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Experiments assessing the effects of preanalytical variables on molecular research

Speed, T (UC, Berkeley)
Tuesday 12 August 2008, 12:00-12:30

Seminar Room 1, Newton Institute


When the abundance of mRNA, proteins or metabolites in cell samples is measured using a genomic, proteomic or metabolomic assay, it may happen that the measurement is more influenced by uncontrolled preanalytical variables than by the measurement process itself. For example, if the cells are from a tissue sample taken during surgery, variables such as drugs, type or duration of anesthesia, and arterial clamp time can greatly affect the final molecular measurements, as can a host of post-acquisition variables such as time at room temperature, temperature of the room prior to fixing, type of fixative, time in fixative, rate of freezing, and so on. Lack of awareness of these possible effects can lead to incorrect diagnosis, incorrect treatment, and irreproducible results in research. How do we determine which of these variables matter for a given assay, and how do we derive standard procedures for sample acquisition, handling, processing and storage, prior to the assay? The answer is, of course, through experimentation. We will need to combine screening experiments, as the number of potentially important variables is large, with later experiments to determine robust combinations of factors which might become new standard operating procedures. The experiments must be on human tissue, we'd like replicates, and we'd like to be able to distinguish intra-person and inter-person variability. There are significant practical and ethical constraints surrounding such experiments. Nevertheless, the US National Cancer Institute's Office of Biorepositories and Biospecimen Research is committed to carrying out such experiments, to address the problems mentioned above. In this talk I will discuss some of the design challenges they are meeting, illustrating my discussion with an example concerning blood drawing.


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