Around the Bases

Thursday, June 26, 2003 Issue 19   VOLUME 2 ISSUE 19  
In This Issue
First Base: And the Winners Are . . .
Second Base: Broad Collaboration
Third Base: New Cancer Chief
Sliding Home: Y Bother?
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First Base: And the Winners Are . . .

The National Press Club in Washington, D.C., was the venue for the presentation of the inaugural Bio-IT World Best Practices awards. 150 invited guests attended the event, in which the winners of a rigorous competition that drew entries from 50 organizations were announced.

The Grand Prize in the Discovery and Development category went to Millennium Pharmaceuticals for the development of PARIS (Pathway Resource Information System), a computational application based on InGenuity's Pathway Knowledge Base for high-throughput data, which contributed to the development of Velcade and other drugs.

In Clinical Trials, the Grand Prize went to Baylor College of Medicine for BRAIN (Biomedical Research and Information Network), a series of paperless Institutional Review Board (IRB) procedures that save time and expand collaborations.

And in the Drug Manufacturing category, Solutia Pharmaceutical Systems won the Grand Prize for the API (Active Pharmaceutical Ingredient) project management system, to monitor utilization of human, capital, and material resources.

Other winners were Infinity Pharmaceuticals, Perlegen Sciences, Pharmacia, Pfizer, St. Jude Children's Research Hospital, Vertex Pharmaceuticals, and Wyeth.

Read further coverage of the Best Practices 2003 Awards.

For information on the 2004 Best Practices Awards, please contact Special Projects Editor Tony Strattner at:

Second Base: Broad Collaboration

During last week's press conference to announce the $300-million Broad Institute, Eric Lander cited a new study published online by Nature Genetics as an example of the collaborative research on complex diseases that will be the hallmark of the new venture. The new study, which Lander co-authored with founding Broad Institute faculty David Altshuler, Todd Golub, and others, adds important new insight into the origins of type 2 (adult-onset) diabetes. The disease affects more than 110 million people worldwide, but dissecting the genetic and environmental risk factors is a mammoth challenge.

The new study presents a novel microarray method called Gene Set Enrichment Analysis, which examines the coordinated changes in activity of genes that congregate in biological pathways, rather than just individually. By monitoring the activity of 22,000 genes in muscle biopsies from 43 individuals, including 18 diabetics, and sorting the results according to gene sets, the group identified a set of genes involved in energy metabolism (oxidative phosphorylation) that is less active in diabetes. This is exciting because previous studies have implicated mutations in factors known to regulate the activity of genes in this pathway as causes of rare inherited forms of diabetes.

Lander hopes this "self-assembled" collaboration between researchers at several MIT- and Harvard-affiliated institutions and hospitals is a harbinger of things to come at the Broad Institute.
*V.K. Mootha et al. "PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes."
Nature Genetics July 2003: doi:10.1038/ng1180

Webcast:  "Addressing Data Access Challenges in Life Sciences with Data Grids" - Tune in Now
Learn how leading pharmaceutical companies are accelerating drug discovery by implementing data grid technology to provide scientists with secure, wide area data access. Join your colleagues today for this informative webcast discussion.


Third Base: New Cancer Chief

Britain's Cancer Research UK, the world's largest cancer charity formed by the merger of the Imperial Cancer Research Fund and the Cancer Research Campaign, has a new boss. Alex Markham has been tapped to succeed Nobel laureate Sir Paul Nurse, who becomes president of Rockefeller University later this year.

Markham is currently Director of the Molecular Medicines Unit at the University of Leeds. "My job will be to maintain the charity's world-class research and build on recent advances to take new knowledge into the clinic for the benefit of cancer patients," said Markham, who assumes his new post on September 1. He will be aided by a war chest that swelled by $450 million last year. The charity spends about $250 million a year on research.

Read the Cancer Research UK press release.

Sliding Home: Y Bother?

Some 13 years ago, Whitehead Institute geneticist David Page thought he had discovered the male sex-determining gene, located on the tip of the Y chromosome. Alas, it was a false lead, and the true 'testis-determining factor' was identified a short time later by Britain's Peter Goodfellow and Robin Lovell-Badge.

Page maintained his interest in the Y chromosome, however, and over the past few years, his team has produced a string of beautiful papers on the structure and evolution of the male chromosome, identifying the genetic basis for at least some forms of male infertility in the process.

Last week, Page, Robert Waterston, and coworkers had the satisfaction of publishing the complete sequence of the Y chromosome. At the Washington, D.C., press conference, Page jokingly presented the Rodney Dangerfield map of the Y chromosome -- a cartoon depicting such hypothetical (or not) male-only traits such as 'air guitar' and 'inability to express affection over the phone.'

The true story of Y is fascinating in its own right, with the researchers discovering eight massive tracks of palindromic sequence, most of which contain testis-specific genes. The sequence of the Y chromosome offers the genetic equivalent of an archaeological dig - a chance to reconstruct events over hundreds of millions of years that transformed an anonymous ancestral chromosome into a pair of misfit sex chromosomes.

The Y chromosome paper is freely available online from Nature:
H. Skaletsky et al. "The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes."
Nature 423, 825-837 (2003).

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Applying fundamental advances in oncogenomics to the pathogenesis, diagnosis and treatment of cancer.

The 2004 CNIO (Spanish National Cancer Centre) Symposium
Madrid, Spain: 3-6 February, 2004

Announcing an outstanding international symposium analyzing the remarkable advances in cancer research, diagnosis and clinical oncology, co-organized by Todd Golub (Whitehead Institute/Dana Farber), Miguel-Angel Piris (CNIO), and Kevin Davies (Bio-IT World).

Speakers include: Mariano Barbacid, Josep Baselga, Gerard Evan, Todd Golub, Peter Goodfellow, Colin Hill, Olli Kallioniemi, Mary-Claire King, Greg Hannon, Sir John Maddox, Alex Matter, Martin Nowak, Miguel A. Piris, John Quackenbush, Chris Sander, Luis Serrano, Louis Staudt, Michael Stratton, Laura Vanīt Veer, Karen Vousden, and Bob Weinberg.

Further details and registration information:


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