January 2009

With the start of the new year, the IGSP will turn six years old and begin a new phase of focus and growth, concentrated in four key areas: understanding human genome variation and its role in shaping biological traits, including disease; personalizing medicine through the use of genomic data related to disease and clinical management; building the expertise in the quantitative sciences required to organize, move, analyze and work with incredible volumes of data; and redoubling our efforts to explore the interface of genetics and society in the age of personal genomics. To learn more, read a message from Hunt Willard.

To follow our progress in these important areas, be sure to look to GenomeLIFE. Last issue, we brought you a story on the passage of the Genetic Information Nondiscrimination Act (GINA) and an interview with David Goldstein on human genome variation. In the issue available on the newsstands now (be sure to pick up your copy if you don’t have it already!!), you’ll find a feature on team science, and particularly the critical role of partnerships between IGSP scientists working in "wet" laboratories and those with the quantitative skills needed to distill meaning out of mass quantities of data. In our next issue, you can expect to learn about the work of the IGSP-CHAVI team, which is using genome resequencing to discover individual genome variants involved in resistance to HIV, as well as the IGSP's Clinical Genomics Studies Unit, which is engaged in clinical trials aimed at translating genomic discoveries into clinical practice.

Genes Seem to Affect Tissues Differently
David Goldstein and colleagues have found that the same gene acting very differently in different tissues may contribute to certain human traits, including how likely a person is to get a disease, according to a Health Day report at usnews.com.

Scientists Test Equipment Critical to MURDOCK Study
In an article in the Salisbury Post about the testing of the first instrument in the Murdock Research Institute's proteomics core, the IGSP's Arthur Moseley said that they are "very excited about the fact that we will have a component of the lab up and running and starting to generate some data."

Researchers Use Genes to Predict Cancer Recurrence
A WRAL report featuring gastroenterology fellow Katherine Garman, who works in Anil Potti's lab, says that IGSP research could lead to newer drugs tailored to specific tumor types.

Gene Mutations Linked to Statin Resistance
Scientists led by Geoff Ginsburg and Deepak Voora have identified genetic mutations that may help explain why some people don't respond very well to statins, drugs taken by millions of Americans to fight cholesterol and prevent coronary artery disease. Read a Q&A with Voora at usnews.com or read the original article in Circulation: Cardiovascular Genetics.

Sharing the Burden, and the Wealth
In a Duke Research feature about the Duke Shared Cluster Resource, IGSP Director of Computing Operations Mark Delong says he expects 100 IGSP researchers to be working on the cluster by year's end.

Putting Primates in Sequence
A new Primate Genomics Initiative, involving the IGSP's Center for Evolutionary Genomics and the Department of Evolutionary Anthropology in Trinity College, will train graduate students how to incorporate new genetic and genomic methods into their research, says research director Julie Horvath.

New Test Aims to Predict Breast Cancer Better
IGSP Member Kelly Marcom says that results showing that a new test to predict an ordinary woman's odds of getting breast cancer works better than a method doctors have relied on for decades are encouraging, but more research in other population groups are needed.

Gene Could Drive Species Separation
A gene in fruit flies that appears to drive the creation of new species reveals that internal genetic environments may be just as important as external factors when it comes to speciation, a discovery that IGSP Member Mohamed Noor says "represents a dramatic change in the context of the field."

HHS Committee Will Seek Public Comment on Upcoming Gene IP Policy Draft Report
SACGHS developed policy recommendations about gene patenting by commissioning a series of case studies conducted by the IGSP’s Center for Genome Ethics, Law and Policy. GELP reviewed case samples related to tests for BRCA1 and BRCA2 for breast and ovarian cancer, as well as tests for Alzheimer’s disease and hearing loss.

Leave This Child Behind
An article in Slate about a genetic test that predicts toddlers' athletic potential cites a comment from Misha Angrist's blog genomeboy pointing out that the ACTN3 testing isn't actually new, but counters that sometimes a technology itself isn't as important as how it's understood and used.

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits
New results reported in PLoS Biology by Erin Heinzen, David Goldstein and colleagues suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.

The Genomic Analysis of Lactic Acidosis and Acidosis Response in Human Cancers
In PLoS Genetics, an IGSP team led by Ashley Chi reports results identifying causal roles of lactic acidosis pathway activity on cellular responses and tumor development.

Complexity Reduction in Context-Dependent DNA Substitution Models
Uwe Ohler and William Majoros report in the journal Bioinformatics that context-dependent DNA substitution models can be substantially reduced in complexity without reducing predictive accuracy.

Childhood IQ and Adult Mental Disorders: A Test of the Cognitive Reserve Hypothesis
Avshalom Caspi and Terrie Moffitt report in The American Journal of Psychiatry that lower childhood IQ is an antecedent of several common psychiatric disorders and also predicts persistence and comorbidity.

The National Institute on Alcoholism and Alcohol Abuse is seeking research into how genetic variants may be linked to alcohol dependence in adults and adolescents.

The National Cancer Institute wants to fund scientists aiming to develop novel ideas and technologies that use molecular or cellular analysis in cancer detection and risk assessment, and will support them with up to $500,000.

The National Institute of Biomedical Imaging and Bioengineering is seeking to fund research into novel imaging methods that can detect and create images of in vivo molecular activities, under a follow-up to an earlier request under the National Institutes of Health’s Roadmap for Medical Research program.

The National Institute of Mental Health has issued a request for applications seeking to fund researchers conducting systems biology studies that expand on findings from genome-wide association studies and other genomic approaches. The studies would be conducted as part of the National Institutes of Health’s Genes, Environment and Health Initiative.

For full details and the latest updates on IGSP seminars and events, see the Events Calendar

A selection of upcoming events:

Tuesday, January 6th
Tuesday Seminar Series
Susan Rosenberg from Baylor College of Medicine will present "Mutation as a stress response and the regulation of evolvability."

Tuesday, January 13th
Genome Biology Meeting
Leyna Denapoli from the MacAlpine Lab presents.

Wednesday, January 14th
Computational Biology Seminar
Matthew Eaton, a CBB student in the MacAlpine lab, will present.

Wednesday, January 14th
Systems Biology Seminar
Blanche Capel, a professor of cell biology, presents.

Thursday, January 15th
Genomic Medicine Forum
Jeannette McCarthy presents "Effect of gene and sex hormone interactions on serum lipids and related metabolic traits."

Wednesday, January 21st
Race, Genetics and Health Seminar
Malinda Maynor Lowery presents on race classification and the Lumbees.
RSVP by January 14th.

Friday, January 23rd
Science & Society Journal Club
Audrey Howell will present.
RSVP Required.

Summer Fellowships in Genome Sciences & Policy offer undergraduate freshmen and sophomores who have completed one course in biology the opportunity to investigate major questions in the field under the mentorship of IGSP faculty representing many relevant disciplines.

The deadline for application is February 18, 2009. Learn more.

Uwe Ohler was named one of "tomorrow’s PIs" in a special year-end issue of Genome Technology magazine profiling rising young investigators. In it, he says that in the genome sciences "the technology's not going to be the limiting part. It will be more a matter of keeping up with the pace of the technology development as a computational person and adjusting our models to actually deal with the data in terms of just basic infrastructure."

Duke senior Sally Liu, who works in IGSP Member Nina Sherwood's lab, has been awarded a prestigious Marshall Scholarship that will finance two years of graduate level studies at a college or university in the United Kingdom.

Caitlin Milligan, an undergraduate senior who does independent research in Hunt Willard's lab studying X chromosome inactivation, has been elected to membership in the Duke chapter of Phi Beta Kappa, the nation's oldest and largest academic honor society.