February 2009

Advances in genome sciences and the approaches used to study them have developed at an incredible pace. The Genome Academy is intended to help researchers at all levels gain the background to begin or enhance their own genomics research projects through various topical learning series. The offerings will vary each year to reflect novel technologies as well as demand. Please see the schedule below for current offerings. Each series is offered free of charge to the Duke Community. Register early as some series may fill up quickly. For more information or to register, contact Shandra Robertson at 684-3156.

There will be two classes offered in February. The first class will be taught by Arthur Moseley PhD, Director, Proteomics Core Facility. Dr. Moseley will give a workshop on the topic of "Data Mining in Qualitative and Quantitative Proteomic Data Sets" The class will be held on Wednesday, February 4, 2009 from 1:00 p.m. - 2:00 p.m. in Nanaline Duke Auditorium, Room 147. The second class in February will be given by the following instructors: Andrea Novicki, PhD, Darin London, and Teddy Gray. The topic is "Keeping Up: The Art of Discovering What's New in Research". The class will be held on Wednesday, February 18, 2009 from 1:00 p.m. - 2:00 p.m. in Bostock Library Computer Lab—Room 023. To get additional details and class descriptions, visit http://genome.duke.edu/education/genomeacademy/

Genome Variation Separates Individuals With and Without Full Jewish Ancestry in a Large Random Sample of European Americans
David Goldstein and his team conclude that within Americans of European ancestry there is a perfect genetic correlation of Jewish ancestry, which, in principle, would permit near perfect genetic inference of Ashkenazi Jewish ancestry.

Gene Variation May Lead to Early Cardiovascular Disease
A study that includes Geoff Ginsburg as a collaborator has identified a variation in a particular gene that increases a person's susceptibility to early coronary artery disease. Read the original article in PLoS Genetics.

Team Spirit
In a Science News article about cooperation among bacteria and other microbes, IGSP Investigator Lingchong You says bugs sometimes get around metabolic burdens by "dividing the labor between two or more species."

2009: The Year of Personal Genomics
In a Portfolio article about the convergence of technology, science, medicine and business into tailored medical care, writer David Ewing Duncan says that a host of books documenting the revolution are already in the works, including one by the IGSP's Misha Angrist on his own experience being genetically screened for diseases and other traits.

A New Study Will Help Explain Why Some People Are Able to Fend Off Infection Even When Repeatedly Exposed to HIV
A collaborative agreement with Ilumina will allow Duke IGSP researchers to study the resistance to HIV infection among 50 individuals that were highly exposed to the virus, but who remain uninfected. Duke University researchers in the IGSP Center for Human Genome Variation will sequence the complete genome of at least 50 individuals with the desired phenotype.

Lawmakers Need a Crash Course in Science
In an opinion piece, Susanne Haga, an IGSP Investigator, writes "With the exception of a small group of doctors and scientists, most members of Congress lack the background to understand the process of science and the subtle nuances that justify investments in science or changes in existing priorities."

Non-coding RNA Prediction and Verification in Saccharomyces cerevisiae
Laura Kavanaugh and Fred Dietrich report in PLoS Genetics that thermodynamic stability, coupled with comparative genomics, can be used to predict non-coding RNA with significant structural elements.

Selective Gene Amplification for High-Throughput Sequencing
Jun Zhu and his team review patents that can enrich target genomic regions of interest to harness the power of NextGen sequencing technology for basic and translational biomedical research.

Genomic and Molecular Profiling Predicts Response to Temozolomide in Melanoma
A research team including Anil Potti and Joseph Nevins reported in Clinical Cancer Research that melanoma resistance to temozolomide is conferred predominantly by MGMT activity and suggests that MGMT expression could potentially be a useful tool for predicting the response of melanoma patients to temozolomide therapy.

A Transcription Factor Affinity Based Code for Mammalian Transcription Initiation
In Genome Research, an IGSP team led by Uwe Ohler proposes a new model for single-peaked transcription start sites based solely on known transcription factors and their respective regions of positional enrichment.

