Weekly Scientist: Researchers Hope New Database Becomes Universal Cancer Genomics Tool

Saturday, August 18, 2012

Researchers Hope New Database Becomes Universal Cancer Genomics Tool

By Mike Martin for the Journal of the National Cancer Institute

Swiss scientists hope that a new online database called “arrayMap” will bring cancer genomics to the desktop, laptop, and tablet computers of pathologists and researchers everywhere.

The database combines genomic information from three sources: large repositories such as the NCBI Gene Expression Omnibus (GEO) and Cancer Genome Atlas (CGA); journal literature; and submissions from individual investigators. It incorporates more than 42,000 genomic copy number arrays—normal and abnormal DNA comparisons—from 195 cancer types.

“arrayMap includes a wider range of human cancer copy number samples than any single repository,” said principal investigator Michael Baudis, M.D. Ease of access, visualization, and data manipulation, he added, are top priorities in its ongoing development.

A product of the University of Zurich Institute for Molecular Life Sciences, where Baudis researches bioinformatics and oncogenomics, arrayMap illustrates the importance of copy number abnormalities (CNA)—dysfunctional DNA gains or losses that visibly lengthen or shorten certain chromosomes—in the diagnosis, staging, and treatment of various malignancies.

Click here for full story.

No comments:

About Mike Martin

A former senior science writer for United Press International, Mike Martin has written articles for Science, The Scientist, Harvard Magazine, MIT's Technology Review, and the Journal of the National Cancer Institute.

His clients include the Epilepsy Foundation, the Association of American Medical Colleges, the U.S. Department of Energy, and the California, Oregon, and Missouri university systems.

A member of the National Press Club and the National Association of Science Writers, Martin specializes in news about early-stage university and laboratory research.

He was a science journalism fellow at Duke University's National Evolutionary Synthesis Center in Fall 2011, where he completed two stories about Margie Profet -- one for the Journal of the National Cancer Institute and a second for Psychology Today. The latter piece led to a happy ending to her 8-year missing person story.

Reader Raves

Mike, You have a real ability to suss out the great stories!
-- Amber Jones, Science Information Officer, National Science Foundation

Once again, you've hit the nail on the head. Sharp, concise, smooth. Nice work.
-- Marc Kaufman, Editor, Science & Spirit

Just writing to praise your exceptionally well-written article on the quantum dots. It is a pleasure to read one's work so accessibly and accurately described. Warmest wishes,
-- Prof. Edward (Ted) H. Sargent, Nortel Networks - Canada Research Chair in Emerging Technologies, Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto

Thanks for your stellar work on this assignment. We're really pleased. I'm glad you thought of us with this story.
-- Bob Marshall, assistant managing editor, MacLeans

Good God -- that's the best Zodiac piece I've ever seen. Absolutely brilliant work, Mike. Brilliant.

-- Alan Cabal, journalist, Counterpunch and New York Press, on With Malice Aforethought

Mike, Thanks for a great job and a very nice story!
-- Caroline McNeil, News Editor, Journal of the National Cancer Institute

Her Majesty would very much like to read your article. I would appreciate it if you can send it to this address.
-- Ghadeer Taher, Media Advisor Office of Her Majesty Queen Noor, Amman, Jordan

I’m writing from InkWell Management, a literary agency in New York. I recently had the pleasure of reading your exceptional article about Margie Profet. Have you considered book-writing? -- Nathaniel Jacks, InkWell Management, New York, NY on Margie Profet's Unfinished Symphony

I loved your piece on Margie Profet in Psychology Today. It was well done and well reported -- as interesting a piece on the nature of science, madness and genius as I’ve read. -- Daniel Levine, Partner, Levine Greenberg Literary Agency, on Margie Profet's Unfinished Symphony

Thanks for a great story. I really appreciate the job you are doing.
-- Maria Zemankova, Ph.D., Program Director, Information and Data Management, Division of Information and Intelligent Systems, National Science Foundation

Boy, your coverage is pretty widespread. Kudos on being a quick study.
-- M. Dickman, Public Information Officer, AT&T Labs

You got it right. Good job. Hope it gets widely read, quoted and acted upon!
-- Mary Dee Wenniger, Editor and Publisher, Women in Higher Education

Thanks much for your superb article. Your piece has made my day. -- Kevin McCaffrey, Associate Director, Office of Communications, Mount Holyoke College

Thank you for a wonderfully written piece on the enigmatic Margie Profet. Her three revolutionary papers have always fascinated me, and now her life, or lack thereof, does as well. -- Barry X. Kuhle, Visiting Assistant Professor, Department of Psychology, Dickinson College on Margie Profet's Unfinished Symphony

I really enjoyed your piece on Mark Twain.
-- Jeff Hardison, Fleishman-Hillard Public Relations

You do some great work. I'd love to have you contribute to Small Times.
-- Howard Lovy, News Editor Small Times Media

A very fine story, Mike. Thank you for this. -- Harvey Mansfield, William R. Kenan, Jr. Professor of Government, Harvard University, on Margie Profet's Unfinished Symphony

I knew Margie well during her time at the University of Washington. I agree with what is said near the end of the article: she was very innovative but was accepted, even embraced, by the scientific community for all of her innovation and oddness. I like that this article takes the optimistic view, implying that we will someday see her again. But I can't see her living a backwoods hermetic life. I fear that she is gone and I will forever miss her. -- George Lake, Professor of Theoretical Physics, Head, Computational Science Program Institute for Theoretical Physics, University of Zurich, Switzerland, on Margie Profet's Unfinished Symphony. [Note: Margie was found shortly after the story appeared].

