November 2009

The announcement last spring that billions of dollars would go to the National Institutes of Health and other funding institutions as part of The American Recovery and Reinvestment Act of 2009 sparked a flurry of grant-writing activity at the IGSP, as it did across the campus and at research institutions around the country. Now, the results are in, and it is clear that the extra effort paid off. Duke as a whole has done quite well, ranking sixth in the nation among its peers with more than $150 million, and the IGSP is no exception.

Overall, the IGSP and its affiliated faculty have won at least 15 ARRA grants, for a total of more than $14 million. Congratulations to all the awardees! We woud also like to give special recognition and thanks to Donna Crutchfield, Louise Wilson and Wendy Conklin, who worked long hours to get the proposals in under very tight deadlines.

We've been keeping you posted in Genomes@Duke since June about individual grants as they have come in. For the latest updates, see the Honors & Awards section below. For more information about where the federal stimulus money is going, see www.recovery.gov. For more on awards to Duke, go to Duke's official Economic Stimulus site.

Op-ed: Weighing Consent in Babies' Screening
In a News & Observer op-ed, Susanne Haga says that doubts over storage and use of newborns' blood samples must not compromise the program's success in catching treatable diseases early.

What ELSI is New?
GenomeWeb highlights a special series in The Genomic Law Report, which includes an essay from Misha Angrist about clinical geneticists' role in the burgeoning personal genomics arena and another by Bob Cook-Deegan on ethical challenges as whole-genome sequencing takes off.

Some Bacteria Zig When Others Zag
A new set of experiments by Lingchong You and colleagues has uncovered the existence of "bistability" in which an individual cell has the potential to live in either of two states, depending on which state it was in when stimulated. Read the original report in Nature Chemical Biology.

New Classification Proposed for Stomach Cancers
A new method for classifying stomach cancers based on signaling pathways "gives us the first way to truly offer our gastric cancer patients personalized medicine," says IGSP Investigator Patrick Tan. Read the original paper in PLoS Genetics.

Genome Sequence Published for Important Biofuels Yeast
A Duke team including Fred Dietrich has sequenced the complete genome of a strain of yeast that thrives on turning sugar cane into ethanol for biofuel. Read the original report in Genome Research.

Comparing Gene Set Enrichment Methods Head-to-Head
Biostatistics researchers including Sayan Mukherjee recently compared four gene set enrichment methods on cancer-related datasets and identified the strengths and weaknesses of each, GenomeWeb reports. Read the original paper in BMC Bioinformatics.

Outside the Lines: Athletes and Genetics
In an ESPN Outside the Lines report, Hunt Willard says "we know that genes are important for elite athletic performance...we just haven't been able to put our finger on the particular genes that are involved yet."

Sniffing Out Swine Flu
Slate.com reports on efforts by the Duke team led by Geoff Ginsburg to find better ways to diagnose swine flu and other infectious diseases.

Human Genetics: Hit or Miss?
In a Nature News feature, David Goldstein says that the discovery of SNPs associated with very high or low levels of fetal haemoglobin is "a tour de force illustration of the value of GWAS," but it's on a short list.

Common Gene Mutation Linked to Statin Side Effects
Deepak Voora and Geoff Ginsburg report new evidence that a common gene variant may underlie differences among people in experiencing side effects of cholesterol-lowering statins. Read the original report in the Journal of the American College of Cardiology.

miRGen 2.0: a Database of microRNA Genomic Information and Regulation
In Nucleic Acids Research, Molly Megraw and colleagues report on a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data.

Multiplex PCR to Diagnose Blood Stream Infections in Patients Admitted from the Emergency Department with Sepsis
Chris Woods and colleagues show in the Journal of Clinical Microbiology that real-time multiplex PCR has the potential to serve as an adjunct to conventional blood culture, adding diagnostic yield and shortening the time to pathogen identification.

Next-Generation Disparities in Human Genomics: Concerns and Remedies
In Trends in Genetics, Anna Need and David Goldstein say it is important to adopt measures to ensure that populations of diverse ancestry are included in genomic studies, and that no major population groups are excluded.

A Genomic Approach to Improve Prognosis and Predict Therapeutic Reponse in Chronic Lymphocytic Leukemia
A microarray analysis of chronic lymphocytic leukemia lymphocytes can be used to refine prognosis and predict response to therapies, Joe Nevins and colleagues report in Clinical Cancer Research.

