[Cowystats] CO/WY ASA Baggerly Talk CORRECTION and lunch/ dinner announcement

[Matt Pocernich]

My apologies - I need to correct the times and dates on Dr. Baggerly's 
talks. Dr. Baggerly is giving two talks next week.  The titles, times
and places are 

######################33

Proteomics, Ovarian Cancer, and Experimental Design
Cancer Center, Wed 3/28 12-1pm Fitzsimons campus
12-1pm RC 1 North Tower - West (Research) Auditorium

and


Cell Lines, Microarrays, Drugs and Disease: Trying to Predict Response to Chemotherapy

Preventive Medicine and Biometrics Seminar, Thurs 3/29 12-1pm
9th Street campus, CPH Auditorium


Lunches are being organized  after each seminar and dinner on both days
during Keith's visit Wed 3/28 and 3/29. If you are interested in attending any
of these, please contact Katerina Kechris  at katerina.kechris at uchsc.edu .

**********************

Directions

Here's the map to 9th Street:
http://www.uchsc.edu/maps/9th.htm
The CPH auditorium is next to lot C
http://www.uchsc.edu/facilities/parking/docs/9thmap.pdf

to Fitzsimons:
http://www.uchsc.edu/maps/fitz.htm
You can find RC-1 North at
http://www.ucdhsc.edu/admin/facilities/parking/docs/FitzMap.pdf


Abstracts

Proteomics, Ovarian Cancer, and Experimental Design

Cancer Center, Wed 3/28 12-1pm Fitzsimons campus
12-1pm RC 1 North Tower - West (Research) Auditorium

Keith Baggerly
Department of Bioinformatics and Computational Biology
UT M.D. Anderson Cancer Center

Abstract:

Just as microarrays allow us to measure the relative RNA expression
levels of thousands of genes at once, mass spectrometry profiles
can provide quick summaries of the expression levels of hundreds
of proteins. Using spectra derived from easily available
biological samples such as serum, we hope to identify proteins
linked with a difference of interest such as the presence
or absence of cancer. With respect to ovarian cancer, this
approach has been claimed to provide diagnostic tests with
near perfect sensitivity and specificity. Based on the strength
of these results, a home-brew test known as OvaCheck was advertised
as "coming soon". Unsurprisingly, such tests are of great interest
at MD Anderson, and we have explored proteomic patterns in depth.

In this talk, we will briefly introduce the mechanics underlying
the mass spectrometry variant known as matrix-assisted laser
desorption and ionization/time of flight (MALDI-TOF), and the
special case known as surface-enhanced laser desorption and
ionization/time of flight (SELDI-TOF). We then take a pictorial
tour through some of the raw data, looking for interesting
structure both in a single experiment and over multiple experiments.
However, what the data most clearly shows is not biological
structure, but rather the need for careful experimental design,
data cleaning, and data preprocessing to ensure that the structure
found is not due to systematic bias.

--------------------------------------------------------

Cell Lines, Microarrays, Drugs and Disease: Trying to Predict Response 
to Chemotherapy 

Preventive Medicine and Biometrics Seminar, Thurs 3/28 12-1pm
9th Street campus, CPH Auditorium

Keith Baggerly
Bioinformatics and Computational Biology
UT M. D. Anderson Cancer Center

Over the past few years, microarray experiments have
supplied much information about the disregulation of
biological pathways associated with various types of
cancer. Many studies focus on identifying subgroups of
patients with particularly agressive forms of disease,
so that we know who to treat. A corresponding question
is how to treat them. Given the treatment options
available today, this means trying to predict which
chemotherapeutic regimens will be most effective,
which we can attack with microarrays by defining
signatures of drug sensitivity. In establishing such
signatures, we would really like to use samples from
cell lines, as these can (a) be grown in abundance,
(b) be tested with the agents under controlled conditions,
and (c) be assayed without poisoning patients.

Recent studies have suggested how this approach might
work using a widely-used panel of cell lines, the NCI60,
to assemble the response signatures for several drugs.
Unfortunately, ambiguities associated with analyzing the
data have made these results difficult to reproduce.

In this talk, we will discuss the steps involved in
attacking response prediction, and describe how we have
analyzed the data. We will cover some specific ambiguities
we have encountered, and in some cases how these can be
resolved. Finally, we will describe methods for making
such analyses more reproducible, so that progress can
be made more steadily.

-- 
Matt Pocernich
National Center for Atmospheric Research
Research Applications Laboratory
(303) 497-8312