Congratulations -- I think you did a great job. I really liked the way you explained how information can be fundamental, and the image about the big bang being like a supercomputer downloading information is brilliant. I'm going to quote you on that! -- Raphael Bousso, Professor of Physics, University of California Santa Barbara

You've written a fine article. Well-researched and on target. Thanks for including me and I appreciate your sending me the link. -- John Baldoni, Management Consultant

Really enjoyed reading your story "The Great Green Grid" in E: The Environmental Magazine! Nicely done!
-- Anne M. Haas, News & Media Services, Energy & Environment, Pacific Northwest National Laboratory

Glad to help Mike. The story turned out really well.
--Heath Shackleford, PR Manager, American Healthways

Nice piece on Googling.
--D. Kent Pingel, Public Relations Director, CI Host

I got a lot of responses from the story on Google.
Everyone's reading your articles!
-- Molly Parsley, Marketing & PR Manager, Carat Interactive

Great story. Thank you for sharing this with me.
-- Tracey L. Linkous, CTM, Director of Communications, Diffusion Pharmaceuticals LLC

Congratulations on a very well-balanced story!
-- Vwani Roychowdhury, Professor, Electrical Engineering Department, University of California, Los Angeles

Thank you very much for forwarding to me the article from the ST. LOUIS JOURNALISM REVIEW. The article is very nicely done and I appreciate your including my comments in it. Keep up the nice work and feel free to contact me again in the future if I can be of assistance.
-- Jeff McCall, Professor of Communications, DePauw University

Cool story! I like the flow of it. Great job!
-- Luis Lehner, physics professor, University of British Columbia

I think think the story reads quite well -- you pulled off keeping the focus on the find well without completely burying or ignoring the tension created by the creation angle.
-- Ken MacLeod, Geology professor and paleontologist, University of Missouri

Well written. Good, interesting science deserves publicity.
-- Piotr Pieranski, Poznan University of Technology, Poznan, Poland

I think your work is terrific, and I am happy to be associated with you and WeeklyScientist!
-- Mike LaSalle, Editor, MensNewsDaily

Great story. Interesting and fair. Thank you. Keep up the good work. Your other articles are also very interesting and thought provoking. -- Doug Phillips, President, Vision Forum Ministries

Thanks for the update on the dino fossil discovery. Nice story. You write very well. -- Pat Housley, Director of College Relations, Central Michigan University

You wrote an excellent, excellent story. Accurate, balanced. Just terrific! Many thanks! -- Mikhail Gershteyn, physicist, MIT

Nicely done; many thanks. -- Robin Goldsmith, Public Information Officer, Scripps Institute

Thank you very much for the great article you wrote. It reads very well! -- Peter Pfeifer, Department of Physics, University of Missouri

Thanks much for sending the story. Fast & great work. I'm totally impressed. Feel free to pick up my stories anytime!
-- A. Lynn, University of Illinois Media Relations

Keep up the good work.
-- Gary Martin, Express-News.net

Mike: I enjoyed the article! Thanks for writing it!
-- D. Callaway, Ph.D., Theoretical & Applied Mechanics

Thanks Mike! Keep 'em coming!
-- G. Cleere, Information Director, Office of Naval Research

Thanks. Well written article.
-- W. Fitzgerald, Senior Scientist and voice-activated software researcher

This is a great article. Thanks again for sending it along.
-- Alan Stern, Southwest Research Institute

Good one...you're going to earn me big brownie points from all the member's press secretaries with that one.
-- Jeffrey Donald, US House of Representatives Science Committee

Thanks, Michael! GREAT story!
-- George Hastings, Astronomy instructor, Virginia Commonwealth University

Thanks for the great story !!!
-- Laszlo Kish, Assoc. Professor, Electrical Engineering, Texas A & M University

Nice story. Thanks so much. -- Sandra Mauceli, Xerox Corporation, www.xerox.com

The science and technology information you cover is very insightful and great stories. -- Seung Oh, VP, Business Development, Competitive Technologies

Thanks for your clips, Mike. Always good to meet someone who's covering science on the outside (as we PIO's say).
-- Chad Boutin, Purdue University Media Relations

Nice article. Glad I could be of help.
-- Bette Price, CMC Coauthor: True Leaders (Dearborn Trade Press) The Price Group

Great article! Thanks for letting me be part of it.
-- John Baschab, Impactinnovations.com

The controversy in flat lenses made most interesting reading. Overall very interesting. Best regards --Richard H. Tullis, Ph.D., Chief Science Officer, Aethlon Medical, Inc.