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Proteomics, ovarian cancer, and experimental design

Baggerly, K (Texas)
Tuesday 12 August 2008, 11:30-12:00

Seminar Room 1, Newton Institute


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 for public consumption. 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.




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