Molecular Profiling

Over the past twenty years, scientists have developed and refined laboratory techniques, such as PCR, protein and cDNA microarrays, fluorescent imaging and microdissection, to the point that many of these techniques are now standardized "kit" protocols and are performed in secondary school laboratory classrooms. By no means does this indicate a decline in scientific advancement. Quite to the contrary, standardization of protocols and widespread availability of reagents is spurring the next scientific revolution: molecular profiling. The vast array of data generated from genome sequencing and in vitro experiments begs scientists to ask the next logical questions: a) how can we use this information for diagnosis and prognosis, b) how does this information correlate with treatment options, c) how can in vitro experimental information be used in conjunction with in vivo information, and d) how can this information be transferred out of the laboratory to the patient bedside?Molecular profiling utilizes the latest advancements in genomics, proteomics, imaging and bioinformatics to answer these questions by providing a molecular portrait of an individual patients' disease. This portrait aids in the design of treatment regimens tailored specifically to each patient. Initially it may seem daunting to cover such varied topics in one volume but each discipline contributes an integral element of an individual's molecular profile. The aim of this volume is to describe protocols for the current state of the art in molecular profiling, as well as discuss unique facets of the future for molecular medicine.Although many of the techniques discussed in this volume use commercially available reagents and instrumentation, it is imperative for the user/reader to understand the principles and nuances of these techniques as they are designed for use with irreplaceable human tissue specimens. This volume hopefully will have a broad readership base, so in an attempt to provide basic assay information, we have included basic test principles in the introduction to each analytical chapter as well as providing troubleshooting tips and tricks for the competent scientist.Molecular Profiling covers eight topics in relation to human disease: genomics, proteomics, bioinformatics, imaging, intellectual property, tissue preservation/biobanking, individualized therapy regimens, and grant funding. The first four topics illustrate current laboratory protocols for generating data relevant to molecular medicine. Each of these disciplines is complimentary and the grouping simply provides a means for differentiating the molecular basis of the protocols. The latter four topics are a unique aspect of this volume of the Methods in Molecular Biology series. These chapters discuss, in a narrative style, future real-world needs in molecular medicine. Important points are highlighted in the Notes section for each chapter.Molecular Profiling is designed to step the reader through a project/experiment in molecular medicine. The protocol chapters describe detailed techniques for evaluating tissue samples, tissue collection and storage, analytical platforms, and bioinformatics/biostatistics. The narrative chapters are designed to provide the reader with a well-rounded discussion of intellectual property issues in biotechnology, human subjects research requirements, regulatory agency approval processes, and an overview of technology transfer (patent) issues. Although other books have been published covering the topics of genomic profiling, or proteomic profiling, we believe this is the first book dedicated to incorporating genomics, proteomics, and bioinformatics with discussions of future requirements in molecular profiling.A topic as broad as Molecular Profiling is primarily aimed toward scientists, pathologists, oncologists, residents, biotechnologists, medical students and nurses involved in clinical trial research. Our hope is that basic research scientists, physicians, venture capitalists, lawyers, and entrepreneurs will find this volume informative and that it spurs development of a routine, standard of care for individualized therapy regimens.