of the genome in schiziphrenia risk, consistent with the idea that the disorder has an immune component.

The Scientific Foundation for Personal Genomics: Recommendations for a National Insitutes of Health-Centers for Disease Control and Prevention Multidisciplinary Workshop
Participants in a workshop convened by the NIH and CDC, including Geoff Ginsburg, conclude in Genetics In Medicine that fulfilling the promise of personal genomics will require a rigorous multidisciplinary research agenda.

Functional Consequences of Genetic Variation in Primates on Tyrosine Hydroxylase (TH) Expression in vitro
Lisa Warner and Greg Wray report in Brain Research evidence highlighting the functional consequences of tyrosine hydroxylase genetic variation in primates.

Racial Differences in the Interaction between Family History and Risk Factors Associated with Diabetes in the National Health and Nutritional Examination Survey, 1999-2004.
A report by Jeanette McCarthy and colleagues in Genetics in Medicine suggests possible race/ethnic-specific differences in gene by environment interaction.

Advancing High-Throughput Gene Synthesis Technology
Jingdong Tian and colleagues say in Molecular Biosystems that "the capability of generating unlimited supplies of DNA molecules of any sequence or size will transform biomedical research in the near future."

The National Institute of Allergy and Infectious Diseases will fund five to eight research programs to develop technologies that can contribute to the prevention, diagnosis or treatment of neglected infectious diseases.

The National Institutes of Health will issue a request for multidisciplinary research proposals to unravel possible environmental influences on breast cancer risk, including studies of how genes interact with environmental factors to influence disease risk.

The National Cancer Institute will fund studies that develop high-throughput enrichment methods to detect very low levels of materials from tumors, such as DNA.

The NIH will fund studies of how dietary factors influence epigenetics and other processes involved in cancer prevention and development through R01 grants and R21 grants.

Anna Need has been appointed Assistant Research Professor in the IGSP and is an Associate Investigator in the IGSP Center for Human Genome Variation. Welcome, Anna!

The IGSP welcomes Nicolas Buchler, an assistant professor in the departments of biology and physics, as its newest investigator. His lab takes an interdisciplinary approach to understanding threshold responses, combinatorial control, bistability and oscillation in regulatory networks that are essential for patterning, cell proliferation and differentiation in developmental systems.

Registration is open for the Duke Bioinformatics Workshop, to be held August 17-18 and 19-20. Instructors include the IGSP's Holly Dressman, Phil Febbo, Arthur Moseley and Terry Furey.

ARRA Update: Anil Potti has received an NIH R01 grant courtesy of ARRA funding for a project entitled "Refining and Validating Genomic Signatures of Lung Cancer Biology."

ARRA Update: Jeanette McCarthy has received an ARRA Summer Research Supplement for a functional analysis of polymorphisms in the SCARB1 gene that affect serum lipids in an estrogen-specific manner.

Sandeep Dave has received an award from the Alexander and Margaret Stewart Trust for a project entitled "Therapeutic target identification in lymphoma using high throughput RNA-interference." The Pruden Estate and the Duke Comprehensive Cancer Center Core Grant will provide additional funding support for the effort.

David Goldstein was elected vice-chair of the Human Genetics and Genomics Gordon Research Conference, one of the major meetings in the field. He will vice-chair the 2011 conference and then chair the conference held in the year 2013.