Abstract
Liquid chromatograph mass spectrometry (LC-MS) proteomic analysis has the ability to quantify and track thousands of peptides from tissues and body fluids. We investigated the ability of LC-MS proteomics to reproducibly detect blood-based markers in the plasma of metastatic renal cancer patients. We used the differential quantification ability of LC-MS to interrogate the plasma of two separate clinical site collections of metastatic renal cancer patients and healthy individuals.

Our goal was to examine the ability of the method to reproducibly find renal cancer specific markers. We demonstrated that there are over 100 plasma proteins enriched in renal cancer patients compared to healthy controls and that these proteins are highly reproducibly detected in two separate clinical collections. Regression analysis, unsupervised hierarchical clustering and PCA detected no systematic bias in the data related to site of sample collection and processing. Using a genetic algorithm, support vector machine classification method we were able to correctly classify disease samples at 88% sensitivity and 94% specificity with an independent validation set. The disease enriched plasma proteins included acute phase reactant proteins, multiple proteins previously associated with renal cancer, and many others with no previous renal cancer association. 2D-LC-MS can be a highly reproducible biomarker discovery platform when used to assess plasma samples.

Speaker Background
Keith Wilson received his Ph.D. from Oregon Health Sciences University in Biochemistry and Molecular Biology and did his postdoctoral work at Stanford University. He joined Eos Biotechnology in 1997 which was an early genomics company utilizing emerging microarray technology and was involved in technological platform design, software and algorithm development, and applying the technology to drug discovery and clinical applications. He has continued to be involved in applying cutting edge technology to drug discovery and development at PDL BioPharma, including recently proteomics, high density SNP/CNV arrays, and massively parallel sequencing.

Dr. Wilson is Director of Computational Biology at PDL BioPharma in Redwood City.

Meeting details

Date:	Thursday	April 29, 2008
Time:	6:00 pm	Social hour, registration (no-host cocktails)
	7:00 pm	Dinner
	8:00 pm	Presentation
Dinner:	featuring:	Salmon
		Chicken Florentine
		Grilled Vegetable Brochette
Cost:	$30	BAMS members*
	$40	Non-members
	$60	BAMS membership plus dinner cost
	$20	Students only
	$300	2008 Corporate Sponsors
		Dinner reservations required by noon on Friday April 25, 2008

*Note:  BAMS memberships are for the calendar year and should be renewed with the first event you attend in 2008.  Dues ($30.00) may be paid while registering for dinner.  If you are unsure of your Membership status, please email Tim Hawkins.

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2960 N.Shoreline Blvd
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