August 1, 2005 (Vol. 1, No. 3) Scientific Updates Administrative Updates Biomarker Team Spotlight Key Web Pages at FHCRC

Dear Colleagues:

The consortium now consists of two teams in Korea and teams in China, Singapore, Taiwan and the United States. We may also have teams forming in Australia and Canada.

This month our newsletter is highlighting news from the National Cancer Institute regarding the newly-approved proteomics initiative. In addition, the newsletter includes a team profile for one of the U.S. teams. This is an example of the kind of profile we would like to post for each team on our website. Also included in the newsletter are the usual updates on meetings, including updates on the Informatics meeting in August and the consortium-wide meeting in October.

I look forward to our meeting in October.

Best regards,

Lee Hartwell
President and Director
Fred Hutchinson Cancer Research Center

National Cancer Institute Approves Proteomics Initiative

NCI's Board of Scientific Advisors (BSA) approved the Clinical Proteomics Technologies Initiative, a $104 million program aimed at optimizing current proteomics technologies and developing the new technologies, reagents, systems, and working consortia to significantly advance the field of cancer proteomics research.

"The revised proposal reflecting BSA's input builds on a 2-year process that sought feedback from the research community through workshops and meetings," said Dr. Anna Barker, NCI deputy director for Advanced Technologies and Strategic Partnerships. "We heard over and over again from across the cancer research enterprise that we need to provide the community with specific support to advance the field of proteomics," Dr. Barker stated, especially in the areas of technology, reagents, bioinformatics, and data standards to ensure reproducibility and comparability of data.

The initiative, she added, is not "all encompassing." Rather, it's "a step forward," meant to bring the field of proteomics "to a point where we can move ahead ... hopefully very quickly."

The initiative, explained Dr. Greg Downing, director of NCI's Office of Technology and Industrial Relations, encompasses a three-pronged strategy:

• Establishment of Clinical Proteomic Technology Assessment Consortia, which will be comprised of multidisciplinary teams from different institutions focused on evaluating tools, such as proteomic technologies and reference reagents; developing protocols and performing cross-laboratory studies of common sample sets; and also providing consultative services and training to the community. This component will use the U24 funding mechanism.
• Support of research into overcoming barriers to protein/peptide feature detection, identification, and quantification; and development of mathematical, computational, and predictive approaches for analysis of large scale data. This component will use the R01 and R21/R3 (phased innovation) award mechanisms.
• Creation of a virtual, centralized clinical proteomics reagents resource, which will include resources such as antibodies, peptides, and proteins. This component will use an RFP contracts funding mechanism.

Steering Committee

The Consortium Steering Committee is currently comprised of the principal investigator from each team, Drs. Myeong-Hee Yu, Hyang-Sook Yoo, Chia-Chu Pao, Fuchu He, Sir David Lane, Lee Hartwell and Drs. Steve Carr, Ruedi Aebersold, Richard Smith, Leigh Anderson, Richard Caprioli and Martin McIntosh.

Informatics Meeting

We are moving forward with the preparations for the August 22-23 Informatics Pre-Meeting in Seoul, Korea from August 22-23 at the International Cooperation Building at the Korea Institute of Science and Technology (KIST, 39-1 Hawalgok-dong, Sungbuk-gu, Seoul 136-791, Korea).

For hotel arrangements, please make hotel reservations through Mr. Eung Cheon Hwang (rmhec@kist.re.kr).

KIST will support hotel lodging $130 x up to 3 nights and the accommodation suggested accommodations are as follows:

1. Holiday Inn Seongbuk (5 min drive from KIST)
   Room rates including breakfast: about $130
2. Hotel Sofitel Ambassador (20-30 min drive from KIST) - more comfortable Room rates including breakfast: about $220
   ? The above price is what we negotiated with them.

If you plan to attend the Informatics Meeting, please send Mr. Hwang (e-mail: rmhec@kist.re.kr) the following information of yours.

1. Hotel name that you want to lodge
2. Smoker or Non-Smoker
3. Arriving and departing schedule
4. Brief C.V. for processing of financial support.

First International Biomarker Consortium Meeting – October 11-12, 2005

The International Cancer Biomarker Consortium Meeting is planned for October 11-12, 2005 in Seattle, Washington. The Steering Committee is currently developing the agenda and a draft agenda will be circulated in the coming weeks. Please contact Karma Kreizenbeck (kkreizen@fhcrc.org) with any questions.

Team Profiles

We are working to put together the public interface for the International Cancer Biomarker Consortium website. For each biomarker discovery team, we would like to post a brief team profile. Wendy Law has contacted each site with draft profiles for review. As soon as we receive the final documents, we will move forward with putting the site up. Below is an example of the profile for one of the U.S. Teams.

Brief Description of Project:

"Improving Early Detection of Breast Cancer with a Blood Test" is a multi-institutional research project to identify biomarkers (proteins) that reveal the presence of breast cancer in a blood test and then to determine which are effective markers of early disease and which of therapeutic response. Multiple nationally-recognized laboratories expert in proteomics technology have been brought together, each of which will take a different and complementary approach to the discovery process. This will be the first study of its kind conducted across expert Consortium laboratories sharing methodologies. In addition, the sharing of common specimen samples, data, and data analysis tools will allow researchers to extend their knowledge to one another and ultimately to their colleagues in the scientific community.

The basic strategy of the Consortium will be to employ two discovery modes. One is a candidate approach which first identifies the most likely disease-specific proteins in the tumor or its proximal fluids, then evaluates the blood of patients compared to normal individuals for the presence/absence of these candidates. Since the candidates are likely to be present in blood at very low concentration, a suite of techniques to identify very low abundance proteins suspected of being useful diagnostic agents will be used. These techniques include glycopeptide enrichment, antibody enrichment, and abundant serum protein depletion followed by mass spectrometry. A second approach is to compare directly the blood of cancer patients with that of normal controls using unique instrumentation and techniques developed by Consortium members including intact protein analysis system (IPAS) and visible isotope-coded affinity tags (VICAT). Biomarkers diagnostic of cancer will be identified and quantitated by these methods.

Key Investigators:

Ruedi Aebersold
Gordon Anderson
David Camp
Steven Carr
Ronald Depinho
Francisco Esteva
Michael Gillette
Todd Golub
Sam Hanash
Leroy Hood
Gabriel Hortobagyi
Peter Laird
Eric Lander
Biaoyang Lin
Martin McIntosh
Amanda Paulovich
Aysegul Sahin
Nathalie Scholler
Richard Smith
Nicole Urban
Hui Zhang

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