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SUMMARY:DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS
  AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY - Florian Markowetz
DTSTART:20100111T153000Z
DTEND:20100111T163000Z
UID:TALK21996@talks.cam.ac.uk
CONTACT:Stefan Gräf
DESCRIPTION:By Keith A. Baggerly and Kevin R. Coombes\n\nU.T. M.D. Anderso
 n Cancer Center\n\nhttp://www.e-publications.org/ims/submission/index.php/
 AOAS/user/submissionFile/5816?confirm=cfad51b7\n\nHigh-throughput biologic
 al assays such as microarrays let us ask very detailed questions about how
  diseases operate\, and promise to let us personalize therapy. Data proces
 sing\, however\, is often not described well enough to allow for exact rep
 roduction of the results\, leading to exercises in “forensic bioinformat
 ics” where aspects of raw data and reported results are used to infer wh
 at methods must have been employed. Unfortunately\, poor documentation can
  shift from an inconvenience to an active danger when it obscures not just
  methods but errors. In this report\, we examine several related papers pu
 rporting to use microarray-based signatures of drug sensitivity derived \n
 from cell lines to predict patient response. Patients in clinical trials a
 re currently being allocated to treatment arms on the basis of these resul
 ts. However\, we show in five case studies that the results incor- \npora
 te several simple errors that may be putting patients at risk. One theme t
 hat emerges is that the most common errors are simple (e.g.\, row or colum
 n offsets)\; conversely\, it is our experience that the most simple errors
  are common. We then discuss steps we are taking to avoid such errors in o
 ur own investigations.
LOCATION:Room 132\, CRI
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