Multicenter Clinical Sample Collection for Microarray Analysis
In this chapter, we describe numerous methods to extract RNA, DNA, and protein from tissue, represented by kidney transplant biopsies, and from peripheral blood cells collected at various clinical sites. Gene expression profiling and SNP-based genome-wide
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1. Introduction The analysis of clinical samples utilizing microarray technology has advanced the field of clinical research including transplan tation medicine (1–6). Our research group, the Transplant Genomics Collaborative Group (TGCG; http://www.genetics. ucla.edu/transplant-genomics/index2.php) is involved in a large study of kidney transplantation outcomes with an emphasis on defining genomic biomarkers that could be used to monitor and individualize the adequacy and efficacy of immunosuppressive drug therapy. Organizing the Transplant Genomics project has provided a better understanding of the challenges facing anyone
Sridar V. Chittur (ed.), Microarray Methods for Drug Discovery, Methods in Molecular Biology, vol. 632, DOI 10.1007/978-1-60761-663-4_1, © Humana Press, a part of Springer Science+Business Media, LLC 2010
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Mondala, Salomon, and Head
planning a large, multicenter clinical project that involves collection of multiple sample types, at multiple predefined time points, with multiple sample handling protocols and where obtaining precise clinical data and outcomes are necessary. The key to success of any study involving multiple clinical centers is the efficient collection, preservation, and transport of clinical material from collection sites to a central processing facility where samples can be prepared for analysis using microarrays and other analytical techniques. Organizing a multicenter research study requires effective training and support of physicians, nurse coordinators, and laboratory personnel in order to guarantee adherence to enrollment (inclusion/exclusion) criteria, proper sample collection, preshipment specimen processing, and documentation of patient/subject data. A key insight is that physicians, nurses, and laboratory personnel all have different jobs, training, and work environments so that strategies to effectively communicate study objectives and monitor sample collection and data integrity must be developed for each. As with any research study involving human subjects, Institutional Review Board approval of a Human Subjects Protocol is required as well as informed consent for study participants. Setting up a central processing center is necessary to create, test, and then provide kits for sample collection and transport. The central processing center is also tasked with the tracking of all collected specimens from the various clinical centers as well as coordinating sample preparation and archiving. Finally, it is critical to have a highly secure clinical database that is readily accessible to all the participating centers and a parallel, but integrated, specimen tracking database in the central processing center. The wealth of scientific information that can be obtained through the establishment of a well-organized system to collect, document, and process clinical research samples provides a foundation for advancing clinical research and translational medicine. The purpose of this chapter is to discuss our experience in a large multicenter clinical study, specificall
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