Childhood IQ and Adult Mental Disorders: A Test of the Cognitive Reserve Hypothesis
In The American Journal of Psychiatry Avshalom Caspi and Terrie Moffit report that lower childhood IQ is associated with increased risk of developing schizophrenia spectrum disorder, adult depression, and adult anxiety.

Pharmacogenetics of Antipsychotic Response in the CATIE Trial: A Candidate Gene Analysis
In the European Journal of Human Genetic, a team led by David Goldstein illustrates a requirement for dissemination of association statistics without undue emphasis on select findings by presenting association statistics for 2769 polymorphisms in 118 candidate genes evaluated for 21 pharmacogenetic phenotypes.

Genome Characterization Centers and Genome Data Analysis Centers for The Cancer Genome Atlas Research Network
Application Receipt Date(s): March 13, 2009

Centers (P50) and Exploratory Grants for Centers (P20) for Excellence in Ethical, Legal and Social Implications (ELSI) Research (CEERs)
Application Receipt Date(s): May 14, 2009

Transdisciplinary Cancer Genomics Research: Post-Genome Wide Association
Application Receipt Date(s): May 29, 2009

Three institutes of the National Institutes of Health plan to fund molecular and genomics studies aimed at developing small-molecule probes that could be used to study biological functioning in the nervous system, specifically in order to develop pharmacological therapeutic targets.

The National Science Foundation has pledged $12 million for research aimed at filling in the tree of life. They plan to fund between three and six awards with up to $3 million for five years for "innovative research that will resolve evolutionary relationships for large groups of organisms throughout the history of life".

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

A selection of upcoming events:

Monday, February 2nd
Cancer Genomics Meeting
Herbert Hurwitz will present "Colorectal Cancer: A Clinical Update"

Tuesday, February 3rd
Tuesday Seminar Series
Edward Buckler from Cornell University will present "The Genetic Architecture of an Adaptive Trait: Maize Flowering Time"

Tuesday, February 3rd
Genome Biology Meeting
Han Wu from the Zhu Lab presents.

Wednesday, February 4th
Genome Academy
Arthur Moseley from Duke's IGSP Proteomics Facility will present "Data Mining in Qualitative and Quantitative Proteomic Data Sets"

Wednesday, February 4th
Computational Biology Seminar
Katie Pollard from the Gladstone Institutes, University of California San Francisco will present "Accelerated evolution in the human genome"

Wednesday, February 11th
Systems Biology Seminar
Greg Wray from Duke's Department of Biology and IGSP will present "Gene networks behaving badly"

Thursday, February 12th
Genomic Medicine Forum
Qing Cheng will present "Pharmacogenomics for Individualized Medicine: Cancer vs. Host"

Wednesday, February 18th
Genome Academy
Andrea Novicki, Darrin London and Teddy Gray will present "Keeping Up: The Art of Discovering What's New in Research"

Wednesday, February 18th
David Goldstein presents a talk on race and pharmacogenetics.
RSVP by February 11th.

Anil Potti is the recipient of a grant award from the National Institutes of Health for a project entitled "Prospective Validation of Genomic Signatures of Chemosensitivity in Non-Small Cell Lung Cancer."

Jong Wook Kim, a post-doc in Joe Nevins' lab, received a fellowship from the Department of Defense for a project entitled "Elucidating the Role of microRNAs in Breast Cancer through Integrative Genomic Analysis of Oncogenic Pathways."

David Goldstein is the recipient of an award from Schering-Plough Corporation for a project entitled "Genome Wide Association Study to Identify Genetic Determinants of HCV Patient’s Response to Pegylated Interferon/Ribavir".

Mark DeLong is the recipient of a grant award from the North Carolina Biotechnology Center for a project entitled "High-Performance Computing System for Bioinformatics".

Thomas Urban, a post-doc in David Goldstein’s lab received a one year fellowship from the Epilepsy Foundation.