Genetic Regulation of Alpha-Synuclein mRNA Expression in Various Human Brain Tissues
Ornit Chiba-Falek reports in PLoS One new evidence for functional consequences of Parkinson's-disease-associated SNCA gene variatns in disease relevant brain tissues, suggesting that regulation of the gene may play a role in the disease.

DNAaseI Hypersensitivity at Gene-Poor, FSH Dystrophy-Linked 4q35.2
In a Nucleic Acids Research report, researchers including Terry Furey and Greg Crawford, conclude that two large gene desert regions may have functional significance despite their paucity of known genes.

Host Genetics Influences on HIV type-1 Disease
In an Antiviral Therapy review, Jacques Fellay discusses several genotype-phenotype associations that have shed new light on HIV pathogenesis in the context of the new genome-wide approaches that make it possible to globally assess the influence of the host genome on HIV-1 related outcomes.

As of October 1st, Arthur Moseley, director of the Proteomics Core Facility, became an IGSP Investigator and an Associate Research Professor. Please join us in welcoming Arthur to the faculty.

The IGSP also welcomes Amy Schmid, a new faculty member in the biology department, as its newest IGSP Member.

Undergraduates Brandon Ruderman and Jason Klein have founded a new student club - the Genome Research & Education Society (GRES) - dedicated to promoting scholarship and research at Duke and educating others about the genome sciences and their implications. In support of the GRES mission, Brandon has already won an award from The Duke Center for Science Education for Science Saturdays at the North Carolina Museum of Life & Science, and Jason has won an award in support of a Science Policy, Ethics & Law Course at the North Carolina School of Science and Mathematics. Jason and Brandon are also approved to teach the house course From Science to Society: Decoding Your Genome at Duke in Spring 2010. If you would like to get involved in the new group, subscribe to the GRES listserv and/or join them on facebook.

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

A selection of upcoming events:

Monday, November 2nd
Cancer Genomics
David Hsu presents "Genomic Strategies to Guide Treatment of Colorectal Cancer."

Tuesday, November 3rd
Tuesday Seminar Series
Gary Karpen presents "Epigenetic Tails of Genome Stability."

Tuesday, November 3rd
Genome Biology Series
Lingyun Song from the Crawford lab presents "Mapping Dnase Hypersensitive Sites in Human Cell Lines."

Wednesday, November 4th
Systems Biology Seminar
Cheemeng Tan from the You lab presents "Emergent Bistability in Bacteria and Implications for Effective Antibiotic Treatment."

Thursday, November 5th
Special CBB Seminar
Bill Noble presents "Unsupervised Discovery of Patterns in Multiple Tracks of Functional Genomics Data."

Thursday, November 5th
Genomic Medicine Forum
Allen Roses presents "Clinical Genetic Implications of a New Phylogenetic Poly-T Repeat Test in Alzheimer's."

Thursday, November 5th
Communication Series
Rochelle Schwartz-Bloom presents "Visualizations to Learn and Communicate Science."

Monday, November 9th
Special Seminars
Rick Kittles presents two special seminars entitled "DNA Testing and the Illusion of Native American Ancestry" and "The Role of Diverse Populations in Personalized Genetic Medicine."

Wednesday, November 11th
Genome Academy
Genomes 101 features Alex Cho on Personalized Medicine.

Monday, November 23rd
Mosquito Biology and Biotechnology Conference
The conference will focus on mosquito biology, molecular biology, field interventions and policies that help individuals to access health biotechnology. Registration required.

Tuesday, November 24th
Mosquito Biology and Biotechnology Conference
The conference continues. Registration required.

ARRA Update: Geoff Ginsburg has received two awards for a project entitled "Phase I Clinical Trial Describing the Pharmacogenomics of Aspirin" and one entitled "Programs in Clinical Effectiveness of Cancer Pharmacogenomics."

ARRA Update: David Goldstein has received an award for a project entitled "Whole-genome Sequencing in Multiplex Epilepsy Families."

ARRA Update: Greg Crawford has received an award for a project entitled "Comprehensive Identification of Active Functional Elements in Human Chromatin."

ARRA Update: Laura Beskow has received an award for a project entitled "Ethical Approaches to Genotype-Driven Research Recruitment."

ARRA Update: Phil Febbo is the principal investigator on a grant subcontract for a project entitled "Mechanism-based Classification and Targeting of Castration-Resistant Prostate Cancer."